hi Note: There is no RefPlanePath. Will remove RefPlanePath variable. InputDir=/opt/data OutputDir=/opt/result/ OrigSifPath=/cromwell-executions/tangent_workflow/aab0f674-d28f-4eb4-bb20-2def0b1b4f9a/call-tangent/inputs/871759661/example.mysif.txt OrigDataPath=/cromwell-executions/tangent_workflow/aab0f674-d28f-4eb4-bb20-2def0b1b4f9a/call-tangent/inputs/871759661/example.mydata.DOC_interval.avg_cvg.txt RefPlanePath= Tag=run SeqPlatform=exome NormalCeiling=0.18 Alpha=0.01 Nsplit=3 Evects=150 doGenRefPlane=false doTangentSteps=true doPseudoTangent=false MCRROOT=/opt/MATLAB/MATLAB_Compiler_Runtime/v714/ Working directory /cromwell-executions/tangent_workflow/aab0f674-d28f-4eb4-bb20-2def0b1b4f9a/call-tangent/execution RefPlanePath is required if doGenRefPlane is false and doTangentSteps is true, using default refplane. /opt/252_refplane/ ===================================================== Skipping Step 1: Will not generate reference plane. ===================================================== Step 2: Running Tangent steps... RefPlanePath=/opt/252_refplane/ OutputDir does not exist. Creating OutputDir /opt/result//run/tangent_output_run... InputDir does not exist. Creating InputDir /opt/data/run/tangent_input_run... Creating symlink for sif file... OrigSifPath: /cromwell-executions/tangent_workflow/aab0f674-d28f-4eb4-bb20-2def0b1b4f9a/call-tangent/inputs/871759661/example.mysif.txt NewSifPath: /opt/data/run/tangent_input_run/run.sif.txt Creating symlink for D file... OrigDataPath: /cromwell-executions/tangent_workflow/aab0f674-d28f-4eb4-bb20-2def0b1b4f9a/call-tangent/inputs/871759661/example.mydata.DOC_interval.avg_cvg.txt NewDataPath: /opt/data/run/tangent_input_run/run.D.txt Running Tangent and post-Tangent on run sequenced on the exome platform: Output directory: /opt/result//run/tangent_output_run Reference Plane: /opt/252_refplane/ Input directory: /opt/data/run/tangent_input_run doTangent: true Normal Ceiling Threshold: 0.18 doGermline: false Step 1: Tangent... MATLAB env: /opt/MATLAB/MATLAB_Compiler_Runtime/v714/ ...confirming there is more than 1 tumor sample in this run. ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/opt/MATLAB/MATLAB_Compiler_Runtime/v714//runtime/glnxa64:/opt/MATLAB/MATLAB_Compiler_Runtime/v714//bin/glnxa64:/opt/MATLAB/MATLAB_Compiler_Runtime/v714//sys/os/glnxa64:/opt/MATLAB/MATLAB_Compiler_Runtime/v714//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/MATLAB/MATLAB_Compiler_Runtime/v714//sys/java/jre/glnxa64/jre/lib/amd64/server:/opt/MATLAB/MATLAB_Compiler_Runtime/v714//sys/java/jre/glnxa64/jre/lib/amd64/client:/opt/MATLAB/MATLAB_Compiler_Runtime/v714//sys/java/jre/glnxa64/jre/lib/amd64 noCNVs_filename: 'run.doc_interval.posttangent_woCNV.txt' withCNVs_filename: 'run.doc_interval.posttangent_wCNV.txt' cnvfile: '/opt/lib/CNV.hg19.bypos.111213.txt' probelist: [1x71 char] normal_blacklist: '/opt/lib/normal.blacklist.txt' seq_platform: 'exome' normal_ceiling: 0.1800 Data loaded and returned from early_gistic_prep. Splitting tumors from normals... Separated tumors from normals. normal_ceiling value: 0.18 mean_windat stats: Min: 0.2151 Max: 0.2241 Mean: 0.22018 Median: 0.22071 mean_windat size: 1 5 Saved /opt/result//run/tangent_output_run/run.early_gistic_prep_output._disruption_scores.txt. Completed tangent against historic planes. Writing tangent projections... Completed writing /opt/result//run/tangent_output_run/run.tangent_projections.full_plane.txt tangent projection files Completed writing tangent projections. Completed saving weights. Returned unnormalized autosome cnv markers to D. Returned unnormalized X cnv markers. Returned unnormalized Y markers to Dfc. Writing file... Completed writing file /opt/result//run/tangent_output_run/run.doc_interval.posttangent_woCNV.txt. Completed writing /opt/result//run/tangent_output_run/run.doc_interval.posttangent_woCNV.txt. Writing file... Completed writing file /opt/result//run/tangent_output_run/run.doc_interval.posttangent_wCNV.txt. Completed writing /opt/result//run/tangent_output_run/run.doc_interval.posttangent_wCNV.txt. ans = dat: [165443x10 single] chr: {165443x1 cell} start: [165443x1 double] stop: [165443x1 double] chrn: [165443x1 double] pos: [165443x1 double] sdesc: {1x10 cell} islog: 0 bad_markers: [] bad_samples: [] marker: {165443x1 cell} normal_files: [1x1 struct] tangent_method: 'classic' ref_center: [165443x1 single] weights: [114x10 double] ...end of tangent_package function In deployed mode, exiting MATLAB. Warning: No display specified. You will not be able to display graphics on the screen. Opening log file: /root/java.log.67 ...step 1 completed. Step 1: Checking the list of suspect normals... Threshold for disruption_scores: 0.180 There are 5 suspect normals out of a total of 5 normals. Step 2: Run stripLocation... For exome analysis, we do not need to run stripLocation (since we do not need to run LiftOver.) ...step 2 completed. Step 3: Run Liftover... For exome analysis, we will not do liftover from hg18 to hg19. The data is already in hg19. ...step 3 completed. Step 4: Run CBS... Running CBS in parallel... Analyzing: LGG.PT5.NB current chromosome: 1 current chromosome: 10 Analyzing: LGG.PT5.TP current chromosome: 1 Analyzing: LGG.PT4.TP Analyzing: LGG.PT1.TP current chromosome: 1 current chromosome: 1 Analyzing: LGG.PT3.TP Analyzing: LGG.PT2.NB current chromosome: 11 Analyzing: LGG.PT3.NB current chromosome: 1 current chromosome: 1 Analyzing: LGG.PT4.NB current chromosome: 1 current chromosome: 1 Analyzing: LGG.PT1.NB current chromosome: 10 current chromosome: 1 current chromosome: 12 Analyzing: LGG.PT2.TP current chromosome: 10 current chromosome: 1 current chromosome: 13 current chromosome: 14 current chromosome: 11 current chromosome: 12 current chromosome: 10 current chromosome: 10 current chromosome: 10 current chromosome: 10 current chromosome: 11 current chromosome: 10 current chromosome: 11 current chromosome: 11 current chromosome: 12 current chromosome: 11 current chromosome: 11 current chromosome: 10 current chromosome: 15 current chromosome: 12 current chromosome: 16 current chromosome: 11 current chromosome: 12 current chromosome: 11 current chromosome: 12 current chromosome: 13 current chromosome: 13 current chromosome: 17 current chromosome: 14 current chromosome: 14 current chromosome: 12 current chromosome: 12 current chromosome: 15 current chromosome: 12 current chromosome: 13 current chromosome: 14 current chromosome: 13 current chromosome: 13 current chromosome: 16 current chromosome: 13 current chromosome: 14 current chromosome: 14 current chromosome: 14 current chromosome: 15 current chromosome: 15 current chromosome: 16 current chromosome: 13 current chromosome: 17 current chromosome: 17 current chromosome: 15 current chromosome: 18 current chromosome: 15 current chromosome: 10 current chromosome: 14 current chromosome: 15 current chromosome: 13 current chromosome: 16 current chromosome: 19 current chromosome: 16 current chromosome: 16 current chromosome: 14 current chromosome: 15 current chromosome: 2 current chromosome: 20 current chromosome: 18 current chromosome: 16 current chromosome: 21 current chromosome: 22 current chromosome: 18 current chromosome: 16 current chromosome: 3 current chromosome: 11 current chromosome: 17 current chromosome: 12 current chromosome: 19 current chromosome: 19 current chromosome: 17 current chromosome: 15 current chromosome: 2 current chromosome: 17 current