PARADIGM Execution Log 4:36 AM Thu Mar 29, '12

Running as user: cgaadm_deadline

preprocessPARADIGM1 evidence prefix COADREAD
preprocessPARADIGM1 expression file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/COADREAD/718810/0.GDAC_mRNA_Preprocess_Median.Finished/COADREAD.medianexp.txt
preprocessPARADIGM1 copynumber file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/COADREAD/1064763/1.GetReducedSegments.Finished/COADREAD.RS.tsv
PARADIGMLite2 config file file:/xchip/cga/reference/PARADIGM/config.txt
PARADIGMLite2 run id 1
Execution Times:
Submitted: 04:36:12 29-03-12
Completed:
Elapsed: 00 hrs 08 mins 37 secs

step 1. preprocessPARADIGM [id: 68430] Preprocessing module for broad data input to PARADIGM

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00238:25
evidence prefix COADREAD
expression file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mRNA_Preprocess_Median/COADREAD/718810/0.GDAC_mRNA_Preprocess_Median.Finished/COADREAD.medianexp.txt
copynumber file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/writeReducedSegments/COADREAD/1064763/1.GetReducedSegments.Finished/COADREAD.RS.tsv
Output Files:
 Evidence_COADREAD.zip
 stdout.txt
Execution Times:
Submitted: 04:36:12 29-03-12
Completed: 04:38:45 29-03-12
Elapsed: 00 hrs 02 mins 33 secs

step 2. PARADIGMLite [id: 68431] PARADIGM allows for pathway level inference using libdai (Written by: Steve Benz and Charles Vaske)

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00237:26
evidence zip Evidence_COADREAD.zip
pathway zip
config file file:/xchip/cga/reference/PARADIGM/config.txt
run id 1
Output Files:
 1-COADREAD_pathlette_IPA-paradigmlite-dev.txt
 stdout.txt
Execution Times:
Submitted: 04:36:12 29-03-12
Completed: 04:44:48 29-03-12
Elapsed: 00 hrs 08 mins 35 secs