getCopyNumberExpCor Execution Log 11:50 AM Thu Jun 6, '13

Running as user: cgaadm

getCNExpCorrelation1 reducedseg file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/KIRC-TP/3471884/all_data_by_genes.txt
getCNExpCorrelation1 mrnaexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRC-TP/3471886/KIRC-TP.medianexp.txt
getCNExpCorrelation1 featurename Hybridization.REF
getCNExpCorrelation1 threshold none
getCNExpCorrelation1 method pearson
getCNExpCorrelation1 cortablename KIRC-TP
getCNExpCorrelation1 figurename OUTPUT
getCNExpCorrelation1 qatablename STATS
writeCorReport2 type mRNA
Execution Times:
Submitted: 11:50:25 06-06-13
Completed:
Elapsed: 00 hrs 03 mins 54 secs

step 1. getCNExpCorrelation [id: 417170] Calculates the correlations between the copy number and expression data

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00287:19
reducedseg file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/KIRC-TP/3471884/all_data_by_genes.txt
mrnaexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRC-TP/3471886/KIRC-TP.medianexp.txt
featurename Hybridization.REF
threshold none
method pearson
cortablename KIRC-TP
figurename OUTPUT
qatablename STATS
Output Files:
 OUTPUT.CORS.png
 STATS.QA.tsv
 KIRC-TP.CORS.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 11:50:30 06-06-13
Completed: 11:54:02 06-06-13
Elapsed: 00 hrs 03 mins 31 secs

step 2. writeCorReport [id: 417171] Generates the html report based on the correlation data

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00288:42
pngname OUTPUT.CORS.png
tablename KIRC-TP.CORS.tsv
type mRNA
qatablename STATS.QA.tsv
Output Files:
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 11:50:30 06-06-13
Completed: 11:54:17 06-06-13
Elapsed: 00 hrs 03 mins 47 secs