Sender: LSF System <lsf@node1559>
Subject: Job 4406821: <iteration_216172> Done

Job <iteration_216172> was submitted from host <node351> 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/216172> was used as the working directory.
Started at Wed Oct 24 16:41:29 2012
Results reported at Wed Oct 24 16:41:32 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 ${return_code} > exited;
exit 1;
fi
/xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/scatter-gather-iterator.py /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/iterative-scatter-gather.py --job-suffix 216172 --priority 65 cga /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/scatter-gather.xml /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/ProcessCoverageForMutSig.77.3706/
return_code=$?
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/216172
rmdir iteration*
fi
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :      0.57 sec.
    Max Memory :         4 MB
    Max Swap   :        40 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 216172 --priority 65 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@node1728>
Subject: Job 4406817: <gather_216172> Done

Job <gather_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1728>, 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/216172/iteration1> was used as the working directory.
Started at Wed Oct 24 16:38:22 2012
Results reported at Wed Oct 24 16:41:26 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 69 ]; 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/" "READ" "/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/READ/1910979/0.MutSigPreprocess.Finished/READ.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/READ/1910979/0.MutSigPreprocess.Finished/READ.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   :    160.62 sec.
    Max Memory :       939 MB
    Max Swap   :      1817 MB

    Max Processes  :         8
    Max Threads    :        66

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
69 files found
69 files found
69 files found
Creating summed FWB coverage file: ./READ.summed_coverage.fwb
Loading target file: /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
Opening files: 10/69 20/69 30/69 40/69 50/69 60/69 
Summing and writing output file:
1/4293390 Elapsed time is 0.001286 seconds.
100001/4293390 Elapsed time is 1.076808 seconds.
200001/4293390 Elapsed time is 1.837642 seconds.
300001/4293390 Elapsed time is 1.958596 seconds.
400001/4293390 Elapsed time is 2.080780 seconds.
500001/4293390 Elapsed time is 2.221073 seconds.
600001/4293390 Elapsed time is 2.347987 seconds.
700001/4293390 Elapsed time is 2.478838 seconds.
800001/4293390 Elapsed time is 2.609445 seconds.
900001/4293390 Elapsed time is 2.740093 seconds.
1000001/4293390 Elapsed time is 2.963838 seconds.
1100001/4293390 Elapsed time is 3.092355 seconds.
1200001/4293390 Elapsed time is 3.220770 seconds.
1300001/4293390 Elapsed time is 3.352936 seconds.
1400001/4293390 Elapsed time is 3.483225 seconds.
1500001/4293390 Elapsed time is 3.608726 seconds.
1600001/4293390 Elapsed time is 3.738847 seconds.
1700001/4293390 Elapsed time is 3.867684 seconds.
1800001/4293390 Elapsed time is 3.993160 seconds.
1900001/4293390 Elapsed time is 4.123573 seconds.
2000001/4293390 Elapsed time is 4.249125 seconds.
2100001/4293390 Elapsed time is 4.382328 seconds.
2200001/4293390 Elapsed time is 4.507080 seconds.
2300001/4293390 Elapsed time is 4.626278 seconds.
2400001/4293390 Elapsed time is 4.748113 seconds.
2500001/4293390 Elapsed time is 4.867110 seconds.
2600001/4293390 Elapsed time is 4.990253 seconds.
2700001/4293390 Elapsed time is 5.113119 seconds.
2800001/4293390 Elapsed time is 5.235034 seconds.
2900001/4293390 Elapsed time is 5.356755 seconds.
3000001/4293390 Elapsed time is 5.478146 seconds.
3100001/4293390 Elapsed time is 5.600202 seconds.
3200001/4293390 Elapsed time is 5.717967 seconds.
3300001/4293390 Elapsed time is 5.837762 seconds.
3400001/4293390 Elapsed time is 5.959578 seconds.
3500001/4293390 Elapsed time is 6.083932 seconds.
3600001/4293390 Elapsed time is 6.201883 seconds.
3700001/4293390 Elapsed time is 6.320113 seconds.
3800001/4293390 Elapsed time is 6.439572 seconds.
3900001/4293390 Elapsed time is 6.558884 seconds.
4000001/4293390 Elapsed time is 6.679745 seconds.
4100001/4293390 Elapsed time is 6.795640 seconds.
4200001/4293390 Elapsed time is 6.914845 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 21217 N 6187745811  rate 3.43e-06 (1.00x)  ci 3.38e-06 to 3.48e-06

