GDAC_RNAseq_ConsensusClusteringPipeline Execution Log 3:47 PM Fri May 24, '13

Running as user: cgaadm_deadline

GDAC_TopgenesforCluster1 expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/HNSC-TP/3026014/0.GDAC_RPPA_preprocess.Finished/HNSC-TP.rppa.txt
GDAC_TopgenesforCluster1 selectedgenes ALL
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 HNSC-TP
GDAC_selectBestcluster3 inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/HNSC-TP/3026014/0.GDAC_RPPA_preprocess.Finished/HNSC-TP.rppa.txt
GDAC_CnmfReports4 report hclRppa
Execution Times:
Submitted: 15:47:02 24-05-13
Completed:
Elapsed: 00 hrs 31 mins 39 secs

step 1. GDAC_TopgenesforCluster [id: 411763] 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:00205:36
expfile file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/HNSC-TP/3026014/0.GDAC_RPPA_preprocess.Finished/HNSC-TP.rppa.txt
selectedgenes ALL
outputprefix outputprefix
Output Files:
 outputprefix.expclu.gct
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 15:47:02 24-05-13
Completed: 16:11:15 24-05-13
Elapsed: 00 hrs 24 mins 12 secs

step 2. GDAC_ConsensusClustering [id: 411764] 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.sub169.stdev
 outputprefix.expclu.sub169.clsdist
 outputprefix.expclu.sub169.2.gct
 outputprefix.expclu.sub169.5.gct
 outputprefix.expclu.sub169.4.gct
 outputprefix.expclu.sub169.3.gct
 outputprefix.expclu.sub169.7.gct
 outputprefix.expclu.sub169.8.gct
 outputprefix.expclu.sub169.6.gct
 outputprefix.expclu.sub169.3.clu
 outputprefix.expclu.sub169.2.clu
 outputprefix.expclu.sub169.5.clu
 outputprefix.expclu.sub169.6.clu
 outputprefix.expclu.sub169.4.clu
 outputprefix.expclu.sub169.8.clu
 outputprefix.expclu.sub169.7.clu
 outputprefix.expclu.sub169.statistics.pdf
 outputprefix.expclu.sub169.srt.2.gif
 outputprefix.expclu.sub169.srt.2.gct
 outputprefix.expclu.sub169.srt.3.gif
 outputprefix.expclu.sub169.srt.3.gct
 outputprefix.expclu.sub169.srt.4.gct
 outputprefix.expclu.sub169.srt.4.gif
 outputprefix.expclu.sub169.srt.5.gct
 outputprefix.expclu.sub169.srt.5.gif
 outputprefix.expclu.sub169.srt.6.gct
 outputprefix.expclu.sub169.srt.6.gif
 outputprefix.expclu.sub169.srt.7.gct
 outputprefix.expclu.sub169.srt.7.gif
 outputprefix.expclu.sub169.srt.8.gif
 outputprefix.expclu.sub169.srt.8.gct
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 15:47:02 24-05-13
Completed: 16:17:42 24-05-13
Elapsed: 00 hrs 30 mins 40 secs

step 3. GDAC_selectBestcluster [id: 411765]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00207:33
measure Pearson
inputexp outputprefix.expclu.gct
output HNSC-TP
file clu 2 outputprefix.expclu.sub169.2.clu
file clu 3 outputprefix.expclu.sub169.3.clu
file clu 4 outputprefix.expclu.sub169.4.clu
file clu 5 outputprefix.expclu.sub169.5.clu
file clu 6 outputprefix.expclu.sub169.6.clu
file clu 7 outputprefix.expclu.sub169.7.clu
file clu 8 outputprefix.expclu.sub169.8.clu
inputallexp file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_RPPA_preprocess/HNSC-TP/3026014/0.GDAC_RPPA_preprocess.Finished/HNSC-TP.rppa.txt
Output Files:
 HNSC-TP.cormatrix.png
 HNSC-TP.allclusters.txt
 HNSC-TP.bestclus.txt
 HNSC-TP.silfig.png
 HNSC-TP.geneheatmap.png
 HNSC-TP.subclassmarkers.txt
 HNSC-TP.seclectedSubclassmarkers.txt
 HNSC-TP.geneheatmaptopgenes.png
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 15:47:02 24-05-13
Completed: 16:18:10 24-05-13
Elapsed: 00 hrs 31 mins 08 secs

step 4. GDAC_CnmfReports [id: 411766]

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:31