Making sub-directories
Evidence:
    outputFile	clusterFiles/BRCA_cnv.tab
    suffix	BRCA_cnv.tab
    attachment	genome
    spec	file:dataFiles/BRCA_cnv.tab
Evidence:
    outputFile	clusterFiles/BRCA_exp.tab
    suffix	BRCA_exp.tab
    attachment	mRNA
    spec	file:dataFiles/BRCA_exp.tab
running:
    cat dataFiles/BRCA_cnv.tab | /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/taskLib/ParadigmPrepare.12.3260/quantileTransform.py /dev/stdin > BRCA_cnv.tab
 ... done
running:
    cat dataFiles/BRCA_exp.tab | /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/taskLib/ParadigmPrepare.12.3260/quantileTransform.py /dev/stdin > BRCA_exp.tab
 ... done
505 samples, fraction of each matrix: 0.61286407767 0.954631379962
15550 genes, fraction of each matrix: 0.529037525942 0.872908948018
Writing config file for EM
Writing config file for final run
Copying pathway files
running:
    cp pathwayFiles/*_pathway.tab clusterFiles
 ... done
writing EM jobs list
writing jobs list