k=2
                  nonflip   n 20357 N 4125163874  rate 4.93e-06 (1.44x)  ci 4.87e-06 to 5.00e-06
                     flip   n   860 N 2062581937  rate 4.17e-07 (0.12x)  ci 3.90e-07 to 4.46e-07

k=3
                *CpG->mut   n  8123 N  339814029  rate 2.39e-05 (6.97x)  ci 2.34e-05 to 2.44e-05
          *Cp(A/C/T)->mut   n  9590 N 2809081827  rate 3.41e-06 (1.00x)  ci 3.35e-06 to 3.48e-06
                   A->mut   n  3504 N 3038849955  rate 1.15e-06 (0.34x)  ci 1.12e-06 to 1.19e-06

k=4
                  *CpG->T   n  7889 N  113271343  rate 6.96e-05 (20.3x)  ci 6.81e-05 to 7.12e-05
          *Cp(A/C/T)->mut   n  9590 N 2809081827  rate 3.41e-06 (1.00x)  ci 3.35e-06 to 3.48e-06
                   A->mut   n  3504 N 3038849955  rate 1.15e-06 (0.34x)  ci 1.12e-06 to 1.19e-06
              *CpG->(G/A)   n   234 N  226542686  rate 1.03e-06 (0.30x)  ci 9.05e-07 to 1.17e-06

