GDAC_mirnaConsensusClusteringPipeline Execution Log 7:34 PM Thu Apr 4, '13

Running as user: cgaadm_deadline

GDAC_mirnaTopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCAN12-TP/2842501/2.GDAC_MergeDataFiles.Finished/PANCAN12-TP.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt
GDAC_mirnaTopgenesforCluster1 selectedgenes 150
GDAC_ConsensusClustering2 clustering algorithm HIERARCHICAL
GDAC_ConsensusClustering2 cluster by
GDAC_ConsensusClustering2 distance measure PEARSON
GDAC_ConsensusClustering2 normalize type
GDAC_selectBestcluster3 measure Pearson
GDAC_selectBestcluster3 output PANCAN12-TP
GDAC_selectBestcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCAN12-TP/2842501/2.GDAC_MergeDataFiles.Finished/PANCAN12-TP.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt
Execution Times:
Submitted: 19:34:22 04-04-13
Completed:
Elapsed: 00 hrs 25 mins 23 secs

step 1. GDAC_mirnaTopgenesforCluster [id: 363267] This module can be used to selecte top genes with most variation, convert file to gct format, as well as imput missing value

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00284:3
expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCAN12-TP/2842501/2.GDAC_MergeDataFiles.Finished/PANCAN12-TP.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt
selectedgenes 150
outputprefix outputprefix
Output Files:
 outputprefix.expclu.gct
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:34:22 04-04-13
Completed: 19:44:11 04-04-13
Elapsed: 00 hrs 09 mins 49 secs

step 2. GDAC_ConsensusClustering [id: 363268] Resampling-based clustering method

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00158:6
input filename outputprefix.expclu.gct
kmax 8
resampling iterations 20
seed value 12345
clustering algorithm HIERARCHICAL
cluster by
distance measure PEARSON
resample subsample
merge type average
descent iterations 2000
output stub <input.filename_basename>
normalize type
normalization iterations 0
create heat map -p
heat map size 2
Output Files:
 outputprefix.expclu.sub454.stdev
 outputprefix.expclu.sub454.clsdist
 outputprefix.expclu.sub454.2.gct
 outputprefix.expclu.sub454.3.gct
 outputprefix.expclu.sub454.4.gct
 outputprefix.expclu.sub454.5.gct
 outputprefix.expclu.sub454.6.gct
 outputprefix.expclu.sub454.7.gct
 outputprefix.expclu.sub454.8.gct
 outputprefix.expclu.sub454.2.clu
 outputprefix.expclu.sub454.3.clu
 outputprefix.expclu.sub454.4.clu
 outputprefix.expclu.sub454.5.clu
 outputprefix.expclu.sub454.6.clu
 outputprefix.expclu.sub454.7.clu
 outputprefix.expclu.sub454.8.clu
 outputprefix.expclu.sub454.statistics.pdf
 outputprefix.expclu.sub454.srt.2.gct
 outputprefix.expclu.sub454.srt.2.gif
 outputprefix.expclu.sub454.srt.3.gct
 outputprefix.expclu.sub454.srt.3.gif
 outputprefix.expclu.sub454.srt.4.gct
 outputprefix.expclu.sub454.srt.4.gif
 outputprefix.expclu.sub454.srt.5.gct
 outputprefix.expclu.sub454.srt.5.gif
 outputprefix.expclu.sub454.srt.6.gct
 outputprefix.expclu.sub454.srt.6.gif
 outputprefix.expclu.sub454.srt.7.gct
 outputprefix.expclu.sub454.srt.7.gif
 outputprefix.expclu.sub454.srt.8.gct
 outputprefix.expclu.sub454.srt.8.gif
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:34:22 04-04-13
Completed: 19:58:29 04-04-13
Elapsed: 00 hrs 24 mins 06 secs

step 3. GDAC_selectBestcluster [id: 363269]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00207:32
measure Pearson
inputexp outputprefix.expclu.gct
output PANCAN12-TP
file clu 2 outputprefix.expclu.sub454.2.clu
file clu 3 outputprefix.expclu.sub454.3.clu
file clu 4 outputprefix.expclu.sub454.4.clu
file clu 5 outputprefix.expclu.sub454.5.clu
file clu 6 outputprefix.expclu.sub454.6.clu
file clu 7 outputprefix.expclu.sub454.7.clu
file clu 8 outputprefix.expclu.sub454.8.clu
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCAN12-TP/2842501/2.GDAC_MergeDataFiles.Finished/PANCAN12-TP.mirna__h_mirna_8x15kv2__unc_edu__Level_3__unc_DWD_Batch_adjusted__data.data.txt
Output Files:
 PANCAN12-TP.silfig.png
 PANCAN12-TP.bestclus.txt
 PANCAN12-TP.cormatrix.png
 PANCAN12-TP.allclusters.txt
 PANCAN12-TP.subclassmarkers.txt
 PANCAN12-TP.seclectedSubclassmarkers.txt
 PANCAN12-TP.geneheatmap.png
 PANCAN12-TP.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 19:34:22 04-04-13
Completed: 19:59:13 04-04-13
Elapsed: 00 hrs 24 mins 50 secs

step 4. GDAC_mirnaConsensusReport [id: 363270]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00278:13