Sender: LSF System <lsf@node1643>
Subject: Job 5211612: <iteration_162679> Done

Job <iteration_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1643>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679> was used as the working directory.
Started at Sat Sep  8 15:54:26 2012
Results reported at Sat Sep  8 15:54:27 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
echo starting
ls iteration*/exited 2>&1
return_code=$?
if [ ${return_code} -eq 0 ]; then
echo some scatter or gather jobs failed;
echo ${return_code} > exited;
exit 1;
fi
ls exited 2>&1
return_code=$?
if [ ${return_code} -eq 0 ]; then
echo previous iteration failed;
echo ${return_code} > exited;
exit 1;
fi
/xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/scatter-gather-iterator.py /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/iterative-scatter-gather.py --job-suffix 162679 --priority 50 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/
return_code=$?
if [ ${return_code} -ne 0 ]; then
echo iterator failed ${return_code};
echo ${return_code} > exited;
exit ${return_code};
fi
cat iteration1/jobSubmissions.txt >> jobSubmissions.txt
rm -f iteration1/jobSubmissions.txt
echo '*** Scatter Gather stdandard out:' 2>&1
cat iteration1/scatter-gather.out.txt 2>&1
rm -f iteration1/scatter-gather.out.txt 2>&1
echo '*** Scatter Gather stdandard err:' 2>&1
cat iteration1/scatter-gather.err.txt 2>&1
rm -f iteration1/scatter-gather.err.txt 2>&1
ls iteration1/sg-next-iteration.txt 2>&1
return_code=$?
if [ ${return_code} -eq 0 ]; then
rm -f iteration1/sg-next-iteration.txt
else
rm -f scatterGatherParameters.txt
rm -f programParameters.txt
mv iteration1/* /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679
rmdir iteration*
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :      0.31 sec.
    Max Memory :         4 MB
    Max Swap   :        42 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

starting
ls: iteration*/exited: No such file or directory
ls: exited: No such file or directory
Running scatter-gather-iterator with the following args: /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/scatter-gather-iterator.py /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/iterative-scatter-gather.py --job-suffix 162679 --priority 50 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/
Finished in 1 iterations
*** Scatter Gather stdandard out:
Sender: LSF System <lsf@node1559>
Subject: Job 5211607: <gather_162679> Done

Job <gather_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1559>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1> was used as the working directory.
Started at Sat Sep  8 15:42:42 2012
Results reported at Sat Sep  8 15:54:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
ls scatter.*/exited 2>&1
return_code=$?
if [ ${return_code} -eq 0 ]; then
echo some scatter jobs failed;
echo ${return_code} > exited;
exit 1;
fi
if [ `ls -1 scatter.*/success | wc -l` -ne 199 ]; then
echo expected result files missing, try rerunning;
echo 1 > exited;
exit 1;
fi
python /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/run_matlab.py /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ fh_MutSigCoverageGather "/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/" "LAML" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LAML/1688931/0.MutSigPreprocess.Finished/LAML.maf" "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "4" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LAML/1688931/0.MutSigPreprocess.Finished/LAML.patients.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
echo gather failed;
echo ${return_code} > exited;
exit ${return_code};
fi
rm -f prepareResults.out
echo '*** Prepare stdandard out:' 2>&1
cat prepare.out 2>&1
rm -f prepare.out 2>&1
echo '*** Prepare stdandard err:' 2>&1
cat prepare.err 2>&1
rm -f prepare.err 2>&1
echo '*** Scatter stdandard out:' 2>&1
cat scatter.*/scatter.out 2>&1
rm -f scatter.*/scatter.out 2>&1
echo '*** Scatter stdandard err:' 2>&1
cat scatter.*/scatter.err 2>&1
rm -f scatter.*/scatter.err 2>&1
echo '*** Scatter retry log:'
head scatter.*.tries
echo
rm -f scatter.*.tries
rm -f scatter.*/success
rmdir scatter.*
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :    753.86 sec.
    Max Memory :      1254 MB
    Max Swap   :      2166 MB

    Max Processes  :         8
    Max Threads    :        64

The output (if any) follows:

ls: scatter.*/exited: No such file or directory
Warning: No display specified.  You will not be able to display graphics on the screen.
fh_MutSigCoverageGather
100/199 
199 files found
100/199 
199 files found
100/199 
199 files found
Creating summed FWB coverage file: ./LAML.summed_coverage.fwb
Loading target file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Opening files: 10/199 20/199 30/199 40/199 50/199 60/199 70/199 80/199 90/199 100/199 110/199 120/199 130/199 140/199 150/199 160/199 170/199 180/199 190/199 
Summing and writing output file:
1/4293390 Elapsed time is 0.023698 seconds.
100001/4293390 Elapsed time is 4.927783 seconds.
200001/4293390 Elapsed time is 8.261689 seconds.
300001/4293390 Elapsed time is 8.896537 seconds.
400001/4293390 Elapsed time is 9.559462 seconds.
500001/4293390 Elapsed time is 10.249612 seconds.
600001/4293390 Elapsed time is 10.949599 seconds.
700001/4293390 Elapsed time is 11.593910 seconds.
800001/4293390 Elapsed time is 12.210098 seconds.
900001/4293390 Elapsed time is 12.912168 seconds.
1000001/4293390 Elapsed time is 13.671633 seconds.
1100001/4293390 Elapsed time is 14.301921 seconds.
1200001/4293390 Elapsed time is 14.922600 seconds.
1300001/4293390 Elapsed time is 15.516147 seconds.
1400001/4293390 Elapsed time is 16.127320 seconds.
1500001/4293390 Elapsed time is 16.774411 seconds.
1600001/4293390 Elapsed time is 17.382469 seconds.
1700001/4293390 Elapsed time is 18.021364 seconds.
1800001/4293390 Elapsed time is 18.670968 seconds.
1900001/4293390 Elapsed time is 19.310037 seconds.
2000001/4293390 Elapsed time is 19.937979 seconds.
2100001/4293390 Elapsed time is 20.596695 seconds.
2200001/4293390 Elapsed time is 21.261236 seconds.
2300001/4293390 Elapsed time is 21.850928 seconds.
2400001/4293390 Elapsed time is 22.501682 seconds.
2500001/4293390 Elapsed time is 23.144363 seconds.
2600001/4293390 Elapsed time is 23.845826 seconds.
2700001/4293390 Elapsed time is 24.466211 seconds.
2800001/4293390 Elapsed time is 25.069865 seconds.
2900001/4293390 Elapsed time is 25.666390 seconds.
3000001/4293390 Elapsed time is 26.304280 seconds.
3100001/4293390 Elapsed time is 27.024115 seconds.
3200001/4293390 Elapsed time is 27.599817 seconds.
3300001/4293390 Elapsed time is 28.163270 seconds.
3400001/4293390 Elapsed time is 28.802889 seconds.
3500001/4293390 Elapsed time is 29.412054 seconds.
3600001/4293390 Elapsed time is 29.988239 seconds.
3700001/4293390 Elapsed time is 30.565378 seconds.
3800001/4293390 Elapsed time is 31.207302 seconds.
3900001/4293390 Elapsed time is 31.779972 seconds.
4000001/4293390 Elapsed time is 32.395733 seconds.
4100001/4293390 Elapsed time is 33.046399 seconds.
4200001/4293390 Elapsed time is 33.669050 seconds.

Closing input files
Done
Getting covered territory tally... 1933/193324 3866/193324 5799/193324 7732/193324 9665/193324 11598/193324 13531/193324 15464/193324 17397/193324 19330/193324 21263/193324 23196/193324 25129/193324 27062/193324 28995/193324 30928/193324 32861/193324 34794/193324 36727/193324 38660/193324 40593/193324 42526/193324 44459/193324 46392/193324 48325/193324 50258/193324 52191/193324 54124/193324 56057/193324 57990/193324 59923/193324 61856/193324 63789/193324 65722/193324 67655/193324 69588/193324 71521/193324 73454/193324 75387/193324 77320/193324 79253/193324 81186/193324 83119/193324 85052/193324 86985/193324 88918/193324 90851/193324 92784/193324 94717/193324 96650/193324 98583/193324 100516/193324 102449/193324 104382/193324 106315/193324 108248/193324 110181/193324 112114/193324 114047/193324 115980/193324 117913/193324 119846/193324 121779/193324 123712/193324 125645/193324 127578/193324 129511/193324 131444/193324 133377/193324 135310/193324 137243/193324 139176/193324 141109/193324 143042/193324 144975/193324 146908/193324 148841/193324 150774/193324 152707/193324 154640/193324 156573/193324 158506/193324 160439/193324 162372/193324 164305/193324 166238/193324 168171/193324 170104/193324 172037/193324 173970/193324 175903/193324 177836/193324 179769/193324 181702/193324 183635/193324 185568/193324 187501/193324 189434/193324 191367/193324 193300/193324 
k=1
                      mut   n  4630 N 16734462225  rate 2.77e-07 (1.00x)  ci 2.69e-07 to 2.85e-07

k=2
                  transit   n  3290 N 5578154075  rate 5.90e-07 (2.13x)  ci 5.70e-07 to 6.10e-07
                 transver   n  1340 N 11156308150  rate 1.20e-07 (0.43x)  ci 1.14e-07 to 1.27e-07

k=3
                     C->T   n  2693 N 2788947787  rate 9.66e-07 (3.49x)  ci 9.29e-07 to 1.00e-06
                     A->G   n   597 N 2789206288  rate 2.14e-07 (0.77x)  ci 1.97e-07 to 2.32e-07
                 transver   n  1340 N 11156308150  rate 1.20e-07 (0.43x)  ci 1.14e-07 to 1.27e-07

k=4
                  *CpG->T   n  1360 N  278094739  rate 4.89e-06 (17.7x)  ci 4.63e-06 to 5.16e-06
            *Cp(A/C/T)->T   n  1333 N 2510853048  rate 5.31e-07 (1.92x)  ci 5.03e-07 to 5.60e-07
                     A->G   n   597 N 2789206288  rate 2.14e-07 (0.77x)  ci 1.97e-07 to 2.32e-07
                 transver   n  1340 N 11156308150  rate 1.20e-07 (0.43x)  ci 1.14e-07 to 1.27e-07