Saving ./READ.mutcategs.txt
all files are *.bin: will read in BINARY MODE
69 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 ./READ.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/216172/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/ READ /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/READ/1910979/0.MutSigPreprocess.Finished/READ.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/READ/1910979/0.MutSigPreprocess.Finished/READ.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@node1651>
Subject: Job 4406468: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000001> was used as the working directory.
Started at Wed Oct 24 16:17:12 2012
Results reported at Wed Oct 24 16:18:19 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000001.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AF-2689-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AF-2689-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AF-2689-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     13.53 sec.
    Max Memory :      4424 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AF-2689-01.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 = 32603035
Writing coverage FWB file READ-AF-2689-TP.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: READ-AF-2689-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AF-2689-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1558>
Subject: Job 4406472: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000002> was used as the working directory.
Started at Wed Oct 24 16:17:27 2012
Results reported at Wed Oct 24 16:17:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000002.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AF-2691-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AF-2691-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AF-2691-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     23.09 sec.
    Max Memory :         3 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AF-2691-01.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 = 32603035
Writing coverage FWB file READ-AF-2691-TP.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: READ-AF-2691-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AF-2691-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1643>
Subject: Job 4406476: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000003> was used as the working directory.
Started at Wed Oct 24 16:17:47 2012
Results reported at Wed Oct 24 16:18:35 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000003.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AF-2692-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AF-2692-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AF-2692-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     13.18 sec.
    Max Memory :      4399 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AF-2692-01.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 = 32603035
Writing coverage FWB file READ-AF-2692-TP.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: READ-AF-2692-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AF-2692-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1531>
Subject: Job 4406480: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000004> was used as the working directory.
Started at Wed Oct 24 16:18:03 2012
Results reported at Wed Oct 24 16:18:25 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000004.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AF-3400-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AF-3400-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AF-3400-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     23.03 sec.
    Max Memory :         3 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AF-3400-01.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 = 32603035
Writing coverage FWB file READ-AF-3400-TP.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: READ-AF-3400-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AF-3400-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1418>
Subject: Job 4406483: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000005> was used as the working directory.
Started at Wed Oct 24 16:18:45 2012
Results reported at Wed Oct 24 16:20:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000005.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AF-3913-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AF-3913-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AF-3913-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     34.66 sec.
    Max Memory :      4487 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AF-3913-01.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 = 34357158
Writing coverage FWB file READ-AF-3913-TP.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: READ-AF-3913-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AF-3913-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1705>
Subject: Job 4406486: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000006> was used as the working directory.
Started at Wed Oct 24 16:18:48 2012
Results reported at Wed Oct 24 16:19:01 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000006.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3574-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3574-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3574-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.49 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3574-01.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 = 32603035
Writing coverage FWB file READ-AG-3574-TP.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: READ-AG-3574-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3574-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1655>
Subject: Job 4406492: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1655>, 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/216172/iteration1/scatter.0000000007> was used as the working directory.
Started at Wed Oct 24 16:19:08 2012
Results reported at Wed Oct 24 16:20:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000007.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3575-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3575-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3575-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     13.40 sec.
    Max Memory :      4391 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3575-01.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 = 32603035
Writing coverage FWB file READ-AG-3575-TP.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: READ-AG-3575-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3575-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1535>
Subject: Job 4406498: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1535>, 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/216172/iteration1/scatter.0000000008> was used as the working directory.
Started at Wed Oct 24 16:19:27 2012
Results reported at Wed Oct 24 16:19:48 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000008.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3578-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3578-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3578-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     23.94 sec.
    Max Memory :         3 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3578-01.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 = 32603035
Writing coverage FWB file READ-AG-3578-TP.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: READ-AG-3578-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3578-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1554>
Subject: Job 4406505: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1554>, 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/216172/iteration1/scatter.0000000009> was used as the working directory.
Started at Wed Oct 24 16:19:27 2012
Results reported at Wed Oct 24 16:20:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000009.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3580-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3580-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3580-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     33.31 sec.
    Max Memory :      4483 MB
    Max Swap   :      5453 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3580-01.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 = 32603035
Writing coverage FWB file READ-AG-3580-TP.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: READ-AG-3580-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3580-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1710>
Subject: Job 4406513: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1710>, 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/216172/iteration1/scatter.0000000010> was used as the working directory.
Started at Wed Oct 24 16:19:27 2012
Results reported at Wed Oct 24 16:19:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000010.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3581-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3581-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3581-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     11.91 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3581-01.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 = 32603035
Writing coverage FWB file READ-AG-3581-TP.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: READ-AG-3581-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3581-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1709>
Subject: Job 4406519: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000011> was used as the working directory.
Started at Wed Oct 24 16:19:42 2012
Results reported at Wed Oct 24 16:19:56 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000011.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3582-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3582-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3582-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     13.57 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3582-01.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 = 32603035
Writing coverage FWB file READ-AG-3582-TP.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: READ-AG-3582-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3582-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1705>
Subject: Job 4406524: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000012> was used as the working directory.
Started at Wed Oct 24 16:19:49 2012
Results reported at Wed Oct 24 16:20:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000012.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3583-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3583-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3583-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.18 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3583-01.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 = 32603035
