lsf stdout
Sender: LSF System <lsf@node1650>
Subject: Job 4596979: </xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/scripts/bsub_mem.sh cga 2 "/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/getCNUseMe.19.1396/mergeSegData.R getCNToUse -k -l -m/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PRAD/421946/1.GDAC_MergeDataFiles.Finished/PRAD.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt -n -oPRAD.Use_Me_Level_3__segmented_cna__seg.tsv >> cmd.out> Done

Job </xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/scripts/bsub_mem.sh cga 2 "/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/getCNUseMe.19.1396/mergeSegData.R getCNToUse -k -l -m/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PRAD/421946/1.GDAC_MergeDataFiles.Finished/PRAD.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt -n -oPRAD.Use_Me_Level_3__segmented_cna__seg.tsv >> cmd.out> was submitted from host <tcga-gdac-genepattern> 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/42049> was used as the working directory.
Started at Wed Aug 10 12:44:12 2011
Results reported at Wed Aug 10 12:44:28 2011

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/scripts/bsub_mem.sh cga 2 "/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/getCNUseMe.19.1396/mergeSegData.R getCNToUse -k -l -m/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PRAD/421946/1.GDAC_MergeDataFiles.Finished/PRAD.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt -n -oPRAD.Use_Me_Level_3__segmented_cna__seg.tsv >> cmd.out
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Successfully completed.

Resource usage summary:

    CPU time   :      0.44 sec.
    Max Memory :         3 MB
    Max Swap   :        39 MB

    Max Processes  :         1
    Max Threads    :         1

The output (if any) follows:



PS:

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

lsf stderr
cat: cmd.out: input file is output file