Saving ./LAML.mutcategs.txt
all files are *.bin: will read in BINARY MODE
100/199 
199 files found
No effect information available in category list: will not be able to test NS/S ratios
Loading target file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Collapsing targets to genes...
10000/193324 20000/193324 30000/193324 40000/193324 50000/193324 60000/193324 70000/193324 80000/193324 90000/193324 100000/193324 110000/193324 120000/193324 130000/193324 140000/193324 150000/193324 160000/193324 170000/193324 180000/193324 190000/193324 
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Saving ./LAML.coverage.mat
Deleting intermediate files
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1
mFile: fh_MutSigCoverageGather
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/fh_MutSigCoverageGather /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ LAML /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LAML/1688931/0.MutSigPreprocess.Finished/LAML.maf /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt /xchip/cga1/lawrence/db/context65 hg18 /xchip/cga1/annotation/db/ucsc/hg18 4 /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/LAML/1688931/0.MutSigPreprocess.Finished/LAML.patients.txt
*** Prepare stdandard out:
cat: prepare.out: No such file or directory
*** Prepare stdandard err:
cat: prepare.err: No such file or directory
*** Scatter stdandard out:
Sender: LSF System <lsf@node1419>
Subject: Job 5210608: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000001> was used as the working directory.
Started at Fri Sep  7 00:22:53 2012
Results reported at Fri Sep  7 00:24:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000001.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000001.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2802" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2802.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2802-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000001.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     43.36 sec.
    Max Memory :      4701 MB
    Max Swap   :      5459 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2802-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2802.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2802.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2802.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1647>
Subject: Job 5210613: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1647>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000002> was used as the working directory.
Started at Fri Sep  7 00:23:05 2012
Results reported at Fri Sep  7 00:24:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000002.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000002.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2803" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2803.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2803-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000002.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.62 sec.
    Max Memory :      4696 MB
    Max Swap   :      5460 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2803-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2803.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2803.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2803.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1534>
Subject: Job 5210618: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1534>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000003> was used as the working directory.
Started at Fri Sep  7 00:23:31 2012
Results reported at Fri Sep  7 00:25:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000003.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000003.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2804" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2804.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2804-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000003.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     40.34 sec.
    Max Memory :      4699 MB
    Max Swap   :      5458 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2804-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2804.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2804.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2804.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210621: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000004> was used as the working directory.
Started at Fri Sep  7 00:25:53 2012
Results reported at Fri Sep  7 00:26:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000004.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000004.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2805" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2805.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2805-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000004.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.34 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2805-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2805.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2805.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2805.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1647>
Subject: Job 5210626: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1647>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000005> was used as the working directory.
Started at Fri Sep  7 00:25:53 2012
Results reported at Fri Sep  7 00:26:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000005.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000005.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2806" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2806.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2806-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000005.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.39 sec.
    Max Memory :        10 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2806-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2806.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2806.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2806.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1420>
Subject: Job 5210629: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1420>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000006> was used as the working directory.
Started at Fri Sep  7 00:25:53 2012
Results reported at Fri Sep  7 00:27:26 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000006.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000006.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2807" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2807.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2807-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000006.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     41.80 sec.
    Max Memory :      4699 MB
    Max Swap   :      5456 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2807-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2807.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2807.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2807.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 5210633: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000007> was used as the working directory.
Started at Fri Sep  7 00:26:05 2012
Results reported at Fri Sep  7 00:27:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000007.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000007.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2808" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2808.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2808-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000007.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.03 sec.
    Max Memory :      4693 MB
    Max Swap   :      5456 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2808-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2808.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2808.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2808.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210638: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000008> was used as the working directory.
Started at Fri Sep  7 00:27:02 2012
Results reported at Fri Sep  7 00:27:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000008.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000008.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2809" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2809.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2809-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000008.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.20 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2809-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2809.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2809.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2809.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1642>
Subject: Job 5210642: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1642>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000009> was used as the working directory.
Started at Fri Sep  7 00:27:35 2012
Results reported at Fri Sep  7 00:29:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000009.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000009.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2810" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2810.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2810-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000009.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     19.48 sec.
    Max Memory :      4695 MB
    Max Swap   :      5474 MB