Writing coverage FWB file READ-AG-3583-TP.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: READ-AG-3583-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3583-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1647>
Subject: Job 4406532: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000013> was used as the working directory.
Started at Wed Oct 24 16:20:05 2012
Results reported at Wed Oct 24 16:21:04 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000013.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3584-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3584-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3584-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     14.12 sec.
    Max Memory :      4384 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3584-01.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 = 32603035
Writing coverage FWB file READ-AG-3584-TP.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: READ-AG-3584-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3584-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1544>
Subject: Job 4406536: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000014> was used as the working directory.
Started at Wed Oct 24 16:20:05 2012
Results reported at Wed Oct 24 16:21:05 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000014.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3586-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3586-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3586-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     31.65 sec.
    Max Memory :      4035 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3586-01.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 = 32603035
Writing coverage FWB file READ-AG-3586-TP.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: READ-AG-3586-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3586-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1651>
Subject: Job 4406540: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000015> was used as the working directory.
Started at Wed Oct 24 16:20:14 2012
Results reported at Wed Oct 24 16:20:26 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000015.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3587-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3587-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3587-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.27 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3587-01.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 = 32603035
Writing coverage FWB file READ-AG-3587-TP.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: READ-AG-3587-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3587-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1540>
Subject: Job 4406548: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1540>, 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/216172/iteration1/scatter.0000000016> was used as the working directory.
Started at Wed Oct 24 16:20:20 2012
Results reported at Wed Oct 24 16:21:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000016.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3593-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3593-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3593-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     32.64 sec.
    Max Memory :      4055 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3593-01.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 = 32603035
Writing coverage FWB file READ-AG-3593-TP.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: READ-AG-3593-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3593-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1647>
Subject: Job 4406553: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000017> was used as the working directory.
Started at Wed Oct 24 16:21:05 2012
Results reported at Wed Oct 24 16:21:18 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000017.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3594-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3594-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3594-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.34 sec.
    Max Memory :        11 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3594-01.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 = 32603035
Writing coverage FWB file READ-AG-3594-TP.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: READ-AG-3594-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3594-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1547>
Subject: Job 4406559: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1547>, 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/216172/iteration1/scatter.0000000018> was used as the working directory.
Started at Wed Oct 24 16:21:10 2012
Results reported at Wed Oct 24 16:21:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000018.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3598-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3598-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3598-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     23.73 sec.
    Max Memory :         3 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3598-01.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 = 32603035
Writing coverage FWB file READ-AG-3598-TP.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: READ-AG-3598-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3598-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1705>
Subject: Job 4406564: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000019> was used as the working directory.
Started at Wed Oct 24 16:21:51 2012
Results reported at Wed Oct 24 16:22:06 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000019.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3599-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3599-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3599-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.91 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3599-01.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 = 32603035
Writing coverage FWB file READ-AG-3599-TP.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: READ-AG-3599-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3599-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1651>
Subject: Job 4406568: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000020> was used as the working directory.
Started at Wed Oct 24 16:22:16 2012
Results reported at Wed Oct 24 16:22:29 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000020.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3600-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3600-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3600-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     14.11 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3600-01.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 = 32603035
Writing coverage FWB file READ-AG-3600-TP.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: READ-AG-3600-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3600-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1700>
Subject: Job 4406574: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000021> was used as the working directory.
Started at Wed Oct 24 16:22:16 2012
Results reported at Wed Oct 24 16:23:10 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000021.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3601-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3601-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3601-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     14.14 sec.
    Max Memory :      4414 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3601-01.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 = 32603035
Writing coverage FWB file READ-AG-3601-TP.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: READ-AG-3601-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3601-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1542>
Subject: Job 4406577: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000022> was used as the working directory.
Started at Wed Oct 24 16:22:37 2012
Results reported at Wed Oct 24 16:23:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000022.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3602-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3602-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3602-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     33.11 sec.
    Max Memory :      4083 MB
    Max Swap   :      5520 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3602-01.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 = 32603035
Writing coverage FWB file READ-AG-3602-TP.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: READ-AG-3602-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3602-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1647>
Subject: Job 4406583: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000023> was used as the working directory.
Started at Wed Oct 24 16:23:09 2012
Results reported at Wed Oct 24 16:23:23 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000023.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3605-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3605-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3605-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     13.36 sec.
    Max Memory :        11 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3605-01.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 = 32603035
Writing coverage FWB file READ-AG-3605-TP.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: READ-AG-3605-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3605-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1641>
Subject: Job 4406587: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000024> was used as the working directory.
Started at Wed Oct 24 16:23:17 2012
Results reported at Wed Oct 24 16:23:30 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000024.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3608-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3608-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3608-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     13.09 sec.
    Max Memory :        11 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3608-01.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 = 32603035
Writing coverage FWB file READ-AG-3608-TP.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: READ-AG-3608-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3608-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1419>
