getCopyNumberExpCor Execution Log 11:09 PM Mon Apr 8, '13

Running as user: cgaadm_deadline

getCNExpCorrelation1 reducedseg file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/LUSC-TP/2859876/all_data_by_genes.txt
getCNExpCorrelation1 mrnaexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/LUSC-TP/2900882/0.GDAC_mRNA_Preprocess_Median.Finished/LUSC-TP.medianexp.txt
getCNExpCorrelation1 featurename Hybridization.REF
getCNExpCorrelation1 threshold none
getCNExpCorrelation1 method pearson
getCNExpCorrelation1 cortablename LUSC-TP
getCNExpCorrelation1 figurename OUTPUT
getCNExpCorrelation1 qatablename STATS
writeCorReport2 type mRNA
Execution Times:
Submitted: 23:09:25 08-04-13
Completed:
Elapsed: 01 hrs 18 mins 06 secs

step 1. getCNExpCorrelation [id: 373639] 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/LUSC-TP/2859876/all_data_by_genes.txt
mrnaexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/LUSC-TP/2900882/0.GDAC_mRNA_Preprocess_Median.Finished/LUSC-TP.medianexp.txt
featurename Hybridization.REF
threshold none
method pearson
cortablename LUSC-TP
figurename OUTPUT
qatablename STATS
Output Files:
 OUTPUT.CORS.png
 STATS.QA.tsv
 LUSC-TP.CORS.tsv
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 23:09:25 08-04-13
Completed: 00:20:15 09-04-13
Elapsed: 01 hrs 10 mins 49 secs

step 2. writeCorReport [id: 373640] Generates the html report based on the correlation data

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00288:42
pngname OUTPUT.CORS.png
tablename LUSC-TP.CORS.tsv
type mRNA
qatablename STATS.QA.tsv
Output Files:
 nozzle.html
 .lsf.out
 nozzle.RData
 stdout.txt
Execution Times:
Submitted: 23:09:25 08-04-13
Completed: 00:27:30 09-04-13
Elapsed: 01 hrs 18 mins 04 secs