    Max Processes  :         4
    Max Threads    :        32

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2810-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2810.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2810.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2810.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210647: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000010> was used as the working directory.
Started at Fri Sep  7 00:28:08 2012
Results reported at Fri Sep  7 00:28:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000010.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000010.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2811" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2811.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2811-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000010.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.82 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2811-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2811.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2811.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2811.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 5210652: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000011> was used as the working directory.
Started at Fri Sep  7 00:28:32 2012
Results reported at Fri Sep  7 00:28:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000011.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000011.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2812" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2812.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2812-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000011.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.23 sec.
    Max Memory :         6 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2812-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2812.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2812.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2812.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1416>
Subject: Job 5210656: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1416>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000012> was used as the working directory.
Started at Fri Sep  7 00:28:38 2012
Results reported at Fri Sep  7 00:30:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000012.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000012.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2813" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2813.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2813-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000012.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     43.35 sec.
    Max Memory :      4694 MB
    Max Swap   :      5462 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2813-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2813.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2813.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2813.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210660: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000013> was used as the working directory.
Started at Fri Sep  7 00:29:09 2012
Results reported at Fri Sep  7 00:29:33 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000013.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000013.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2814" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2814.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2814-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000013.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.80 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2814-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2814.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2814.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2814.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1534>
Subject: Job 5210664: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1534>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000014> was used as the working directory.
Started at Fri Sep  7 00:29:18 2012
Results reported at Fri Sep  7 00:29:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000014.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000014.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2815" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2815.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2815-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000014.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.24 sec.
    Max Memory :         3 MB
    Max Swap   :        45 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2815-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2815.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2815.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2815.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210669: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000015> was used as the working directory.
Started at Fri Sep  7 00:30:14 2012
Results reported at Fri Sep  7 00:30:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000015.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000015.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2816" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2816.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2816-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000015.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.99 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2816-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2816.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2816.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2816.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1533>
Subject: Job 5210674: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1533>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000016> was used as the working directory.
Started at Fri Sep  7 00:30:49 2012
Results reported at Fri Sep  7 00:32:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000016.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000016.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2817" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2817.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2817-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000016.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     40.84 sec.
    Max Memory :      4636 MB
    Max Swap   :      5454 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2817-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2817.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2817.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2817.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210677: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000017> was used as the working directory.
Started at Fri Sep  7 00:31:14 2012
Results reported at Fri Sep  7 00:31:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000017.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000017.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2818" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2818.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2818-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000017.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.27 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2818-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2818.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2818.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2818.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1544>
Subject: Job 5210680: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1544>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000018> was used as the working directory.
Started at Fri Sep  7 00:31:54 2012
Results reported at Fri Sep  7 00:33:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000018.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000018.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2819" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2819.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2819-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000018.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     38.00 sec.
    Max Memory :      4697 MB
    Max Swap   :      5455 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2819-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2819.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2819.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2819.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210687: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000019> was used as the working directory.
Started at Fri Sep  7 00:32:15 2012
Results reported at Fri Sep  7 00:32:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000019.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000019.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2820" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2820.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2820-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000019.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.59 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2820-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2820.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2820.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2820.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1641>
Subject: Job 5210701: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1641>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000020> was used as the working directory.
Started at Fri Sep  7 00:32:15 2012
Results reported at Fri Sep  7 00:33:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000020.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000020.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2821" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2821.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2821-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000020.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.58 sec.
    Max Memory :      4696 MB
    Max Swap   :      5458 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2821-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2821.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2821.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2821.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210705: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000021> was used as the working directory.
Started at Fri Sep  7 00:33:15 2012
Results reported at Fri Sep  7 00:33:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000021.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000021.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2822" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2822.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2822-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000021.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     26.99 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2822-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2822.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2822.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2822.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5210711: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000022> was used as the working directory.
Started at Fri Sep  7 00:33:39 2012
Results reported at Fri Sep  7 00:34:16 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000022.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000022.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2823" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2823.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2823-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000022.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.74 sec.
    Max Memory :      4699 MB
    Max Swap   :      5460 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2823-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2823.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2823.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2823.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1420>
Subject: Job 5210715: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1420>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000023> was used as the working directory.
Started at Fri Sep  7 00:33:45 2012
Results reported at Fri Sep  7 00:34:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000023.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000023.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2824" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2824.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2824-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000023.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.13 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2824-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2824.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2824.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2824.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210722: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000024> was used as the working directory.
Started at Fri Sep  7 00:34:16 2012
Results reported at Fri Sep  7 00:34:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000024.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000024.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2825" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2825.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2825-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000024.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.83 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2825-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2825.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2825.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2825.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1544>
Subject: Job 5210726: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1544>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000025> was used as the working directory.
Started at Fri Sep  7 00:34:32 2012
Results reported at Fri Sep  7 00:34:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000025.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000025.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2826" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2826.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2826-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000025.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.69 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2826-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2826.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2826.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2826.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5210729: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000026> was used as the working directory.
Started at Fri Sep  7 00:34:43 2012
Results reported at Fri Sep  7 00:35:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000026.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000026.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2827" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2827.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2827-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000026.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.77 sec.
    Max Memory :         4 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2827-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2827.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2827.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2827.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 5210734: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000027> was used as the working directory.
Started at Fri Sep  7 00:35:10 2012
Results reported at Fri Sep  7 00:35:29 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000027.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000027.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2828" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2828.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2828-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000027.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.88 sec.
    Max Memory :         6 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2828-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2828.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2828.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2828.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210742: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000028> was used as the working directory.
Started at Fri Sep  7 00:35:17 2012
Results reported at Fri Sep  7 00:35:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000028.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000028.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2829" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2829.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2829-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000028.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.58 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2829-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2829.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2829.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2829.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1528>
Subject: Job 5210746: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1528>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000029> was used as the working directory.
Started at Fri Sep  7 00:35:47 2012
Results reported at Fri Sep  7 00:37:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000029.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000029.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2830" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2830.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2830-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000029.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     41.10 sec.
    Max Memory :      4700 MB
    Max Swap   :      5455 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2830-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2830.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2830.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2830.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 5210750: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000030> was used as the working directory.
Started at Fri Sep  7 00:36:13 2012
Results reported at Fri Sep  7 00:36:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000030.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000030.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2831" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2831.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2831-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000030.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.67 sec.
    Max Memory :         6 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2831-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2831.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2831.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2831.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210752: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000031> was used as the working directory.
Started at Fri Sep  7 00:36:17 2012
Results reported at Fri Sep  7 00:36:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000031.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000031.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2832" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2832.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2832-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000031.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.70 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2832-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2832.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2832.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2832.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1420>
Subject: Job 5210755: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1420>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000032> was used as the working directory.
Started at Fri Sep  7 00:36:44 2012
Results reported at Fri Sep  7 00:37:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000032.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000032.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2833" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2833.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2833-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000032.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.06 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2833-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2833.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2833.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2833.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 5210756: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000033> was used as the working directory.
Started at Fri Sep  7 00:36:44 2012
Results reported at Fri Sep  7 00:39:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000033.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000033.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2834" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2834.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2834-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000033.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.69 sec.
    Max Memory :      4696 MB
    Max Swap   :      5458 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2834-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2834.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2834.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2834.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210759: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000034> was used as the working directory.
Started at Fri Sep  7 00:37:20 2012
Results reported at Fri Sep  7 00:37:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000034.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000034.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2835" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2835.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2835-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000034.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.84 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2835-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2835.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2835.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2835.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1556>
Subject: Job 5210761: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1556>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000035> was used as the working directory.
Started at Fri Sep  7 00:37:20 2012
Results reported at Fri Sep  7 00:39:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000035.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000035.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2836" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2836.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2836-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000035.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     38.24 sec.
    Max Memory :      4698 MB
    Max Swap   :      5457 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2836-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2836.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2836.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2836.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1422>
Subject: Job 5210763: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1422>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000036> was used as the working directory.
Started at Fri Sep  7 00:37:58 2012
Results reported at Fri Sep  7 00:39:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000036.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000036.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2837" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2837.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2837-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000036.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     39.81 sec.
    Max Memory :      4697 MB
    Max Swap   :      5457 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2837-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2837.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2837.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2837.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210765: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000037> was used as the working directory.
Started at Fri Sep  7 00:38:25 2012
Results reported at Fri Sep  7 00:38:59 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000037.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000037.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2838" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2838.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2838-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000037.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.35 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2838-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2838.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2838.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2838.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 5210768: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000038> was used as the working directory.
Started at Fri Sep  7 00:39:17 2012
Results reported at Fri Sep  7 00:40:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000038.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000038.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2839" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2839.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2839-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000038.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     25.08 sec.
    Max Memory :      4699 MB
    Max Swap   :      5457 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2839-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2839.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2839.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2839.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1537>
Subject: Job 5210774: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1537>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000039> was used as the working directory.
Started at Fri Sep  7 00:39:34 2012
Results reported at Fri Sep  7 00:41:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000039.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000039.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2840" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2840.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2840-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000039.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     39.63 sec.
    Max Memory :      4643 MB
    Max Swap   :      5457 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2840-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2840.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2840.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2840.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1420>
Subject: Job 5210780: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1420>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000040> was used as the working directory.
Started at Fri Sep  7 00:39:37 2012
Results reported at Fri Sep  7 00:40:23 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000040.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000040.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2841" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2841.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2841-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000040.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.27 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2841-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2841.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2841.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2841.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210789: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000041> was used as the working directory.
Started at Fri Sep  7 00:40:33 2012
Results reported at Fri Sep  7 00:41:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000041.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000041.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2842" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2842.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2842-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000041.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.45 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2842-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2842.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2842.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2842.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1421>
Subject: Job 5210794: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1421>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000042> was used as the working directory.
Started at Fri Sep  7 00:41:04 2012
Results reported at Fri Sep  7 00:42:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000042.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000042.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2843" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2843.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2843-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000042.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     38.60 sec.
    Max Memory :      4699 MB
    Max Swap   :      5456 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2843-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2843.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2843.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2843.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1642>
Subject: Job 5210798: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1642>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000043> was used as the working directory.
Started at Fri Sep  7 00:41:17 2012
Results reported at Fri Sep  7 00:41:43 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000043.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000043.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2844" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2844.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2844-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000043.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.43 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2844-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2844.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2844.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2844.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210804: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000044> was used as the working directory.
Started at Fri Sep  7 00:41:34 2012
Results reported at Fri Sep  7 00:42:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000044.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000044.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2845" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2845.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2845-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000044.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     26.84 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2845-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2845.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2845.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2845.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 5210809: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000045> was used as the working directory.
Started at Fri Sep  7 00:41:38 2012
Results reported at Fri Sep  7 00:42:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000045.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000045.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2846" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2846.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2846-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000045.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.72 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2846-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2846.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2846.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2846.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1422>
Subject: Job 5210814: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1422>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000046> was used as the working directory.
Started at Fri Sep  7 00:42:06 2012
Results reported at Fri Sep  7 00:42:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000046.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000046.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2847" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2847.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2847-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000046.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.96 sec.
    Max Memory :         3 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2847-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2847.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2847.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2847.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210817: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000047> was used as the working directory.
Started at Fri Sep  7 00:42:34 2012
Results reported at Fri Sep  7 00:42:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000047.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000047.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2848" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2848.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2848-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000047.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.57 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2848-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2848.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2848.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2848.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1420>
Subject: Job 5210825: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1420>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000048> was used as the working directory.
Started at Fri Sep  7 00:42:55 2012
Results reported at Fri Sep  7 00:43:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000048.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000048.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2849" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2849.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2849-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000048.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.36 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2849-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2849.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2849.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2849.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1422>
Subject: Job 5210827: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1422>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000049> was used as the working directory.
Started at Fri Sep  7 00:43:10 2012
Results reported at Fri Sep  7 00:43:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000049.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000049.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2850" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2850.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2850-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000049.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.92 sec.
    Max Memory :         3 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2850-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2850.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2850.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2850.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1549>
Subject: Job 5210831: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1549>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000050> was used as the working directory.
Started at Fri Sep  7 00:43:26 2012
Results reported at Fri Sep  7 00:45:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000050.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000050.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2851" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2851.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2851-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000050.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     40.60 sec.
    Max Memory :      4703 MB
    Max Swap   :      5402 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2851-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2851.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2851.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2851.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210833: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000051> was used as the working directory.
Started at Fri Sep  7 00:43:35 2012
Results reported at Fri Sep  7 00:44:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000051.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000051.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2853" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2853.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2853-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000051.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.72 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2853-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2853.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2853.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2853.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1416>
Subject: Job 5210836: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1416>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000052> was used as the working directory.
Started at Fri Sep  7 00:44:07 2012
Results reported at Fri Sep  7 00:44:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000052.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000052.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2854" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2854.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2854-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000052.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.56 sec.
    Max Memory :      4696 MB
    Max Swap   :      5456 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2854-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2854.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2854.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2854.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1642>
