[choose_run_matlab2.sh] DOTKIT  .matlab-2010a
[choose_run_matlab2.sh] CMD     /xchip/tcga/gdac_prod/source/analysis_pipeline/scripts/run_matlab2.py /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Gistic2_Analysis/broadinstitute.org/cancer.genome.analysis/00264/127/ /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Gistic2_Analysis/broadinstitute.org/cancer.genome.analysis/00264/127/call_gistic2 . 4 /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/BLCA-TP/22506898/segmentationfile.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/BLCA-TP/22506898/markersfile.txt /xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.mat /xchip/gistic/CNV/SNP6.merged.151117.hg19.CNV.txt 0.3 0.3 2 0.5 0 0.99 10 1 10000 0 extreme /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Gistic2_Analysis/broadinstitute.org/cancer.genome.analysis/00264/127/version.txt
[run_matlab2.py] [command line] matlab_exe = /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Gistic2_Analysis/broadinstitute.org/cancer.genome.analysis/00264/127/call_gistic2
[run_matlab2.py] [command line] matlab_args = ['.', '4', '/xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/BLCA-TP/22506898/segmentationfile.txt', '/xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/BLCA-TP/22506898/markersfile.txt', '/xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.mat', '/xchip/gistic/CNV/SNP6.merged.151117.hg19.CNV.txt', '0.3', '0.3', '2', '0.5', '0', '0.99', '10', '1', '10000', '0', 'extreme', '/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Gistic2_Analysis/broadinstitute.org/cancer.genome.analysis/00264/127/version.txt']
[run_matlab2.py] [command line] with_display = False
[run_matlab2.py] [command line] libdir = /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Gistic2_Analysis/broadinstitute.org/cancer.genome.analysis/00264/127/
[run_matlab2.py] LD_LIBRARY_PATH = .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2010a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2010a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2010a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2010a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2010a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2010a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2010a/sys/java/jre/glnxa64/jre/lib/amd64
[run_matlab2.py] MCR_CACHE_ROOT = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/BLCA-TP/22507482
[run_matlab2.py] Matlab command = /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Gistic2_Analysis/broadinstitute.org/cancer.genome.analysis/00264/127/call_gistic2 . 4 /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/BLCA-TP/22506898/segmentationfile.txt /xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/BLCA-TP/22506898/markersfile.txt /xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.mat /xchip/gistic/CNV/SNP6.merged.151117.hg19.CNV.txt 0.3 0.3 2 0.5 0 0.99 10 1 10000 0 extreme /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Gistic2_Analysis/broadinstitute.org/cancer.genome.analysis/00264/127/version.txt
Warning: No display specified.  You will not be able to display graphics on the screen.
Running GISTIC version 2.0.21

fields = 

    {1x1 cell}    {1x1 cell}


cgaRevision =

Firehose task version: 127


inputInfoFilename =

gisticInputs.txt


fid =

     3


ans =

     9


ans =

   118


ans =

   108


ans =

    76


ans =

    60


ans =

    28


ans =

    23


ans =

    13


ans =

    24


ans =

    22


ans =

    22


ans =

    21


ans =

    21


ans =

    30


ans =

    17


ans =

    29


ans =

     0

...Matching fields to Array List File:
      Array  --->  array

conf_level =

    0.9900


params = 

         array_list_file: 'array_list.txt'
                cnv_file: {[1x49 char]}
                   t_amp: 0.3000
                   t_del: 0.3000
             genepattern: 0
       join_segment_size: 10
                     ext: ''
                remove_X: 0
      run_broad_analysis: 1
                   ziggs: [1x1 struct]
        broad_len_cutoff: 0.5000
               qv_thresh: 0.2500
              conf_level: [0.9900 0.9900]
                     cap: 2
                   alpha: [2.5145 2.1653]
          do_gene_gistic: 0
         save_data_files: 1
     conserve_disk_space: 0
            use_segarray: 1
        write_gene_files: 1
           use_two_sided: 0
          do_arbitration: 1
              peak_types: ''
           save_seg_data: 1
             arm_peeloff: 1
    gene_collapse_method: 'extreme'

Checking inputs...
Making D struct
Reading Markers File '/xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/BLCA-TP/22506898/markersfile.txt'
Reading Seg File '/xchip/cga/gdac-prod/tcga-gdac/jobResults/PrepareGisticDNASeq/BLCA-TP/22506898/segmentationfile.txt'
CL = 
               sdesc: {112x1 cell}
                chrn: [27158x1 double]
                 pos: [27158x1 double]
              marker: {27158x1 cell}
                 chr: {1x27158 cell}
    suppress_history: 1
               islog: 1
                isMB: 0
                 dat: [27158x112 SegArray]

Sub-selecting samples...
...Matching fields to Array List File:
      Array  --->  array
Matched all 112 samples in array list file
CL = 
               sdesc: {112x1 cell}
                chrn: [27158x1 double]
                 pos: [27158x1 double]
              marker: {27158x1 cell}
                 chr: {1x27158 cell}
    suppress_history: 1
               islog: 1
                isMB: 0
                 dat: [27158x112 SegArray]