Subject: Job 4406592: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000025> was used as the working directory.
Started at Wed Oct 24 16:24:46 2012
Results reported at Wed Oct 24 16:25:54 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000025.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3609-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3609-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3609-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     33.04 sec.
    Max Memory :      4420 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3609-01.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 = 32603035
Writing coverage FWB file READ-AG-3609-TP.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: READ-AG-3609-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3609-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1542>
Subject: Job 4406597: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000026> was used as the working directory.
Started at Wed Oct 24 16:25:10 2012
Results reported at Wed Oct 24 16:25:49 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000026.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3611-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3611-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3611-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     26.36 sec.
    Max Memory :         4 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3611-01.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 = 32603035
Writing coverage FWB file READ-AG-3611-TP.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: READ-AG-3611-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3611-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1647>
Subject: Job 4406602: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000027> was used as the working directory.
Started at Wed Oct 24 16:25:10 2012
Results reported at Wed Oct 24 16:25:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000027.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3612-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3612-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3612-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     13.05 sec.
    Max Memory :        11 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-3612-01.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 = 32603035
Writing coverage FWB file READ-AG-3612-TP.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: READ-AG-3612-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3612-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1709>
Subject: Job 4406607: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000028> was used as the working directory.
Started at Wed Oct 24 16:25:21 2012
Results reported at Wed Oct 24 16:25:37 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000028.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3726-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3726-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3726-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     13.10 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3726-01.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 = 34357158
Writing coverage FWB file READ-AG-3726-TP.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: READ-AG-3726-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3726-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1652>
Subject: Job 4406613: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1652>, 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/216172/iteration1/scatter.0000000029> was used as the working directory.
Started at Wed Oct 24 16:26:20 2012
Results reported at Wed Oct 24 16:27:11 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000029.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3727-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3727-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3727-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     14.66 sec.
    Max Memory :      4412 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3727-01.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 = 34357158
Writing coverage FWB file READ-AG-3727-TP.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: READ-AG-3727-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3727-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1558>
Subject: Job 4406618: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000030> was used as the working directory.
Started at Wed Oct 24 16:27:02 2012
Results reported at Wed Oct 24 16:27:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000030.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3878-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3878-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3878-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     32.52 sec.
    Max Memory :      4365 MB
    Max Swap   :      5513 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3878-01.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 = 34357158
Writing coverage FWB file READ-AG-3878-TP.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: READ-AG-3878-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3878-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1651>
Subject: Job 4406622: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000031> was used as the working directory.
Started at Wed Oct 24 16:27:02 2012
Results reported at Wed Oct 24 16:27:17 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000031.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3881-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3881-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3881-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.36 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3881-01.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 = 34357158
Writing coverage FWB file READ-AG-3881-TP.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: READ-AG-3881-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3881-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1707>
Subject: Job 4406627: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000032> was used as the working directory.
Started at Wed Oct 24 16:27:34 2012
Results reported at Wed Oct 24 16:28:08 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000032.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3882-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3882-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3882-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     14.64 sec.
    Max Memory :         4 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3882-01.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 = 34357158
Writing coverage FWB file READ-AG-3882-TP.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: READ-AG-3882-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3882-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1644>
Subject: Job 4406633: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1644>, 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/216172/iteration1/scatter.0000000033> was used as the working directory.
Started at Wed Oct 24 16:27:34 2012
Results reported at Wed Oct 24 16:28:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000033.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3883-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3883-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3883-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     13.45 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3883-01.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 = 34357158
Writing coverage FWB file READ-AG-3883-TP.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: READ-AG-3883-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3883-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1652>
Subject: Job 4406639: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1652>, 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/216172/iteration1/scatter.0000000034> was used as the working directory.
Started at Wed Oct 24 16:27:34 2012
Results reported at Wed Oct 24 16:27:47 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000034.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3887-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3887-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3887-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.66 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3887-01.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 = 34357158
Writing coverage FWB file READ-AG-3887-TP.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: READ-AG-3887-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3887-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1640>
Subject: Job 4406644: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000035> was used as the working directory.
Started at Wed Oct 24 16:28:06 2012
Results reported at Wed Oct 24 16:28:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000035.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3890-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3890-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3890-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     14.20 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3890-01.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 = 34357158
Writing coverage FWB file READ-AG-3890-TP.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: READ-AG-3890-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3890-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1547>
Subject: Job 4406648: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1547>, 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/216172/iteration1/scatter.0000000036> was used as the working directory.
Started at Wed Oct 24 16:28:14 2012
Results reported at Wed Oct 24 16:28:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000036.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3892-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3892-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3892-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     25.17 sec.
    Max Memory :         3 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3892-01.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 = 34357158
Writing coverage FWB file READ-AG-3892-TP.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: READ-AG-3892-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3892-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1708>
Subject: Job 4406655: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000037> was used as the working directory.
Started at Wed Oct 24 16:28:14 2012
