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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/getCNExpCorrelation.18.1573/findCNExpCorrelation.R")
> result <- getmRNACor("-r/xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/OV/868533/1.GetReducedSegments.Finished/OV.RS.tsv", "-m/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/856547/1.GDAC_MergeDataFiles.Finished/OV.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt", "-fHybridization.REF", "-tnone", "-wpearson", "-oOV.CORS.tsv", "-pOUTPUT.CORS.png", "-d/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/getCNExpCorrelation.18.1573/", "-aSTATS.QA.tsv")
> q(save="no")
lsf stdout
Sender: LSF System <lsf@node1428>
Subject: Job 2000162: </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/getCNExpCorrelation.18.1573/findCNExpCorrelation.R getmRNACor -r/xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/OV/868533/1.GetReducedSegments.Finished/OV.RS.tsv -m/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/856547/1.GDAC_MergeDataFiles.Finished/OV.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt -fHybridization.REF -tnone -wpearson -oOV.CORS.tsv -pOUTPUT.CORS.png -d/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/getCNExpCorrelation.18.1573/ -aSTATS.QA.tsv >> 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/getCNExpCorrelation.18.1573/findCNExpCorrelation.R getmRNACor -r/xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/OV/868533/1.GetReducedSegments.Finished/OV.RS.tsv -m/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/856547/1.GDAC_MergeDataFiles.Finished/OV.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt -fHybridization.REF -tnone -wpearson -oOV.CORS.tsv -pOUTPUT.CORS.png -d/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/getCNExpCorrelation.18.1573/ -aSTATS.QA.tsv >> cmd.out> was submitted from host <tcga-gdac-genepattern> by user <cgaadm> in cluster <cromwell>.
Job was executed on host(s) <node1428>, in queue <cga>, as user <cgaadm> in cluster <cromwell>.
</home/unix/cgaadm> was used as the home directory.
</xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/56306> was used as the working directory.
Started at Sat Feb 25 11:47:00 2012
Results reported at Sat Feb 25 11:47:39 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/getCNExpCorrelation.18.1573/findCNExpCorrelation.R getmRNACor -r/xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/OV/868533/1.GetReducedSegments.Finished/OV.RS.tsv -m/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/OV/856547/1.GDAC_MergeDataFiles.Finished/OV.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt -fHybridization.REF -tnone -wpearson -oOV.CORS.tsv -pOUTPUT.CORS.png -d/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/getCNExpCorrelation.18.1573/ -aSTATS.QA.tsv >> cmd.out
------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time   :     38.92 sec.
    Max Memory :       575 MB
    Max Swap   :      9009 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
Warning message:
package 'Cairo' was built under R version 2.7.2 and help may not work correctly 