Matrix size 27158    112
Removing 4882 markers
Removing NaN probes...
Removing 297 markers with NaNs
Matrix size 21979    112
Merging small segments...
currently not taking care of edge of chromosomes!!!
Smoothing segments for sample 1:
Smoothing segments for sample 2:
Smoothing segments for sample 3:
Smoothing segments for sample 4:
Smoothing segments for sample 5:
Smoothing segments for sample 6:
Smoothing segments for sample 7:
Smoothing segments for sample 8:
Smoothing segments for sample 9:
Smoothing segments for sample 10:
Smoothing segments for sample 11:
Smoothing segments for sample 12:
Smoothing segments for sample 13:
Smoothing segments for sample 14:
Smoothing segments for sample 15:
Smoothing segments for sample 16:
Smoothing segments for sample 17:
Smoothing segments for sample 18:
Smoothing segments for sample 19:
Smoothing segments for sample 20:
Smoothing segments for sample 21:
Smoothing segments for sample 22:
Smoothing segments for sample 23:
Smoothing segments for sample 24:
Smoothing segments for sample 25:
Smoothing segments for sample 26:
Smoothing segments for sample 27:
Smoothing segments for sample 28:
Smoothing segments for sample 29:
Smoothing segments for sample 30:
Smoothing segments for sample 31:
Smoothing segments for sample 32:
Smoothing segments for sample 33:
Smoothing segments for sample 34:
Smoothing segments for sample 35:
Smoothing segments for sample 36:
Smoothing segments for sample 37:
Smoothing segments for sample 38:
Smoothing segments for sample 39:
Smoothing segments for sample 40:
Smoothing segments for sample 41:
Smoothing segments for sample 42:
Smoothing segments for sample 43:
Smoothing segments for sample 44:
Smoothing segments for sample 45:
Smoothing segments for sample 46:
Smoothing segments for sample 47:
Smoothing segments for sample 48:
Smoothing segments for sample 49:
Smoothing segments for sample 50:
Smoothing segments for sample 51:
Smoothing segments for sample 52:
Smoothing segments for sample 53:
Smoothing segments for sample 54:
Smoothing segments for sample 55:
Smoothing segments for sample 56:
Smoothing segments for sample 57:
Smoothing segments for sample 58:
Smoothing segments for sample 59:
Smoothing segments for sample 60:
Smoothing segments for sample 61:
Smoothing segments for sample 62:
Smoothing segments for sample 63:
Smoothing segments for sample 64:
Smoothing segments for sample 65:
Smoothing segments for sample 66:
Smoothing segments for sample 67:
Smoothing segments for sample 68:
Smoothing segments for sample 69:
Smoothing segments for sample 70:
Smoothing segments for sample 71:
Smoothing segments for sample 72:
Smoothing segments for sample 73:
Smoothing segments for sample 74:
Smoothing segments for sample 75:
Smoothing segments for sample 76:
Smoothing segments for sample 77:
Smoothing segments for sample 78:
Smoothing segments for sample 79:
Smoothing segments for sample 80:
Smoothing segments for sample 81:
Smoothing segments for sample 82:
Smoothing segments for sample 83:
Smoothing segments for sample 84:
Smoothing segments for sample 85:
Smoothing segments for sample 86:
Smoothing segments for sample 87:
Smoothing segments for sample 88:
Smoothing segments for sample 89:
Smoothing segments for sample 90:
Smoothing segments for sample 91:
Smoothing segments for sample 92:
Smoothing segments for sample 93:
Smoothing segments for sample 94:
Smoothing segments for sample 95:
Smoothing segments for sample 96:
Smoothing segments for sample 97:
Smoothing segments for sample 98:
Smoothing segments for sample 99:
Smoothing segments for sample 100:
Smoothing segments for sample 101:
Smoothing segments for sample 102:
Smoothing segments for sample 103:
Smoothing segments for sample 104:
Smoothing segments for sample 105:
Smoothing segments for sample 106:
Smoothing segments for sample 107:
Smoothing segments for sample 108:
Smoothing segments for sample 109:
Smoothing segments for sample 110:
Smoothing segments for sample 111:
Smoothing segments for sample 112:
Median centering data...
Saving segmented data file...
Running focal analysis...
Using supplied D...
Loading cytoband/refgene file: '/xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.mat'
...Matching fields to Array List File:
      Array  --->  array
Subselecting 112 samples in data.