Results reported at Wed Oct 24 16:28:28 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000037.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3893-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3893-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3893-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.16 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3893-01.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 = 34357158
Writing coverage FWB file READ-AG-3893-TP.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: READ-AG-3893-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3893-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1707>
Subject: Job 4406663: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000038> was used as the working directory.
Started at Wed Oct 24 16:28:37 2012
Results reported at Wed Oct 24 16:28:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000038.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3894-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3894-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3894-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.29 sec.
    Max Memory :         4 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3894-01.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 = 34357158
Writing coverage FWB file READ-AG-3894-TP.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: READ-AG-3894-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3894-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1544>
Subject: Job 4406669: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000039> was used as the working directory.
Started at Wed Oct 24 16:28:37 2012
Results reported at Wed Oct 24 16:28:59 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000039.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3896-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3896-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3896-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     24.98 sec.
    Max Memory :         3 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3896-01.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 = 34357158
Writing coverage FWB file READ-AG-3896-TP.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: READ-AG-3896-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3896-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1644>
Subject: Job 4406676: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1644>, 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/216172/iteration1/scatter.0000000040> was used as the working directory.
Started at Wed Oct 24 16:28:37 2012
Results reported at Wed Oct 24 16:28:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000040.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3898-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3898-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3898-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.38 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3898-01.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 = 34357158
Writing coverage FWB file READ-AG-3898-TP.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: READ-AG-3898-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3898-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1651>
Subject: Job 4406681: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000041> was used as the working directory.
Started at Wed Oct 24 16:29:10 2012
Results reported at Wed Oct 24 16:29:22 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000041.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3901-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3901-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3901-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.14 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3901-01.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 = 34357158
Writing coverage FWB file READ-AG-3901-TP.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: READ-AG-3901-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3901-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1643>
Subject: Job 4406685: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000042> was used as the working directory.
Started at Wed Oct 24 16:29:10 2012
Results reported at Wed Oct 24 16:29:24 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000042.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3902-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3902-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3902-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.52 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3902-01.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 = 34357158
Writing coverage FWB file READ-AG-3902-TP.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: READ-AG-3902-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3902-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1708>
Subject: Job 4406690: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000043> was used as the working directory.
Started at Wed Oct 24 16:29:17 2012
Results reported at Wed Oct 24 16:29:32 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000043.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3909-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3909-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3909-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.17 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3909-01.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 = 34357158
Writing coverage FWB file READ-AG-3909-TP.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: READ-AG-3909-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3909-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1551>
Subject: Job 4406696: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1551>, 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/216172/iteration1/scatter.0000000044> was used as the working directory.
Started at Wed Oct 24 16:29:29 2012
Results reported at Wed Oct 24 16:29:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000044.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-3999-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-3999-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3999-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     27.13 sec.
    Max Memory :         4 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-3999-01.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 = 34357158
Writing coverage FWB file READ-AG-3999-TP.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: READ-AG-3999-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-3999-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1707>
Subject: Job 4406702: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000045> was used as the working directory.
Started at Wed Oct 24 16:29:40 2012
Results reported at Wed Oct 24 16:29:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000045.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-4001-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-4001-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4001-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.72 sec.
    Max Memory :         4 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4001-01.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 = 34357158
Writing coverage FWB file READ-AG-4001-TP.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: READ-AG-4001-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-4001-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1644>
Subject: Job 4406705: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1644>, 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/216172/iteration1/scatter.0000000046> was used as the working directory.
Started at Wed Oct 24 16:29:40 2012
Results reported at Wed Oct 24 16:29:52 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000046.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-4005-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-4005-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4005-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.21 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4005-01.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 = 34357158
Writing coverage FWB file READ-AG-4005-TP.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: READ-AG-4005-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-4005-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1708>
Subject: Job 4406712: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000047> was used as the working directory.
Started at Wed Oct 24 16:30:16 2012
Results reported at Wed Oct 24 16:30:28 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000047.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-4007-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-4007-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4007-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.00 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4007-01.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 = 34357158
Writing coverage FWB file READ-AG-4007-TP.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: READ-AG-4007-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-4007-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1707>
Subject: Job 4406718: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000048> was used as the working directory.
Started at Wed Oct 24 16:30:39 2012
Results reported at Wed Oct 24 16:30:53 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000048.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-4008-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-4008-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4008-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     13.18 sec.
    Max Memory :         4 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4008-01.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 = 34357158
Writing coverage FWB file READ-AG-4008-TP.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: READ-AG-4008-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-4008-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1711>
Subject: Job 4406723: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000049> was used as the working directory.
Started at Wed Oct 24 16:31:12 2012
Results reported at Wed Oct 24 16:31:58 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000049.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-4015-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-4015-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4015-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     13.24 sec.
    Max Memory :      4414 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-4015-01.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 = 34357158
