Gistic2_Pipeline Execution Log 12:08 PM Thu Jan 10, '13

Running as user: cgaadm_deadline

Gistic2_Analysis1 seg_file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COAD-TP/2169270/2.GDAC_MergeDataFiles.Finished/COAD-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
Gistic2_Analysis1 markers_file file:/xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt
Gistic2_Analysis1 refgene_file file:/xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat
Gistic2_Analysis1 cnv_files /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt
Gistic2_Analysis1 amp_thresh 0.1
Gistic2_Analysis1 del_thresh 0.1
Gistic2_Analysis1 cap 1.5
Gistic2_Analysis1 broad length cutoff 0.7
Gistic2_Analysis1 remove X 0
Gistic2_Analysis1 confidence level 0.99
Gistic2_Analysis1 join segment size 4
Gistic2_Analysis1 arm peel 1
Gistic2_Analysis1 max sample segs 2000
Execution Times:
Submitted: 12:08:47 10-01-13
Completed:
Elapsed: 01 hrs 01 mins 32 secs

step 1. Gistic2_Analysis [id: 284157] Wrapper module for Gistic v2 (Note: uses segarray to reduce memory)

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00264:106
seg_file file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COAD-TP/2169270/2.GDAC_MergeDataFiles.Finished/COAD-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
markers_file file:/xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt
refgene_file file:/xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat
cnv_files /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt
amp_thresh 0.1
del_thresh 0.1
cap 1.5
broad length cutoff 0.7
remove X 0
confidence level 0.99
join segment size 4
arm peel 1
max sample segs 2000
Output Files:
 tmp_array_list.txt
 params.mat
 gisticInputs.txt
 array_list.txt
 gistic_inputs.mat
 gisticVersion.txt
 segmented_data.mat
 arraylistfile.txt
 D.cap1.5.mat
 focal_dat.0.7.mat
 focal_input.seg.txt
 scores.0.7.mat
 orig_stats.mat
 gene_stats.mat
 peak_regs.mat
 perm_ads.mat
 wide_peak_regs.mat
 all_lesions.conf_99.txt
 del_genes.conf_99.txt
 table_del.conf_99.txt
 amp_genes.conf_99.txt
 table_amp.conf_99.txt
 regions_track.conf_99.bed
 scores.gistic
 raw_copy_number.fig
 raw_copy_number.png
 raw_copy_number.pdf
 amp_qplot.v2.pdf
 amp_qplot.pdf
 amp_qplot.png
 amp_qplot.fig
 del_qplot.v2.pdf
 del_qplot.pdf
 del_qplot.png
 del_qplot.fig
 freqarms_vs_ngenes.pdf
 broad_results.mat
 freqarms_vs_ngenes.fig
 broad_significance_results.txt
 broad_values_by_arm.txt
 all_data_by_genes.txt
 focal_data_by_genes.txt
 broad_data_by_genes.txt
 sample_cutoffs.txt
 all_thresholded.by_genes.mat
 all_thresholded.by_genes.txt
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:08:54 10-01-13
Completed: 13:09:37 10-01-13
Elapsed: 01 hrs 00 mins 43 secs

step 2. GDAC_Gistic2Report [id: 284158] Gistic2 results report

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00269:49
amp amp_genes.conf_99.txt
del del_genes.conf_99.txt
amplification png amp_qplot.png
deletion png del_qplot.png
segmented_copy_number png raw_copy_number.png
gistic_version txt gisticVersion.txt
arraylistfile txt arraylistfile.txt
broad_sig_res broad_significance_results.txt
gisticInputs txt gisticInputs.txt
Output Files:
 hg19_with_miR_20120227.mat
 CNV.hg19.bypos.111213.txt
 genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt
 nozzle.RData
 nozzle.html
 .lsf.out
 stdout.txt
Execution Times:
Submitted: 12:08:54 10-01-13
Completed: 13:10:16 10-01-13
Elapsed: 01 hrs 01 mins 22 secs