Subject: Job 5210842: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1642>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000053> was used as the working directory.
Started at Fri Sep  7 00:44:20 2012
Results reported at Fri Sep  7 00:44:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000053.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000053.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2855" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2855.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2855-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000053.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.51 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2855-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2855.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2855.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2855.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210847: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000054> was used as the working directory.
Started at Fri Sep  7 00:44:35 2012
Results reported at Fri Sep  7 00:45:06 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000054.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000054.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2856" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2856.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2856-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000054.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.03 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2856-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2856.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2856.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2856.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210852: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000055> was used as the working directory.
Started at Fri Sep  7 00:45:37 2012
Results reported at Fri Sep  7 00:46:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000055.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000055.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2857" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2857.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2857-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000055.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.34 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2857-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2857.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2857.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2857.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1420>
Subject: Job 5210857: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1420>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000056> was used as the working directory.
Started at Fri Sep  7 00:46:25 2012
Results reported at Fri Sep  7 00:46:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000056.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000056.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2858" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2858.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2858-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000056.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.26 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2858-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2858.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2858.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2858.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210862: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000057> was used as the working directory.
Started at Fri Sep  7 00:46:37 2012
Results reported at Fri Sep  7 00:47:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000057.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000057.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2859" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2859.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2859-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000057.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.85 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2859-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2859.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2859.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2859.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1645>
Subject: Job 5210868: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1645>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000058> was used as the working directory.
Started at Fri Sep  7 00:46:47 2012
Results reported at Fri Sep  7 00:48:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000058.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000058.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2860" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2860.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2860-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000058.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     26.21 sec.
    Max Memory :      4696 MB
    Max Swap   :      5456 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2860-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2860.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2860.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2860.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1422>
Subject: Job 5210871: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1422>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000059> was used as the working directory.
Started at Fri Sep  7 00:47:17 2012
Results reported at Fri Sep  7 00:47:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000059.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000059.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2861" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2861.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2861-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000059.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.62 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2861-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2861.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2861.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2861.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210878: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000060> was used as the working directory.
Started at Fri Sep  7 00:47:40 2012
Results reported at Fri Sep  7 00:48:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000060.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000060.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2862" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2862.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2862-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000060.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.02 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2862-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2862.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2862.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2862.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1705>
Subject: Job 5210883: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1705>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000061> was used as the working directory.
Started at Fri Sep  7 00:47:40 2012
Results reported at Fri Sep  7 00:49:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000061.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000061.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2863" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2863.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2863-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000061.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     25.68 sec.
    Max Memory :      4699 MB
    Max Swap   :      5462 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2863-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2863.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2863.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2863.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210887: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000062> was used as the working directory.
Started at Fri Sep  7 00:48:41 2012
Results reported at Fri Sep  7 00:49:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000062.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000062.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2864" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2864.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2864-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000062.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.99 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2864-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2864.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2864.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2864.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210893: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000063> was used as the working directory.
Started at Fri Sep  7 00:49:46 2012
Results reported at Fri Sep  7 00:50:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000063.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000063.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2865" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2865.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2865-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000063.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.59 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2865-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2865.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2865.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2865.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1645>
Subject: Job 5210898: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1645>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000064> was used as the working directory.
Started at Fri Sep  7 00:50:14 2012
Results reported at Fri Sep  7 00:50:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000064.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000064.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2866" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2866.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2866-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000064.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.96 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2866-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2866.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2866.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2866.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5210905: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000065> was used as the working directory.
Started at Fri Sep  7 00:50:14 2012
Results reported at Fri Sep  7 00:50:29 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000065.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000065.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2867" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2867.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2867-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000065.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.79 sec.
    Max Memory :         4 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2867-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2867.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2867.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2867.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210909: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000066> was used as the working directory.
Started at Fri Sep  7 00:50:47 2012
Results reported at Fri Sep  7 00:51:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000066.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000066.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2868" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2868.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2868-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000066.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.22 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2868-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2868.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2868.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2868.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 5210916: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000067> was used as the working directory.
Started at Fri Sep  7 00:50:47 2012
Results reported at Fri Sep  7 00:51:23 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000067.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000067.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2869" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2869.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2869-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000067.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.55 sec.
    Max Memory :      4698 MB
    Max Swap   :      5456 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2869-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2869.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2869.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2869.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5210922: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000068> was used as the working directory.
Started at Fri Sep  7 00:51:16 2012
Results reported at Fri Sep  7 00:51:33 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000068.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000068.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2870" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2870.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2870-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000068.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.73 sec.
    Max Memory :         4 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2870-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2870.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2870.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2870.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210928: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000069> was used as the working directory.
Started at Fri Sep  7 00:51:50 2012
Results reported at Fri Sep  7 00:52:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000069.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000069.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2871" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2871.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2871-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000069.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.52 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2871-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2871.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2871.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2871.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 5210934: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000070> was used as the working directory.
Started at Fri Sep  7 00:51:50 2012
Results reported at Fri Sep  7 00:52:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000070.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000070.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2872" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2872.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2872-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000070.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.28 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2872-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2872.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2872.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2872.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5210939: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000071> was used as the working directory.
Started at Fri Sep  7 00:52:16 2012
Results reported at Fri Sep  7 00:52:32 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000071.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000071.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2873" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2873.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2873-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000071.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.84 sec.
    Max Memory :         4 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2873-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2873.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2873.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2873.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 5210949: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000072> was used as the working directory.
Started at Fri Sep  7 00:52:51 2012
Results reported at Fri Sep  7 00:53:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000072.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000072.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2874" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2874.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2874-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000072.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.45 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2874-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2874.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2874.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2874.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5210951: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000073> was used as the working directory.
Started at Fri Sep  7 00:53:17 2012
Results reported at Fri Sep  7 00:53:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000073.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000073.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2875" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2875.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2875-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000073.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.75 sec.
    Max Memory :         4 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2875-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2875.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2875.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2875.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210954: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000074> was used as the working directory.
Started at Fri Sep  7 00:53:51 2012
Results reported at Fri Sep  7 00:54:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000074.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000074.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2876" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2876.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2876-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000074.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.30 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2876-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2876.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2876.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2876.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 5210955: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000075> was used as the working directory.
Started at Fri Sep  7 00:53:51 2012
Results reported at Fri Sep  7 00:54:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000075.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000075.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2877" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2877.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2877-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000075.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.77 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2877-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2877.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2877.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2877.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1420>
Subject: Job 5210957: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1420>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000076> was used as the working directory.
Started at Fri Sep  7 00:54:13 2012
Results reported at Fri Sep  7 00:54:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000076.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000076.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2878" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2878.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2878-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000076.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.61 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2878-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2878.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2878.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2878.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5210958: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000077> was used as the working directory.
Started at Fri Sep  7 00:54:17 2012
Results reported at Fri Sep  7 00:54:32 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000077.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000077.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2879" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2879.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2879-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000077.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.74 sec.
    Max Memory :         4 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2879-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2879.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2879.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2879.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210960: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000078> was used as the working directory.
Started at Fri Sep  7 00:54:56 2012
Results reported at Fri Sep  7 00:55:29 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000078.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000078.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2880" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2880.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2880-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000078.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.33 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2880-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2880.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2880.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2880.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 5210963: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000079> was used as the working directory.
Started at Fri Sep  7 00:54:56 2012
Results reported at Fri Sep  7 00:55:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000079.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000079.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2881" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2881.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2881-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000079.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.77 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2881-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2881.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2881.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2881.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5210965: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000080> was used as the working directory.
Started at Fri Sep  7 00:55:17 2012
Results reported at Fri Sep  7 00:55:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000080.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000080.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2882" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2882.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2882-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000080.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.94 sec.
    Max Memory :         4 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2882-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2882.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2882.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2882.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 5210967: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000081> was used as the working directory.
Started at Fri Sep  7 00:55:55 2012
Results reported at Fri Sep  7 00:56:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000081.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000081.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2883" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2883.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2883-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000081.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.04 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2883-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2883.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2883.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2883.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5210969: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000082> was used as the working directory.
Started at Fri Sep  7 00:56:18 2012
Results reported at Fri Sep  7 00:56:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000082.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000082.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2884" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2884.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2884-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000082.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.63 sec.
    Max Memory :         4 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2884-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2884.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2884.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2884.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 5210972: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000083> was used as the working directory.
Started at Fri Sep  7 00:56:28 2012
Results reported at Fri Sep  7 00:56:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000083.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000083.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2885" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2885.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2885-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000083.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.60 sec.
    Max Memory :         6 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2885-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2885.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2885.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2885.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1549>
Subject: Job 5210974: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1549>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000084> was used as the working directory.
Started at Fri Sep  7 00:56:32 2012
Results reported at Fri Sep  7 00:57:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000084.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000084.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2886" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2886.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2886-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000084.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     31.64 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2886-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2886.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2886.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2886.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 5210980: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000085> was used as the working directory.
Started at Fri Sep  7 00:56:56 2012
Results reported at Fri Sep  7 00:57:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000085.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000085.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2887" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2887.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2887-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000085.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.22 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2887-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2887.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2887.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2887.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1705>
Subject: Job 5210985: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1705>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000086> was used as the working directory.
Started at Fri Sep  7 00:57:14 2012
Results reported at Fri Sep  7 00:57:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000086.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000086.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2888" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2888.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2888-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000086.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.75 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2888-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2888.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2888.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2888.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5210989: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000087> was used as the working directory.
Started at Fri Sep  7 00:57:18 2012
Results reported at Fri Sep  7 00:57:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000087.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000087.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2889" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2889.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2889-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000087.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.86 sec.
    Max Memory :         4 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2889-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2889.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2889.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2889.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5210993: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000088> was used as the working directory.
Started at Fri Sep  7 00:58:00 2012
Results reported at Fri Sep  7 00:58:32 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000088.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000088.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2890" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2890.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2890-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000088.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.11 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2890-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2890.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2890.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2890.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 5211004: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000089> was used as the working directory.
Started at Fri Sep  7 00:58:00 2012
Results reported at Fri Sep  7 00:58:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000089.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000089.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2891" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2891.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2891-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000089.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.91 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2891-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2891.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2891.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2891.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5211009: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000090> was used as the working directory.
Started at Fri Sep  7 00:58:24 2012
Results reported at Fri Sep  7 00:58:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000090.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000090.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2892" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2892.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2892-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000090.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.59 sec.
    Max Memory :         4 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2892-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2892.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2892.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2892.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1640>
Subject: Job 5211013: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1640>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000091> was used as the working directory.
Started at Fri Sep  7 00:58:43 2012
Results reported at Fri Sep  7 00:59:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000091.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000091.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2893" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2893.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2893-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000091.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.64 sec.
    Max Memory :      4698 MB
    Max Swap   :      5456 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2893-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2893.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2893.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2893.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5211019: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000092> was used as the working directory.
Started at Fri Sep  7 00:59:02 2012
Results reported at Fri Sep  7 00:59:32 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000092.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000092.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2894" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2894.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2894-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000092.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.81 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2894-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2894.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2894.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2894.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 5211023: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000093> was used as the working directory.
Started at Fri Sep  7 00:59:02 2012
Results reported at Fri Sep  7 00:59:19 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000093.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000093.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2895" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2895.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2895-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000093.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.35 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2895-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2895.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2895.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2895.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1647>
Subject: Job 5211029: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1647>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000094> was used as the working directory.
Started at Fri Sep  7 00:59:15 2012
Results reported at Fri Sep  7 00:59:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000094.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000094.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2896" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2896.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2896-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000094.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.90 sec.
    Max Memory :      4697 MB
    Max Swap   :      5457 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2896-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2896.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2896.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2896.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5211032: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000095> was used as the working directory.
Started at Fri Sep  7 00:59:25 2012
Results reported at Fri Sep  7 00:59:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000095.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000095.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2897" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2897.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2897-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000095.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.39 sec.
    Max Memory :         4 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2897-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2897.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2897.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2897.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1558>
Subject: Job 5211044: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1558>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000096> was used as the working directory.
Started at Fri Sep  7 00:59:37 2012
Results reported at Fri Sep  7 01:00:55 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000096.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000096.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2898" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2898.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2898-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000096.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     39.07 sec.
    Max Memory :      4700 MB
    Max Swap   :      5458 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2898-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2898.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2898.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2898.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5211046: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000097> was used as the working directory.
Started at Fri Sep  7 01:00:05 2012