Writing coverage FWB file READ-AG-4015-TP.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: READ-AG-4015-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-4015-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1646>
Subject: Job 4406729: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, 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/216172/iteration1/scatter.0000000050> was used as the working directory.
Started at Wed Oct 24 16:31:22 2012
Results reported at Wed Oct 24 16:32:00 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000050.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A002-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A002-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A002-01.wig.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A002-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     17.01 sec.
    Max Memory :      4703 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A002-01.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 = 34357158
Reading coverage wiggle file 2: /xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A002-01.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 = 35047957
Writing coverage FWB file READ-AG-A002-TP.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: READ-AG-A002-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A002-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1651>
Subject: Job 4406733: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000051> was used as the working directory.
Started at Wed Oct 24 16:32:33 2012
Results reported at Wed Oct 24 16:32:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000051.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A008-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A008-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A008-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.36 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A008-01.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 = 32603035
Writing coverage FWB file READ-AG-A008-TP.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: READ-AG-A008-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A008-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1652>
Subject: Job 4406739: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1652>, 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/216172/iteration1/scatter.0000000052> was used as the working directory.
Started at Wed Oct 24 16:33:16 2012
Results reported at Wed Oct 24 16:33:31 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000052.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A00C-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A00C-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A00C-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     13.32 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A00C-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 = 32603035
Writing coverage FWB file READ-AG-A00C-TP.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: READ-AG-A00C-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A00C-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1547>
Subject: Job 4406744: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1547>, 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/216172/iteration1/scatter.0000000053> was used as the working directory.
Started at Wed Oct 24 16:34:03 2012
Results reported at Wed Oct 24 16:34:27 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000053.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A00H-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A00H-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A00H-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     23.69 sec.
    Max Memory :         3 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A00H-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 = 34357158
Writing coverage FWB file READ-AG-A00H-TP.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: READ-AG-A00H-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A00H-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1711>
Subject: Job 4406748: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000054> was used as the working directory.
Started at Wed Oct 24 16:35:26 2012
Results reported at Wed Oct 24 16:35:39 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000054.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A00Y-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A00Y-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A00Y-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.80 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A00Y-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 = 32603035
Writing coverage FWB file READ-AG-A00Y-TP.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: READ-AG-A00Y-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A00Y-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1646>
Subject: Job 4406754: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, 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/216172/iteration1/scatter.0000000055> was used as the working directory.
Started at Wed Oct 24 16:35:34 2012
Results reported at Wed Oct 24 16:35:50 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000055.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A011-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A011-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A011-01.wig.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A011-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     16.15 sec.
    Max Memory :        11 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A011-01.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 = 34357158
Reading coverage wiggle file 2: /xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A011-01.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 = 35047957
Writing coverage FWB file READ-AG-A011-TP.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: READ-AG-A011-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A011-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1551>
Subject: Job 4406757: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1551>, 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/216172/iteration1/scatter.0000000056> was used as the working directory.
Started at Wed Oct 24 16:35:41 2012
Results reported at Wed Oct 24 16:36:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000056.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A014-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A014-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A014-01.wig.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A014-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     32.12 sec.
    Max Memory :         4 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A014-01.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 = 34357158
Reading coverage wiggle file 2: /xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A014-01.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 = 35047957
Writing coverage FWB file READ-AG-A014-TP.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: READ-AG-A014-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A014-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1649>
Subject: Job 4406762: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000057> was used as the working directory.
Started at Wed Oct 24 16:35:52 2012
Results reported at Wed Oct 24 16:36:38 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000057.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A015-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A015-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A015-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     13.64 sec.
    Max Memory :      4391 MB
    Max Swap   :      5395 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A015-01.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 = 32603035
Writing coverage FWB file READ-AG-A015-TP.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: READ-AG-A015-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A015-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1711>
Subject: Job 4406768: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000058> was used as the working directory.
Started at Wed Oct 24 16:36:31 2012
Results reported at Wed Oct 24 16:36:42 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000058.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A016-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A016-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A016-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.42 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/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A016-01.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 = 32603035
Writing coverage FWB file READ-AG-A016-TP.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: READ-AG-A016-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A016-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1646>
Subject: Job 4406772: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, 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/216172/iteration1/scatter.0000000059> was used as the working directory.
Started at Wed Oct 24 16:36:35 2012
Results reported at Wed Oct 24 16:36:57 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000059.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A01L-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A01L-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A01L-01.wig.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A01L-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     16.32 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A01L-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 = 34357158
Reading coverage wiggle file 2: /xchip/gdac_data/normalized/diced/read/tracerel__solid_dna__bcm_edu__Level_2__Coverage_Calculation__wig/bcm.edu_READ.SOLiD_DNA.Level_2.1.3.0/TCGA-AG-A01L-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 = 35047957
Writing coverage FWB file READ-AG-A01L-TP.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: READ-AG-A01L-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A01L-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1551>
Subject: Job 4406777: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1551>, 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/216172/iteration1/scatter.0000000060> was used as the working directory.
Started at Wed Oct 24 16:36:41 2012
Results reported at Wed Oct 24 16:37:03 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000060.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A01W-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A01W-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A01W-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     24.04 sec.
    Max Memory :         3 MB
    Max Swap   :        40 MB

