
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/LUSC/1676808/1.GetReducedSegments.Finished/LUSC.RS.tsv", "-m/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/LUSC/1676811/0.GDAC_mRNA_Preprocess_Median.Finished/LUSC.medianexp.txt", "-fHybridization.REF", "-tnone", "-wpearson", "-oLUSC.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@node1700>
Subject: Job 3015012: </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/LUSC/1676808/1.GetReducedSegments.Finished/LUSC.RS.tsv -m/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/LUSC/1676811/0.GDAC_mRNA_Preprocess_Median.Finished/LUSC.medianexp.txt -fHybridization.REF -tnone -wpearson -oLUSC.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/LUSC/1676808/1.GetReducedSegments.Finished/LUSC.RS.tsv -m/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/LUSC/1676811/0.GDAC_mRNA_Preprocess_Median.Finished/LUSC.medianexp.txt -fHybridization.REF -tnone -wpearson -oLUSC.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) <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/157895> was used as the working directory.
Started at Tue Aug 28 11:38:27 2012
Results reported at Tue Aug 28 11:40:52 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/LUSC/1676808/1.GetReducedSegments.Finished/LUSC.RS.tsv -m/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/LUSC/1676811/0.GDAC_mRNA_Preprocess_Median.Finished/LUSC.medianexp.txt -fHybridization.REF -tnone -wpearson -oLUSC.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   :    142.21 sec.
    Max Memory :       568 MB
    Max Swap   :     13092 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 