Results reported at Fri Sep  7 01:00:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000097.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000097.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2899" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2899.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2899-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000097.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.43 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2899-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2899.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2899.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2899.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 5211052: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000098> was used as the working directory.
Started at Fri Sep  7 01:00:05 2012
Results reported at Fri Sep  7 01:00:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000098.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000098.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2900" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2900.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2900-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000098.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.20 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2900-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2900.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2900.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2900.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1549>
Subject: Job 5211055: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1549>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000099> was used as the working directory.
Started at Fri Sep  7 01:00:15 2012
Results reported at Fri Sep  7 01:00:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000099.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000099.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2901" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2901.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2901-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000099.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.89 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2901-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2901.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2901.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2901.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1705>
Subject: Job 5211058: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1705>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000100> was used as the working directory.
Started at Fri Sep  7 01:00:18 2012
Results reported at Fri Sep  7 01:00:41 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000100.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000100.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2903" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2903.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2903-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000100.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.36 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2903-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2903.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2903.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2903.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5211062: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000101> was used as the working directory.
Started at Fri Sep  7 01:00:25 2012
Results reported at Fri Sep  7 01:00:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000101.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000101.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2904" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2904.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2904-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000101.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.69 sec.
    Max Memory :         4 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2904-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2904.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2904.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2904.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1640>
Subject: Job 5211067: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1640>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000102> was used as the working directory.
Started at Fri Sep  7 01:00:45 2012
Results reported at Fri Sep  7 01:01:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000102.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000102.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2905" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2905.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2905-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000102.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.20 sec.
    Max Memory :         3 MB
    Max Swap   :        46 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2905-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2905.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2905.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2905.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 5211072: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000103> was used as the working directory.
Started at Fri Sep  7 01:01:13 2012
Results reported at Fri Sep  7 01:01:27 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000103.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000103.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2906" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2906.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2906-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000103.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.83 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2906-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2906.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2906.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2906.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5211075: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000104> was used as the working directory.
Started at Fri Sep  7 01:01:25 2012
Results reported at Fri Sep  7 01:01:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000104.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000104.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2907" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2907.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2907-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000104.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.87 sec.
    Max Memory :         4 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2907-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2907.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2907.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2907.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1422>
Subject: Job 5211079: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1422>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000105> was used as the working directory.
Started at Fri Sep  7 01:01:41 2012
Results reported at Fri Sep  7 01:02:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000105.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000105.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2908" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2908.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2908-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000105.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     30.33 sec.
    Max Memory :      4697 MB
    Max Swap   :      5456 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2908-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2908.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2908.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2908.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5211082: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000106> was used as the working directory.
Started at Fri Sep  7 01:02:14 2012
Results reported at Fri Sep  7 01:02:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000106.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000106.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2909" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2909.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2909-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000106.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.38 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2909-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2909.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2909.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2909.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 5211086: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000107> was used as the working directory.
Started at Fri Sep  7 01:02:14 2012
Results reported at Fri Sep  7 01:02:32 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000107.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000107.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2910" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2910.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2910-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000107.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.62 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2910-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2910.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2910.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2910.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1700>
Subject: Job 5211092: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1700>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000108> was used as the working directory.
Started at Fri Sep  7 01:02:25 2012
Results reported at Fri Sep  7 01:02:43 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000108.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000108.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2911" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2911.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2911-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000108.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.84 sec.
    Max Memory :         4 MB
    Max Swap   :        43 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2911-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2911.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2911.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2911.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1640>
Subject: Job 5211098: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1640>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000109> was used as the working directory.
Started at Fri Sep  7 01:02:46 2012
Results reported at Fri Sep  7 01:03:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000109.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000109.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2912" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2912.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2912-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000109.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.07 sec.
    Max Memory :         3 MB
    Max Swap   :        46 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2912-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2912.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2912.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2912.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5211101: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000110> was used as the working directory.
Started at Fri Sep  7 01:03:14 2012
Results reported at Fri Sep  7 01:03:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000110.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000110.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2913" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2913.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2913-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000110.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.46 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2913-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2913.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2913.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2913.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 5211107: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000111> was used as the working directory.
Started at Fri Sep  7 01:03:14 2012
Results reported at Fri Sep  7 01:03:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000111.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000111.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2914" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2914.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2914-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000111.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.53 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2914-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2914.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2914.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2914.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5211112: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000112> was used as the working directory.
Started at Fri Sep  7 01:04:16 2012
Results reported at Fri Sep  7 01:04:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000112.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000112.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2915" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2915.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2915-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000112.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.33 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2915-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2915.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2915.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2915.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1640>
Subject: Job 5211165: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1640>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000113> was used as the working directory.
Started at Fri Sep  7 01:04:56 2012
Results reported at Fri Sep  7 01:05:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000113.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000113.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2916" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2916.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2916-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000113.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.43 sec.
    Max Memory :         3 MB
    Max Swap   :        46 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2916-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2916.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2916.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2916.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1425>
Subject: Job 5211171: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1425>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000114> was used as the working directory.
Started at Fri Sep  7 01:04:56 2012
Results reported at Fri Sep  7 01:06:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000114.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000114.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2917" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2917.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2917-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000114.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     39.84 sec.
    Max Memory :      4696 MB
    Max Swap   :      5519 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2917-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2917.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2917.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2917.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1420>
Subject: Job 5211178: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1420>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000115> was used as the working directory.
Started at Fri Sep  7 01:05:05 2012
Results reported at Fri Sep  7 01:05:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000115.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000115.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2918" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2918.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2918-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000115.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.66 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2918-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2918.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2918.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2918.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5211184: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000116> was used as the working directory.
Started at Fri Sep  7 01:05:16 2012
Results reported at Fri Sep  7 01:05:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000116.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000116.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2919" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2919.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2919-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000116.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.48 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2919-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2919.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2919.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2919.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1705>
Subject: Job 5211189: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1705>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000117> was used as the working directory.
Started at Fri Sep  7 01:05:38 2012
Results reported at Fri Sep  7 01:05:55 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000117.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000117.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2920" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2920.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2920-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000117.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.16 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2920-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2920.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2920.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2920.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5211194: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000118> was used as the working directory.
Started at Fri Sep  7 01:06:17 2012
Results reported at Fri Sep  7 01:06:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000118.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000118.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2921" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2921.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2921-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000118.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.28 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2921-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2921.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2921.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2921.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1533>
Subject: Job 5211198: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1533>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000119> was used as the working directory.
Started at Fri Sep  7 01:06:57 2012
Results reported at Fri Sep  7 01:08:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000119.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000119.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2922" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2922.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2922-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000119.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     38.48 sec.
    Max Memory :      4697 MB
    Max Swap   :      5456 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2922-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2922.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2922.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2922.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1640>
Subject: Job 5211203: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1640>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000120> was used as the working directory.
Started at Fri Sep  7 01:07:01 2012
Results reported at Fri Sep  7 01:07:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000120.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000120.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2923" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2923.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2923-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000120.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.31 sec.
    Max Memory :         3 MB
    Max Swap   :        46 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2923-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2923.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2923.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2923.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5211209: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000121> was used as the working directory.
Started at Fri Sep  7 01:07:19 2012
Results reported at Fri Sep  7 01:07:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000121.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000121.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2924" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2924.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2924-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000121.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.36 sec.
    Max Memory :         4 MB
    Max Swap   :        40 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2924-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2924.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2924.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2924.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1708>
Subject: Job 5211215: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1708>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000122> was used as the working directory.
Started at Fri Sep  7 01:07:19 2012
Results reported at Fri Sep  7 01:07:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000122.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000122.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2925" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2925.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2925-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000122.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.26 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2925-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2925.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2925.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2925.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1558>
Subject: Job 5211221: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1558>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000123> was used as the working directory.
Started at Fri Sep  7 01:07:34 2012
Results reported at Fri Sep  7 01:08:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000123.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000123.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2926" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2926.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2926-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000123.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.35 sec.
    Max Memory :         4 MB
    Max Swap   :        45 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2926-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2926.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2926.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2926.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1709>
Subject: Job 5211226: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1709>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000124> was used as the working directory.
Started at Fri Sep  7 01:07:48 2012
Results reported at Fri Sep  7 01:08:43 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000124.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000124.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2927" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2927.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2927-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000124.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.78 sec.
    Max Memory :      4694 MB
    Max Swap   :      5455 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2927-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2927.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2927.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2927.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5211232: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000125> was used as the working directory.
Started at Fri Sep  7 01:08:22 2012
Results reported at Fri Sep  7 01:08:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000125.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000125.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2928" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2928.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2928-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000125.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.22 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2928-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2928.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2928.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2928.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1650>
Subject: Job 5211237: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1650>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000126> was used as the working directory.
Started at Fri Sep  7 01:08:36 2012
Results reported at Fri Sep  7 01:09:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000126.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000126.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2929" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2929.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2929-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000126.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.62 sec.
    Max Memory :      4698 MB
    Max Swap   :      5459 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2929-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2929.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2929.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2929.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1420>
Subject: Job 5211243: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1420>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000127> was used as the working directory.
Started at Fri Sep  7 01:09:20 2012
Results reported at Fri Sep  7 01:09:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000127.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000127.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2930" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2930.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2930-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000127.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.40 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2930-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2930.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2930.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2930.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5211246: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000128> was used as the working directory.
Started at Fri Sep  7 01:09:26 2012
Results reported at Fri Sep  7 01:09:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000128.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000128.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2931" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2931.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2931-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000128.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.34 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2931-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2931.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2931.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2931.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1422>
Subject: Job 5211250: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1422>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000129> was used as the working directory.
Started at Fri Sep  7 01:09:44 2012
Results reported at Fri Sep  7 01:10:15 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000129.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000129.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2932" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2932.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2932-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000129.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.66 sec.
    Max Memory :         3 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2932-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2932.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2932.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2932.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1709>
Subject: Job 5211256: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1709>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000130> was used as the working directory.
Started at Fri Sep  7 01:10:21 2012
Results reported at Fri Sep  7 01:10:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000130.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000130.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2933" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2933.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2933-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000130.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.33 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2933-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2933.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2933.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2933.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5211261: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000131> was used as the working directory.
Started at Fri Sep  7 01:10:30 2012
Results reported at Fri Sep  7 01:11:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000131.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000131.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2934" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2934.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2934-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000131.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.50 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2934-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2934.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2934.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2934.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1431>
Subject: Job 5211268: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1431>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000132> was used as the working directory.
Started at Fri Sep  7 01:10:48 2012
Results reported at Fri Sep  7 01:11:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000132.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000132.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2935" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2935.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2935-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000132.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     38.09 sec.
    Max Memory :      4698 MB
    Max Swap   :      5458 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2935-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2935.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2935.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2935.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1558>
Subject: Job 5211273: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1558>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000133> was used as the working directory.
Started at Fri Sep  7 01:10:54 2012
Results reported at Fri Sep  7 01:11:23 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000133.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000133.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2936" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2936.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2936-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000133.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.81 sec.
    Max Memory :         4 MB
    Max Swap   :        45 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2936-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2936.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2936.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2936.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1640>
Subject: Job 5211280: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1640>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000134> was used as the working directory.
Started at Fri Sep  7 01:11:05 2012
Results reported at Fri Sep  7 01:11:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000134.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000134.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2937" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2937.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2937-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000134.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.38 sec.
    Max Memory :         3 MB
    Max Swap   :        46 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2937-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2937.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2937.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2937.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5211287: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000135> was used as the working directory.
Started at Fri Sep  7 01:11:35 2012
Results reported at Fri Sep  7 01:12:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000135.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000135.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2938" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2938.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2938-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000135.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     26.91 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2938-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2938.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2938.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2938.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1647>
Subject: Job 5211294: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1647>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000136> was used as the working directory.
Started at Fri Sep  7 01:11:37 2012
Results reported at Fri Sep  7 01:11:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000136.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000136.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2939" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2939.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2939-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000136.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.99 sec.
    Max Memory :        10 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2939-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2939.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2939.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2939.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1536>
Subject: Job 5211301: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1536>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000137> was used as the working directory.
Started at Fri Sep  7 01:12:35 2012
Results reported at Fri Sep  7 01:13:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000137.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000137.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2940" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2940.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2940-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000137.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     37.65 sec.
    Max Memory :      4707 MB
    Max Swap   :      5465 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2940-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2940.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2940.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2940.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1640>
Subject: Job 5211305: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1640>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000138> was used as the working directory.
Started at Fri Sep  7 01:13:05 2012
Results reported at Fri Sep  7 01:13:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000138.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000138.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2941" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2941.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2941-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000138.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.61 sec.
    Max Memory :         3 MB
    Max Swap   :        46 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2941-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2941.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2941.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2941.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5211311: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000139> was used as the working directory.
Started at Fri Sep  7 01:13:39 2012
Results reported at Fri Sep  7 01:14:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000139.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000139.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2942" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2942.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2942-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000139.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.62 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2942-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2942.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2942.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2942.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1558>
Subject: Job 5211314: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1558>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000140> was used as the working directory.
Started at Fri Sep  7 01:13:39 2012