    Max Processes  :         2
    Max Threads    :         2

The output (if any) follows:

initialized lengths from referenceInfo
Reading coverage wiggle file 1: /xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A01W-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 = 34357158
Writing coverage FWB file READ-AG-A01W-TP.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: READ-AG-A01W-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A01W-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1649>
Subject: Job 4406781: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000061> was used as the working directory.
Started at Wed Oct 24 16:36:54 2012
Results reported at Wed Oct 24 16:37:07 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000061.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A01Y-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A01Y-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A01Y-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.81 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A01Y-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 = 34357158
Writing coverage FWB file READ-AG-A01Y-TP.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: READ-AG-A01Y-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A01Y-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1730>
Subject: Job 4406785: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1730>, 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/216172/iteration1/scatter.0000000062> was used as the working directory.
Started at Wed Oct 24 16:36:59 2012
Results reported at Wed Oct 24 16:37:21 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000062.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A020-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A020-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A020-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.29 sec.
    Max Memory :        11 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A020-01.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 = 34357158
Writing coverage FWB file READ-AG-A020-TP.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: READ-AG-A020-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A020-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1725>
Subject: Job 4406788: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1725>, 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/216172/iteration1/scatter.0000000063> was used as the working directory.
Started at Wed Oct 24 16:37:07 2012
Results reported at Wed Oct 24 16:37:28 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000063.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A025-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A025-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A025-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     13.13 sec.
    Max Memory :        11 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A025-01.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 = 34357158
Writing coverage FWB file READ-AG-A025-TP.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: READ-AG-A025-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A025-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1727>
Subject: Job 4406791: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1727>, 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/216172/iteration1/scatter.0000000064> was used as the working directory.
Started at Wed Oct 24 16:37:12 2012
Results reported at Wed Oct 24 16:37:36 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000064.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A026-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A026-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A026-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.49 sec.
    Max Memory :         5 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A026-01.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 = 34357158
Writing coverage FWB file READ-AG-A026-TP.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: READ-AG-A026-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A026-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1728>
Subject: Job 4406796: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1728>, 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/216172/iteration1/scatter.0000000065> was used as the working directory.
Started at Wed Oct 24 16:37:22 2012
Results reported at Wed Oct 24 16:37:44 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000065.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A02G-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A02G-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A02G-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.85 sec.
    Max Memory :        11 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A02G-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 = 34357158
Writing coverage FWB file READ-AG-A02G-TP.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: READ-AG-A02G-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A02G-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1557>
Subject: Job 4406799: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1557>, 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/216172/iteration1/scatter.0000000066> was used as the working directory.
Started at Wed Oct 24 16:37:31 2012
Results reported at Wed Oct 24 16:38:12 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000066.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A02N-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A02N-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A02N-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     31.12 sec.
    Max Memory :      4297 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A02N-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 = 34357158
Writing coverage FWB file READ-AG-A02N-TP.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: READ-AG-A02N-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A02N-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1711>
Subject: Job 4406803: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> 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/216172/iteration1/scatter.0000000067> was used as the working directory.
Started at Wed Oct 24 16:37:31 2012
Results reported at Wed Oct 24 16:37:45 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000067.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A02X-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A02X-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A02X-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.83 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A02X-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 = 34357158
Writing coverage FWB file READ-AG-A02X-TP.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: READ-AG-A02X-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A02X-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1646>
Subject: Job 4406809: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1646>, 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/216172/iteration1/scatter.0000000068> was used as the working directory.
Started at Wed Oct 24 16:37:34 2012
Results reported at Wed Oct 24 16:37:46 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000068.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A032-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A032-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A032-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     12.42 sec.
    Max Memory :        11 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A032-01.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 = 34357158
Writing coverage FWB file READ-AG-A032-TP.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: READ-AG-A032-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A032-TP.somatic_coverage.txt.bin
chr1chr2chr3chr4chr5chr6chr7chr8chr9chr10chr11chr12chr13chr14chr15chr16chr17chr18chr19chr20chr21chr22chr23chr24
Done.


PS:

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

Sender: LSF System <lsf@node1723>
Subject: Job 4406814: <scatter_216172> Done

Job <scatter_216172> was submitted from host <node351> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1723>, 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/216172/iteration1/scatter.0000000069> was used as the working directory.
Started at Wed Oct 24 16:37:34 2012
Results reported at Wed Oct 24 16:37:51 2012

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/iteration1/scatter.0000000069.tries`
echo -n `expr ${tries} + 1` > /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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 "READ-AG-A036-TP" "hg18" "/xchip/cga1/annotation/db/ucsc/hg18" "READ-AG-A036-TP.somatic_coverage.txt" "/xchip/gdac_data/normalized/diced/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A036-01.wig.txt"

return_code=$?
if [ ${return_code} -ne 0 ]; then
tries=`cat /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/216172/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   :     15.80 sec.
    Max Memory :        11 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/read/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Coverage_Calculation__wig/broad.mit.edu_READ.IlluminaGA_DNASeq.Level_2.1.0.0/TCGA-AG-A036-01.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 = 34357158
Writing coverage FWB file READ-AG-A036-TP.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: READ-AG-A036-TP.somatic_coverage.fwb
Reading categories file: /xchip/cga1/lawrence/db/context65/all.fwb
Writing binary output file: READ-AG-A036-TP.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


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.

