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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/LIHC/1269735/2.GDAC_MergeDataFiles.Finished/LIHC.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", "-rLIHC.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")
> q(save="no")
lsf stdout
Sender: LSF System <lsf@node1545>
Subject: Job 9153489: </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/LIHC/1269735/2.GDAC_MergeDataFiles.Finished/LIHC.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 -rLIHC.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/LIHC/1269735/2.GDAC_MergeDataFiles.Finished/LIHC.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 -rLIHC.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 <tcga-gdac-genepattern> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1545>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/107306> was used as the working directory.
Started at Fri Jun  1 19:28:33 2012
Results reported at Fri Jun  1 19:28:54 2012

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/LIHC/1269735/2.GDAC_MergeDataFiles.Finished/LIHC.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 -rLIHC.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   :     19.51 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
Loading required package: genefilter
Creating a new generic function for "genefilter" in "CNTools"