Results reported at Fri Sep  7 01:14:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000140.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000140.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2943" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2943.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2943-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000140.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.19 sec.
    Max Memory :         4 MB
    Max Swap   :        45 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2943-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2943.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2943.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2943.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1431>
Subject: Job 5211322: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1431>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000141> was used as the working directory.
Started at Fri Sep  7 01:13:55 2012
Results reported at Fri Sep  7 01:14:29 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000141.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000141.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2944" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2944.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2944-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000141.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.29 sec.
    Max Memory :         4 MB
    Max Swap   :        42 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2944-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2944.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2944.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2944.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1640>
Subject: Job 5211324: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1640>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000142> was used as the working directory.
Started at Fri Sep  7 01:17:07 2012
Results reported at Fri Sep  7 01:17:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000142.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000142.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2945" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2945.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2945-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000142.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.15 sec.
    Max Memory :         3 MB
    Max Swap   :        46 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2945-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2945.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2945.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2945.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1423>
Subject: Job 5211331: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1423>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000143> was used as the working directory.
Started at Sat Sep  8 11:08:53 2012
Results reported at Sat Sep  8 11:10:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000143.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000143.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2946" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2946.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2946-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000143.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     38.83 sec.
    Max Memory :      4699 MB
    Max Swap   :      5459 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2946-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2946.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2946.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2946.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1531>
Subject: Job 5211336: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1531>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000144> was used as the working directory.
Started at Sat Sep  8 11:09:44 2012
Results reported at Sat Sep  8 11:11:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000144.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000144.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2947" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2947.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2947-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000144.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     41.29 sec.
    Max Memory :      4702 MB
    Max Swap   :      5459 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2947-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2947.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2947.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2947.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1707>
Subject: Job 5211341: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1707>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000145> was used as the working directory.
Started at Sat Sep  8 11:11:47 2012
Results reported at Sat Sep  8 11:13:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000145.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000145.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2948" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2948.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2948-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000145.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.20 sec.
    Max Memory :      4698 MB
    Max Swap   :      5460 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2948-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2948.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2948.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2948.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1418>
Subject: Job 5211345: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1418>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000146> was used as the working directory.
Started at Sat Sep  8 11:13:53 2012
Results reported at Sat Sep  8 11:16:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000146.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000146.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2949" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2949.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2949-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000146.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     41.00 sec.
    Max Memory :      4697 MB
    Max Swap   :      5456 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2949-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2949.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2949.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2949.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1419>
Subject: Job 5211353: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1419>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000147> was used as the working directory.
Started at Sat Sep  8 11:15:57 2012
Results reported at Sat Sep  8 11:17:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000147.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000147.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2950" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2950.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2950-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000147.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     40.82 sec.
    Max Memory :      4692 MB
    Max Swap   :      5458 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2950-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2950.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2950.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2950.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1645>
Subject: Job 5211358: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1645>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000148> was used as the working directory.
Started at Sat Sep  8 11:16:57 2012
Results reported at Sat Sep  8 11:17:49 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000148.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000148.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2952" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2952.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2952-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000148.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.51 sec.
    Max Memory :      4698 MB
    Max Swap   :      5458 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2952-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2952.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2952.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2952.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1643>
Subject: Job 5211360: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1643>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000149> was used as the working directory.
Started at Sat Sep  8 11:20:05 2012
Results reported at Sat Sep  8 11:20:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000149.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000149.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2954" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2954.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2954-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000149.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     20.56 sec.
    Max Memory :      4698 MB
    Max Swap   :      5460 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2954-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2954.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2954.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2954.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1531>
Subject: Job 5211362: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1531>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000150> was used as the working directory.
Started at Sat Sep  8 11:23:32 2012
Results reported at Sat Sep  8 11:26:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000150.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000150.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2955" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2955.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2955-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000150.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     40.00 sec.
    Max Memory :      4710 MB
    Max Swap   :      5469 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2955-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2955.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2955.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2955.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1703>
Subject: Job 5211364: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1703>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000151> was used as the working directory.
Started at Sat Sep  8 11:24:14 2012
Results reported at Sat Sep  8 11:26:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000151.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000151.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2956" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2956.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2956-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000151.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     21.18 sec.
    Max Memory :      4728 MB
    Max Swap   :      5465 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2956-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2956.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2956.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2956.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1538>
Subject: Job 5211366: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1538>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000152> was used as the working directory.
Started at Sat Sep  8 11:26:32 2012
Results reported at Sat Sep  8 11:28:49 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000152.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000152.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2957" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2957.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2957-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000152.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     41.38 sec.
    Max Memory :      4699 MB
    Max Swap   :      5458 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2957-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2957.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2957.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2957.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 5211370: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000153> was used as the working directory.
Started at Sat Sep  8 11:26:34 2012
Results reported at Sat Sep  8 11:28:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000153.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000153.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2959" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2959.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2959-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000153.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.27 sec.
    Max Memory :      4694 MB
    Max Swap   :      5455 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2959-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2959.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2959.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2959.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1713>
Subject: Job 5211373: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1713>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000154> was used as the working directory.
Started at Sat Sep  8 11:27:27 2012
Results reported at Sat Sep  8 11:29:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000154.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000154.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2963" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2963.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2963-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000154.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.22 sec.
    Max Memory :      4730 MB
    Max Swap   :      5467 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2963-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2963.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2963.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2963.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 5211376: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000155> was used as the working directory.
Started at Sat Sep  8 11:27:34 2012
Results reported at Sat Sep  8 11:29:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000155.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000155.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2964" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2964.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2964-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000155.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.62 sec.
    Max Memory :      4698 MB
    Max Swap   :      5458 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2964-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2964.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2964.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2964.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 5211381: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000156> was used as the working directory.
Started at Sat Sep  8 11:29:10 2012
Results reported at Sat Sep  8 11:29:26 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000156.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000156.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2965" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2965.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2965-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000156.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.30 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2965-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2965.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2965.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2965.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1651>
Subject: Job 5211385: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1651>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000157> was used as the working directory.
Started at Sat Sep  8 11:30:11 2012
Results reported at Sat Sep  8 11:30:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000157.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000157.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2966" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2966.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2966-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000157.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.59 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2966-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2966.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2966.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2966.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1550>
Subject: Job 5211390: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1550>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000158> was used as the working directory.
Started at Sat Sep  8 11:30:35 2012
Results reported at Sat Sep  8 11:31:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000158.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000158.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2967" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2967.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2967-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000158.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     38.16 sec.
    Max Memory :      4706 MB
    Max Swap   :      5464 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2967-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2967.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2967.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2967.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1542>
Subject: Job 5211395: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1542>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000159> was used as the working directory.
Started at Sat Sep  8 11:30:35 2012
Results reported at Sat Sep  8 11:31:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000159.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000159.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2968" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2968.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2968-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000159.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     37.52 sec.
    Max Memory :      4701 MB
    Max Swap   :      5461 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2968-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2968.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2968.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2968.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1558>
Subject: Job 5211401: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1558>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000160> was used as the working directory.
Started at Sat Sep  8 11:30:35 2012
Results reported at Sat Sep  8 11:31:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000160.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000160.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2969" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2969.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2969-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000160.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     36.22 sec.
    Max Memory :      4701 MB
    Max Swap   :      5460 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2969-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2969.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2969.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2969.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 5211406: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000161> was used as the working directory.
Started at Sat Sep  8 11:30:42 2012
Results reported at Sat Sep  8 11:30:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000161.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000161.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2970" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2970.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2970-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000161.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.12 sec.
    Max Memory :         4 MB
    Max Swap   :        46 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2970-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2970.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2970.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2970.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1558>
Subject: Job 5211410: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1558>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000162> was used as the working directory.
Started at Sat Sep  8 11:38:14 2012
Results reported at Sat Sep  8 11:38:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000162.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000162.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2971" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2971.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2971-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000162.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.06 sec.
    Max Memory :         4 MB
    Max Swap   :        45 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2971-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2971.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2971.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2971.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1558>
Subject: Job 5211415: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1558>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000163> was used as the working directory.
Started at Sat Sep  8 11:39:30 2012
Results reported at Sat Sep  8 11:39:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000163.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000163.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2972" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2972.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2972-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000163.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     26.73 sec.
    Max Memory :         4 MB
    Max Swap   :        45 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2972-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2972.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2972.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2972.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1558>
Subject: Job 5211422: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1558>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000164> was used as the working directory.
Started at Sat Sep  8 11:40:30 2012
Results reported at Sat Sep  8 11:40:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000164.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000164.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2973" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2973.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2973-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000164.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     28.11 sec.
    Max Memory :         4 MB
    Max Swap   :        45 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2973-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2973.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2973.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2973.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1537>
Subject: Job 5211424: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1537>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000165> was used as the working directory.
Started at Sat Sep  8 11:40:48 2012
Results reported at Sat Sep  8 11:42:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000165.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000165.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2974" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2974.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2974-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000165.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     38.51 sec.
    Max Memory :      4698 MB
    Max Swap   :      5457 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2974-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2974.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2974.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2974.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1550>
Subject: Job 5211427: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1550>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000166> was used as the working directory.
Started at Sat Sep  8 11:43:21 2012
Results reported at Sat Sep  8 11:43:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000166.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000166.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2976" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2976.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2976-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000166.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     26.94 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2976-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2976.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2976.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2976.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1550>
Subject: Job 5211433: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1550>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000167> was used as the working directory.
Started at Sat Sep  8 11:44:22 2012
Results reported at Sat Sep  8 11:44:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000167.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000167.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2977" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2977.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2977-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000167.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.00 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2977-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2977.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2977.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2977.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 5211440: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000168> was used as the working directory.
Started at Sat Sep  8 11:50:01 2012
Results reported at Sat Sep  8 11:50:20 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000168.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000168.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2978" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2978.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2978-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000168.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.54 sec.
    Max Memory :         4 MB
    Max Swap   :        46 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2978-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2978.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2978.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2978.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1550>
Subject: Job 5211444: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1550>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000169> was used as the working directory.
Started at Sat Sep  8 11:50:01 2012
Results reported at Sat Sep  8 11:50:28 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000169.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000169.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2979" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2979.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2979-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000169.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     26.91 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2979-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2979.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2979.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2979.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 5211450: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000170> was used as the working directory.
Started at Sat Sep  8 11:51:01 2012
Results reported at Sat Sep  8 11:51:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000170.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000170.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2980" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2980.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2980-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000170.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.96 sec.
    Max Memory :         4 MB
    Max Swap   :        46 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2980-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2980.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2980.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2980.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1550>
Subject: Job 5211453: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1550>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000171> was used as the working directory.
Started at Sat Sep  8 11:51:01 2012
Results reported at Sat Sep  8 11:51:26 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000171.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000171.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2981" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2981.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2981-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000171.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.57 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2981-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2981.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2981.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2981.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1421>
Subject: Job 5211457: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1421>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000172> was used as the working directory.
Started at Sat Sep  8 11:51:25 2012
Results reported at Sat Sep  8 11:53:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000172.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000172.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2982" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2982.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2982-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000172.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     40.50 sec.
    Max Memory :      4697 MB
    Max Swap   :      5457 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2982-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2982.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2982.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2982.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 5211463: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000173> was used as the working directory.
Started at Sat Sep  8 11:52:02 2012
Results reported at Sat Sep  8 11:52:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000173.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000173.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2983" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2983.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2983-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000173.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.03 sec.
    Max Memory :         4 MB
    Max Swap   :        46 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2983-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2983.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2983.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2983.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 5211469: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000174> was used as the working directory.
Started at Sat Sep  8 11:53:19 2012
Results reported at Sat Sep  8 11:53:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000174.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000174.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2984" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2984.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2984-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000174.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.26 sec.
    Max Memory :         4 MB
    Max Swap   :        46 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2984-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2984.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2984.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2984.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 5211474: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000175> was used as the working directory.
Started at Sat Sep  8 11:53:19 2012
Results reported at Sat Sep  8 11:55:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000175.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000175.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2985" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2985.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2985-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000175.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.74 sec.
    Max Memory :      4697 MB
    Max Swap   :      5458 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2985-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2985.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2985.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2985.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 5211478: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000176> was used as the working directory.
Started at Sat Sep  8 11:54:22 2012
Results reported at Sat Sep  8 11:54:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000176.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000176.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2986" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2986.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2986-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000176.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.48 sec.
    Max Memory :         4 MB
    Max Swap   :        46 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2986-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2986.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2986.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2986.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1531>
Subject: Job 5211484: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1531>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000177> was used as the working directory.
Started at Sat Sep  8 11:54:53 2012
Results reported at Sat Sep  8 11:55:34 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000177.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000177.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2987" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2987.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2987-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000177.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.69 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2987-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2987.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2987.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2987.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1649>
Subject: Job 5211488: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1649>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000178> was used as the working directory.
Started at Sat Sep  8 11:55:32 2012
Results reported at Sat Sep  8 11:55:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000178.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000178.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2988" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2988.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2988-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000178.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.29 sec.
    Max Memory :         4 MB
    Max Swap   :        46 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2988-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2988.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2988.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2988.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 5211494: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000179> was used as the working directory.
Started at Sat Sep  8 11:55:57 2012
Results reported at Sat Sep  8 11:56:14 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000179.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000179.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2989" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2989.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2989-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000179.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.93 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2989-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2989.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2989.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2989.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1531>
Subject: Job 5211500: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1531>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000180> was used as the working directory.
Started at Sat Sep  8 11:55:57 2012
Results reported at Sat Sep  8 11:56:23 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000180.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000180.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2990" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2990.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2990-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000180.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     29.72 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2990-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2990.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2990.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2990.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1642>
Subject: Job 5211506: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1642>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000181> was used as the working directory.
Started at Sat Sep  8 11:56:37 2012
Results reported at Sat Sep  8 11:58:13 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000181.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000181.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2991" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2991.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2991-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000181.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     26.18 sec.
    Max Memory :      4698 MB
    Max Swap   :      5474 MB

