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Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GetReducedSegments.28.1386/getReducedSegments.R")
> result <- getReducedSegments("-s/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA-TP/2327738/2.GDAC_MergeDataFiles.Finished/BRCA-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt", "-bgene", "-fHybridization.REF", "-iFALSE", "-xFALSE", "-wmedian", "-rBRCA-TP.RS.tsv", "-l/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GetReducedSegments.28.1386/", "-nSample", "-cChromosome", "-tStart", "-eEnd", "-mSegment_Mean")
gcc -std=gnu99 -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/include  -I/usr/local/include    -fpic  -g -O2 -c getratios.c -o getratios.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o CNTools.so getratios.o -L/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1/lib64/R/lib -lR
> q(save="no")
lsf stdout
Sender: LSF System <lsf@node1650>
Subject: Job 3978771: </broad/software/free/Linux/redhat_5_x86_64/pkgs/sun-java-jdk_1.6.0-21_x86_64/bin/java -DR_HOME=/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1 -Dr_flags=--vanilla -cp /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/RunR/ RunR /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GetReducedSegments.28.1386/getReducedSegments.R getReducedSegments -s/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA-TP/2327738/2.GDAC_MergeDataFiles.Finished/BRCA-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt -bgene -fHybridization.REF -iFALSE -xFALSE -wmedian -rBRCA-TP.RS.tsv -l/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GetReducedSegments.28.1386/ -nSample -cChromosome -tStart -eEnd -mSegment_Mean >> cmd.out> Done

Job </broad/software/free/Linux/redhat_5_x86_64/pkgs/sun-java-jdk_1.6.0-21_x86_64/bin/java -DR_HOME=/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1 -Dr_flags=--vanilla -cp /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/RunR/ RunR /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GetReducedSegments.28.1386/getReducedSegments.R getReducedSegments -s/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA-TP/2327738/2.GDAC_MergeDataFiles.Finished/BRCA-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt -bgene -fHybridization.REF -iFALSE -xFALSE -wmedian -rBRCA-TP.RS.tsv -l/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GetReducedSegments.28.1386/ -nSample -cChromosome -tStart -eEnd -mSegment_Mean >> cmd.out> was submitted from host <node1430> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1650>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/300602> was used as the working directory.
Started at Tue Jan 29 15:57:43 2013
Results reported at Tue Jan 29 15:59:16 2013

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
/broad/software/free/Linux/redhat_5_x86_64/pkgs/sun-java-jdk_1.6.0-21_x86_64/bin/java -DR_HOME=/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.10.1 -Dr_flags=--vanilla -cp /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/RunR/ RunR /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GetReducedSegments.28.1386/getReducedSegments.R getReducedSegments -s/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/BRCA-TP/2327738/2.GDAC_MergeDataFiles.Finished/BRCA-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt -bgene -fHybridization.REF -iFALSE -xFALSE -wmedian -rBRCA-TP.RS.tsv -l/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/GetReducedSegments.28.1386/ -nSample -cChromosome -tStart -eEnd -mSegment_Mean >> cmd.out
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     84.58 sec.
    Max Memory :      1369 MB
    Max Swap   :     13754 MB

    Max Processes  :         4
    Max Threads    :        27

The output (if any) follows:



PS:

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

lsf stderr
* installing *source* package 'CNTools' ...
** libs
** R
** data
** inst
** help
*** installing help indices
** building package indices ...
* DONE (CNTools)
Loading required package: genefilter
Creating a new generic function for "genefilter" in "CNTools"
