getCopyNumberExpCor Execution Log 4:28 PM Mon Mar 4, '13

Running as user: cgaadm_deadline

getCNExpCorrelation1 reducedseg file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/KIRC-TP/2661799/all_data_by_genes.txt
getCNExpCorrelation1 mrnaexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRC-TP/2661800/0.GDAC_mRNA_Preprocess_Median.Finished/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: 16:28:22 04-03-13
Completed:
Elapsed: 00 hrs 03 mins 54 secs

step 1. getCNExpCorrelation [id: 334288] 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/2661799/all_data_by_genes.txt
mrnaexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/KIRC-TP/2661800/0.GDAC_mRNA_Preprocess_Median.Finished/KIRC-TP.medianexp.txt
featurename Hybridization.REF
threshold none
method pearson
cortablename KIRC-TP
figurename OUTPUT
qatablename STATS
Output Files:
 STATS.QA.tsv
 OUTPUT.CORS.png
 KIRC-TP.CORS.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 16:28:22 04-03-13
Completed: 16:31:58 04-03-13
Elapsed: 00 hrs 03 mins 36 secs

step 2. writeCorReport [id: 334289] 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.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 16:28:22 04-03-13
Completed: 16:32:15 04-03-13
Elapsed: 00 hrs 03 mins 52 secs