    Max Processes  :         4
    Max Threads    :        32

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2991-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2991.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2991.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2991.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 5211511: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000182> was used as the working directory.
Started at Sat Sep  8 11:57:03 2012
Results reported at Sat Sep  8 11:57:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000182.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000182.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2992" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2992.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2992-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000182.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.80 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2992-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2992.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2992.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2992.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1531>
Subject: Job 5211518: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1531>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000183> was used as the working directory.
Started at Sat Sep  8 11:57:03 2012
Results reported at Sat Sep  8 11:57:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000183.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000183.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2993" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2993.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2993-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000183.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.56 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2993-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2993.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2993.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2993.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 5211525: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000184> was used as the working directory.
Started at Sat Sep  8 11:58:05 2012
Results reported at Sat Sep  8 11:58:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000184.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000184.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2994" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2994.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2994-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000184.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.26 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2994-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2994.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2994.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2994.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1531>
Subject: Job 5211531: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1531>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000185> was used as the working directory.
Started at Sat Sep  8 11:58:05 2012
Results reported at Sat Sep  8 11:58:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000185.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000185.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2995" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2995.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2995-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000185.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.32 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2995-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2995.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2995.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2995.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1550>
Subject: Job 5211536: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1550>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000186> was used as the working directory.
Started at Sat Sep  8 11:58:39 2012
Results reported at Sat Sep  8 11:59:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000186.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000186.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2996" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2996.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2996-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000186.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     27.89 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2996-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2996.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2996.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2996.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1426>
Subject: Job 5211541: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1426>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000187> was used as the working directory.
Started at Sat Sep  8 11:59:33 2012
Results reported at Sat Sep  8 12:00:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000187.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000187.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2997" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2997.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2997-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000187.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     39.13 sec.
    Max Memory :      4702 MB
    Max Swap   :      5462 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2997-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2997.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2997.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2997.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1702>
Subject: Job 5211545: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1702>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000188> was used as the working directory.
Started at Sat Sep  8 11:59:51 2012
Results reported at Sat Sep  8 12:00:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000188.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000188.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2998" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2998.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2998-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000188.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.32 sec.
    Max Memory :      4697 MB
    Max Swap   :      5454 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2998-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2998.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2998.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2998.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1642>
Subject: Job 5211551: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1642>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000189> was used as the working directory.
Started at Sat Sep  8 11:59:51 2012
Results reported at Sat Sep  8 12:00:06 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000189.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000189.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-2999" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-2999.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2999-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000189.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.46 sec.
    Max Memory :         5 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2999-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-2999.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-2999.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-2999.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1643>
Subject: Job 5211555: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1643>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000190> was used as the working directory.
Started at Sat Sep  8 12:01:29 2012
Results reported at Sat Sep  8 12:01:49 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000190.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000190.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3000" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-3000.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3000-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000190.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     17.02 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3000-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-3000.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-3000.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-3000.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1714>
Subject: Job 5211561: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1714>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000191> was used as the working directory.
Started at Sat Sep  8 12:01:33 2012
Results reported at Sat Sep  8 12:02:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000191.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000191.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3001" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-3001.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3001-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000191.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     18.03 sec.
    Max Memory :      4696 MB
    Max Swap   :      5457 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3001-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-3001.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-3001.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-3001.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 5211565: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000192> was used as the working directory.
Started at Sat Sep  8 12:02:23 2012
Results reported at Sat Sep  8 12:02:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000192.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000192.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3002" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-3002.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3002-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000192.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.64 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3002-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-3002.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-3002.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-3002.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 5211570: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000193> was used as the working directory.
Started at Sat Sep  8 12:03:24 2012
Results reported at Sat Sep  8 12:03:40 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000193.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000193.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3005" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-3005.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3005-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000193.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.19 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3005-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-3005.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-3005.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-3005.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 5211575: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000194> was used as the working directory.
Started at Sat Sep  8 12:04:29 2012
Results reported at Sat Sep  8 12:04:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000194.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000194.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3006" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-3006.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3006-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000194.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     16.44 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3006-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-3006.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-3006.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-3006.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1702>
Subject: Job 5211581: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1702>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000195> was used as the working directory.
Started at Sat Sep  8 12:08:44 2012
Results reported at Sat Sep  8 12:08:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000195.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000195.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3007" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-3007.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3007-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000195.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     15.93 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3007-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-3007.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-3007.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-3007.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1711>
Subject: Job 5211585: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1711>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000196> was used as the working directory.
Started at Sat Sep  8 12:09:31 2012
Results reported at Sat Sep  8 12:09:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000196.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000196.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3008" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-3008.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3008-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000196.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     14.96 sec.
    Max Memory :         4 MB
    Max Swap   :        41 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3008-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-3008.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-3008.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-3008.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1550>
Subject: Job 5211589: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1550>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000197> was used as the working directory.
Started at Sat Sep  8 12:09:50 2012
Results reported at Sat Sep  8 12:11:49 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000197.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000197.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3009" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-3009.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3009-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000197.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     39.55 sec.
    Max Memory :      4696 MB
    Max Swap   :      5455 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3009-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-3009.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-3009.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-3009.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1420>
Subject: Job 5211595: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1420>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000198> was used as the working directory.
Started at Sat Sep  8 12:12:04 2012
Results reported at Sat Sep  8 12:12:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000198.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000198.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3011" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-3011.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3011-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000198.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     36.55 sec.
    Max Memory :      4701 MB
    Max Swap   :      5457 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3011-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-3011.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-3011.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-3011.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

Sender: LSF System <lsf@node1559>
Subject: Job 5211601: <scatter_162679> Done

Job <scatter_162679> was submitted from host <node1139> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1559>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000199> was used as the working directory.
Started at Sat Sep  8 12:16:06 2012
Results reported at Sat Sep  8 12:18:33 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000199.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000199.tries
java -Xmx5g -jar /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/ExtractFromWigAllChr.jar "/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt" "/xchip/cga1/lawrence/db/context65/all.fwb" 1 65 "LAML-AB-3012" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "LAML-AB-3012.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3012-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/162679/iteration1/scatter.0000000199.tries`
if [ ${return_code} -ne 130 -a ${tries} -lt 3 ]; then
exit 167;
else
echo ${return_code} > exited;
exit 1;
fi
else
touch success
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     43.04 sec.
    Max Memory :      4709 MB
    Max Swap   :      5470 MB

    Max Processes  :         4
    Max Threads    :        24

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Coverage_Calculation__wig/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3012-01.wig.txt
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
  Total coverage = 57693536
Writing coverage FWB file LAML-AB-3012.somatic_coverage.fwb
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY 
Reading targets file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Reading coverage file: LAML-AB-3012.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: LAML-AB-3012.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

Read file <scatter.err> for stderr output of this job.

