getCopyNumberExpCor Execution Log 3:27 PM Thu May 2, '13

Running as user: cgaadm_deadline

getCNExpCorrelation1 reducedseg file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/LUAD-TP/3140812/all_data_by_genes.txt
getCNExpCorrelation1 mrnaexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/LUAD-TP/3140809/0.GDAC_mRNA_Preprocess_Median.Finished/LUAD-TP.medianexp.txt
getCNExpCorrelation1 featurename Hybridization.REF
getCNExpCorrelation1 threshold none
getCNExpCorrelation1 method pearson
getCNExpCorrelation1 cortablename LUAD-TP
getCNExpCorrelation1 figurename OUTPUT
getCNExpCorrelation1 qatablename STATS
writeCorReport2 type mRNA
Execution Times:
Submitted: 15:27:18 02-05-13
Completed:
Elapsed: 00 hrs 04 mins 32 secs

step 1. getCNExpCorrelation [id: 396890] 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/LUAD-TP/3140812/all_data_by_genes.txt
mrnaexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/LUAD-TP/3140809/0.GDAC_mRNA_Preprocess_Median.Finished/LUAD-TP.medianexp.txt
featurename Hybridization.REF
threshold none
method pearson
cortablename LUAD-TP
figurename OUTPUT
qatablename STATS
Output Files:
 LUAD-TP.CORS.tsv
 STATS.QA.tsv
 .lsf.out
 OUTPUT.CORS.png
 stdout.txt
Execution Times:
Submitted: 15:27:29 02-05-13
Completed: 15:31:15 02-05-13
Elapsed: 00 hrs 03 mins 46 secs

step 2. writeCorReport [id: 396891] Generates the html report based on the correlation data

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00288:42
pngname OUTPUT.CORS.png
tablename LUAD-TP.CORS.tsv
type mRNA
qatablename STATS.QA.tsv
Output Files:
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 15:27:29 02-05-13
Completed: 15:31:49 02-05-13
Elapsed: 00 hrs 04 mins 20 secs