chromosome: 20 current chromosome: 16 current chromosome: 13 current chromosome: 4 current chromosome: 14 current chromosome: 18 current chromosome: 17 current chromosome: 17 current chromosome: 15 current chromosome: 5 current chromosome: 21 current chromosome: 19 current chromosome: 22 current chromosome: 3 current chromosome: 18 current chromosome: 18 current chromosome: 18 current chromosome: 19 current chromosome: 19 current chromosome: 17 current chromosome: 16 current chromosome: 19 current chromosome: 2 current chromosome: 6 current chromosome: 17 current chromosome: 18 current chromosome: 2 current chromosome: 19 current chromosome: 20 current chromosome: 18 current chromosome: 19 current chromosome: 21 current chromosome: 7 current chromosome: 22 current chromosome: 2 current chromosome: 2 current chromosome: 8 current chromosome: 2 current chromosome: 4 current chromosome: 2 current chromosome: 20 current chromosome: 20 current chromosome: 3 current chromosome: 21 current chromosome: 9 current chromosome: 21 current chromosome: 22 current chromosome: 4 current chromosome: 22 current chromosome: 3 current chromosome: 20 current chromosome: 3 current chromosome: 20 current chromosome: 21 current chromosome: 20 current chromosome: 21 current chromosome: 21 current chromosome: 22 current chromosome: 18 current chromosome: 22 current chromosome: 3 current chromosome: X current chromosome: 2 current chromosome: 22 current chromosome: 20 current chromosome: 5 current chromosome: 3 current chromosome: 3 current chromosome: 19 current chromosome: 21 current chromosome: 5 current chromosome: 4 current chromosome: 22 current chromosome: 4 current chromosome: 3 current chromosome: 6 current chromosome: 4 current chromosome: 4 current chromosome: 5 current chromosome: 6 current chromosome: 4 current chromosome: 7 current chromosome: 2 current chromosome: 5 current chromosome: 5 current chromosome: 5 current chromosome: 8 current chromosome: 7 current chromosome: 5 current chromosome: 6 current chromosome: 6 current chromosome: 20 current chromosome: 21 current chromosome: 6 current chromosome: 6 current chromosome: 22 current chromosome: 8 current chromosome: 3 current chromosome: 4 current chromosome: 7 current chromosome: 9 current chromosome: 9 current chromosome: X current chromosome: 7 current chromosome: 5 current chromosome: 7 current chromosome: 8 current chromosome: 8 current chromosome: 7 current chromosome: 9 current chromosome: X current chromosome: 6 current chromosome: X current chromosome: 4 current chromosome: 6 current chromosome: 5 current chromosome: 8 current chromosome: 8 current chromosome: 6 current chromosome: 9 current chromosome: 9 current chromosome: 9 current chromosome: 7 current chromosome: 7 current chromosome: X current chromosome: X current chromosome: X current chromosome: 7 current chromosome: 8 current chromosome: 9 current chromosome: 8 current chromosome: 8 current chromosome: X current chromosome: 9 current chromosome: 9 current chromosome: X current chromosome: X ...step 4 completed. Step 5: Run tblcat to generate.seg ... OutputDir for CBS files: /opt/result//run/tangent_output_run/CBS ...step 5 completed. ...Step 2 completed. ===================================================== Skipping Step 3: Will not run PseudoTangent. ===================================================== CBS run.D.txt run.doc_interval.posttangent_wCNV.txt run.doc_interval.posttangent_woCNV.full_plane_weights.mat run.doc_interval.posttangent_woCNV.txt run.early_gistic_prep_output._disruption_scores.txt run.early_gistic_prep_output._suspect_normals.txt run.sif.txt run.tangent_projections.full_plane.txt run_woCNV_hg19.catted.seg.txt stdout_stderr.log