*** Scatter stdandard err:
*** Scatter retry log:
==> scatter.0000000001.tries <==
1
==> scatter.0000000002.tries <==
1
==> scatter.0000000003.tries <==
1
==> scatter.0000000004.tries <==
1
==> scatter.0000000005.tries <==
1
==> scatter.0000000006.tries <==
1
==> scatter.0000000007.tries <==
1
==> scatter.0000000008.tries <==
1
==> scatter.0000000009.tries <==
1
==> scatter.0000000010.tries <==
1
==> scatter.0000000011.tries <==
1
==> scatter.0000000012.tries <==
1
==> scatter.0000000013.tries <==
1
==> scatter.0000000014.tries <==
1
==> scatter.0000000015.tries <==
1
==> scatter.0000000016.tries <==
1
==> scatter.0000000017.tries <==
1
==> scatter.0000000018.tries <==
1
==> scatter.0000000019.tries <==
1
==> scatter.0000000020.tries <==
1
==> scatter.0000000021.tries <==
1
==> scatter.0000000022.tries <==
1
==> scatter.0000000023.tries <==
1
==> scatter.0000000024.tries <==
1
==> scatter.0000000025.tries <==
1
==> scatter.0000000026.tries <==
1
==> scatter.0000000027.tries <==
1
==> scatter.0000000028.tries <==
1
==> scatter.0000000029.tries <==
1
==> scatter.0000000030.tries <==
1
==> scatter.0000000031.tries <==
1
==> scatter.0000000032.tries <==
1
==> scatter.0000000033.tries <==
1
==> scatter.0000000034.tries <==
1
==> scatter.0000000035.tries <==
1
==> scatter.0000000036.tries <==
1
==> scatter.0000000037.tries <==
1
==> scatter.0000000038.tries <==
1
==> scatter.0000000039.tries <==
1
==> scatter.0000000040.tries <==
1
==> scatter.0000000041.tries <==
1
==> scatter.0000000042.tries <==
1
==> scatter.0000000043.tries <==
1
==> scatter.0000000044.tries <==
1
==> scatter.0000000045.tries <==
1
==> scatter.0000000046.tries <==
1
==> scatter.0000000047.tries <==
1
==> scatter.0000000048.tries <==
1
==> scatter.0000000049.tries <==
1
==> scatter.0000000050.tries <==
1
==> scatter.0000000051.tries <==
1
==> scatter.0000000052.tries <==
1
==> scatter.0000000053.tries <==
1
==> scatter.0000000054.tries <==
1
==> scatter.0000000055.tries <==
1
==> scatter.0000000056.tries <==
1
==> scatter.0000000057.tries <==
1
==> scatter.0000000058.tries <==
1
==> scatter.0000000059.tries <==
1
==> scatter.0000000060.tries <==
1
==> scatter.0000000061.tries <==
1
==> scatter.0000000062.tries <==
1
==> scatter.0000000063.tries <==
1
==> scatter.0000000064.tries <==
1
==> scatter.0000000065.tries <==
1
==> scatter.0000000066.tries <==
1
==> scatter.0000000067.tries <==
1
==> scatter.0000000068.tries <==
1
==> scatter.0000000069.tries <==
1
==> scatter.0000000070.tries <==
1
==> scatter.0000000071.tries <==
1
==> scatter.0000000072.tries <==
1
==> scatter.0000000073.tries <==
1
==> scatter.0000000074.tries <==
1
==> scatter.0000000075.tries <==
1
==> scatter.0000000076.tries <==
1
==> scatter.0000000077.tries <==
1
==> scatter.0000000078.tries <==
1
==> scatter.0000000079.tries <==
1
==> scatter.0000000080.tries <==
1
==> scatter.0000000081.tries <==
1
==> scatter.0000000082.tries <==
1
==> scatter.0000000083.tries <==
1
==> scatter.0000000084.tries <==
1
==> scatter.0000000085.tries <==
1
==> scatter.0000000086.tries <==
1
==> scatter.0000000087.tries <==
1
==> scatter.0000000088.tries <==
1
==> scatter.0000000089.tries <==
1
==> scatter.0000000090.tries <==
1
==> scatter.0000000091.tries <==
1
==> scatter.0000000092.tries <==
1
==> scatter.0000000093.tries <==
1
==> scatter.0000000094.tries <==
1
==> scatter.0000000095.tries <==
1
==> scatter.0000000096.tries <==
1
==> scatter.0000000097.tries <==
1
==> scatter.0000000098.tries <==
1
==> scatter.0000000099.tries <==
1
==> scatter.0000000100.tries <==
1
==> scatter.0000000101.tries <==
1
==> scatter.0000000102.tries <==
1
==> scatter.0000000103.tries <==
1
==> scatter.0000000104.tries <==
1
==> scatter.0000000105.tries <==
1
==> scatter.0000000106.tries <==
1
==> scatter.0000000107.tries <==
1
==> scatter.0000000108.tries <==
1
==> scatter.0000000109.tries <==
1
==> scatter.0000000110.tries <==
1
==> scatter.0000000111.tries <==
1
==> scatter.0000000112.tries <==
1
==> scatter.0000000113.tries <==
1
==> scatter.0000000114.tries <==
1
==> scatter.0000000115.tries <==
1
==> scatter.0000000116.tries <==
1
==> scatter.0000000117.tries <==
1
==> scatter.0000000118.tries <==
1
==> scatter.0000000119.tries <==
1
==> scatter.0000000120.tries <==
1
==> scatter.0000000121.tries <==
1
==> scatter.0000000122.tries <==
1
==> scatter.0000000123.tries <==
1
==> scatter.0000000124.tries <==
1
==> scatter.0000000125.tries <==
1
==> scatter.0000000126.tries <==
1
==> scatter.0000000127.tries <==
1
==> scatter.0000000128.tries <==
1
==> scatter.0000000129.tries <==
1
==> scatter.0000000130.tries <==
1
==> scatter.0000000131.tries <==
1
==> scatter.0000000132.tries <==
1
==> scatter.0000000133.tries <==
1
==> scatter.0000000134.tries <==
1
==> scatter.0000000135.tries <==
1
==> scatter.0000000136.tries <==
1
==> scatter.0000000137.tries <==
1
==> scatter.0000000138.tries <==
1
==> scatter.0000000139.tries <==
1
==> scatter.0000000140.tries <==
1
==> scatter.0000000141.tries <==
1
==> scatter.0000000142.tries <==
1
==> scatter.0000000143.tries <==
1
==> scatter.0000000144.tries <==
1
==> scatter.0000000145.tries <==
1
==> scatter.0000000146.tries <==
1
==> scatter.0000000147.tries <==
1
==> scatter.0000000148.tries <==
1
==> scatter.0000000149.tries <==
1
==> scatter.0000000150.tries <==
1
==> scatter.0000000151.tries <==
1
==> scatter.0000000152.tries <==
1
==> scatter.0000000153.tries <==
1
==> scatter.0000000154.tries <==
1
==> scatter.0000000155.tries <==
1
==> scatter.0000000156.tries <==
1
==> scatter.0000000157.tries <==
1
==> scatter.0000000158.tries <==
1
==> scatter.0000000159.tries <==
1
==> scatter.0000000160.tries <==
1
==> scatter.0000000161.tries <==
1
==> scatter.0000000162.tries <==
1
==> scatter.0000000163.tries <==
1
==> scatter.0000000164.tries <==
1
==> scatter.0000000165.tries <==
1
==> scatter.0000000166.tries <==
1
==> scatter.0000000167.tries <==
1
==> scatter.0000000168.tries <==
1
==> scatter.0000000169.tries <==
1
==> scatter.0000000170.tries <==
1
==> scatter.0000000171.tries <==
1
==> scatter.0000000172.tries <==
1
==> scatter.0000000173.tries <==
1
==> scatter.0000000174.tries <==
1
==> scatter.0000000175.tries <==
1
==> scatter.0000000176.tries <==
1
==> scatter.0000000177.tries <==
1
==> scatter.0000000178.tries <==
1
==> scatter.0000000179.tries <==
1
==> scatter.0000000180.tries <==
1
==> scatter.0000000181.tries <==
1
==> scatter.0000000182.tries <==
1
==> scatter.0000000183.tries <==
1
==> scatter.0000000184.tries <==
1
==> scatter.0000000185.tries <==
1
==> scatter.0000000186.tries <==
1
==> scatter.0000000187.tries <==
1
==> scatter.0000000188.tries <==
1
==> scatter.0000000189.tries <==
1
==> scatter.0000000190.tries <==
1
==> scatter.0000000191.tries <==
1
==> scatter.0000000192.tries <==
1
==> scatter.0000000193.tries <==
1
==> scatter.0000000194.tries <==
1
==> scatter.0000000195.tries <==
1
==> scatter.0000000196.tries <==
1
==> scatter.0000000197.tries <==
1
==> scatter.0000000198.tries <==
1
==> scatter.0000000199.tries <==
1


PS:

Read file <scatter-gather.err.txt> for stderr output of this job.

*** Scatter Gather stdandard err:
ls: iteration1/sg-next-iteration.txt: No such file or directory


PS:

Read file <iterator.err.txt> for stderr output of this job.