Nsamples =

   112

Running focal GISTIC version 2.0.21
params = 
         array_list_file: 'array_list.txt'
                cnv_file: {[1x49 char]}
                   t_amp: 0.3000
                   t_del: 0.3000
             genepattern: 0
       join_segment_size: 10
                     ext: ''
                remove_X: 0
      run_broad_analysis: 1
                   ziggs: [1x1 struct]
        broad_len_cutoff: 0.5000
               qv_thresh: 0.2500
              conf_level: [0.9900 0.9900]
                     cap: 2
                   alpha: [2.5145 2.1653]
          do_gene_gistic: 0
         save_data_files: 1
     conserve_disk_space: 0
            use_segarray: 1
        write_gene_files: 1
           use_two_sided: 0
          do_arbitration: 1
              peak_types: ''
           save_seg_data: 1
             arm_peeloff: 1
    gene_collapse_method: 'extreme'
                     res: 4.4643e-04
                   fname: ''
                   islog: 1

Removed 0 samples with more than 10000 segments
Converting data from log to copy number space...
Performing ziggurat deconstruction!
   100

    25

    50

    75

   100

Reconstructing focal genomes...
Reconstructing genome: amp
Reconstructing genome: aod
Reconstructing genome: del
Reconstructing genome: doa
Saving results to: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/BLCA-TP/22507482/focal_dat.0.5.mat
Scoring segments...
Reconstructing genome: amp
Reconstructing genome: del
Scoring genomes...
Reconstructing genome: amp
Reconstructing genome: aod
Reconstructing genome: del
Reconstructing genome: doa
Saving results to: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/BLCA-TP/22507482/scores.0.5.mat
Performing background permutations...
Amps...
   100

Conv:................................................................................................................
Dels...
   100

Conv:................................................................................................................
Saving stats...
Running arbitrated peel-off...
Finding peaks on chromosome 1
Removing 88 segments from data
Removing 36 segments from data
Removing 20 segments from data
Resolving conflicts...
Computing background score...
Computing score for peak 1 of 2 on chromosome
Amplification peak at chr1:160887451-161070225(1050:1057)
q-value = 4.7578e-09 & residual q-value = 4.7578e-09
Computing score for peak 2 of 2 on chromosome
Amplification peak at chr1:40428006-40433921(277:278)
q-value = 0.031414 & residual q-value = 0.031414
Finding peaks on chromosome 2
Computing background score...
Finding peaks on chromosome 3
Removing 62 segments from data
Removing 10 segments from data
Resolving conflicts...
Computing background score...
Computing score for peak 1 of 1 on chromosome
Amplification peak at chr3:12037673-12181459(3405:3406)
q-value = 6.7568e-07 & residual q-value = 6.7568e-07
Finding peaks on chromosome 4
Removing 39 segments from data
Removing 10 segments from data
Computing background score...
Computing score for peak 1 of 1 on chromosome
Amplification peak at chr4:73630009-73651302(5381:5382)
q-value = 0.18798 & residual q-value = 0.18798
Finding peaks on chromosome 5
Computing background score...
Finding peaks on chromosome 6
Removing 60 segments from data
Removing 22 segments from data
Resolving conflicts...
Removing 12 segments from data
Computing background score...
Computing score for peak 1 of 2 on chromosome
Amplification peak at chr6:19071283-19329929(7913:7923)
q-value = 8.4986e-06 & residual q-value = 0.0076608
Computing score for peak 2 of 2 on chromosome
Amplification peak at chr6:23785507-23861198(7924:7925)
q-value = 0.00014663 & residual q-value = 0.0035245
Finding peaks on chromosome 7
Removing 50 segments from data
Removing 20 segments from data
Resolving conflicts...
Computing background score...
Computing score for peak 1 of 1 on chromosome
Amplification peak at chr7:54801843-55095530(9407:9412)
q-value = 9.8316e-07 & residual q-value = 9.8316e-07
Finding peaks on chromosome 8
Removing 102 segments from data
Removing 30 segments from data
Removing 8 segments from data
Resolving conflicts...
Computing background score...
Computing score for peak 1 of 2 on chromosome
Amplification peak at chr8:102013118-102196067(11049:11056)
q-value = 1.4563e-06 & residual q-value = 1.4563e-06
Computing score for peak 2 of 2 on chromosome
Amplification peak at chr8:37588240-37589461(10313:10314)
q-value = 0.00036926 & residual q-value = 0.00036926
Finding peaks on chromosome 9
Computing background score...
Finding peaks on chromosome 10
Removing 32 segments from data
Removing 15 segments from data
Computing background score...
Computing score for peak 1 of 1 on chromosome
Amplification peak at chr10:8070939-8081931(12434:12435)
q-value = 0.038557 & residual q-value = 0.038557
Finding peaks on chromosome 11
Removing 60 segments from data
Removing 3 segments from data
Computing background score...
Computing score for peak 1 of 1 on chromosome
Amplification peak at chr11:70219906-70402506(13905:13912)
q-value = 3.0331e-09 & residual q-value = 3.0331e-09
Finding peaks on chromosome 12
Removing 45 segments from data
Removing 8 segments from data
Resolving conflicts...
Computing background score...
Computing score for peak 1 of 1 on chromosome
Amplification peak at chr12:69183509-69479730(15248:15253)
q-value = 4.9358e-06 & residual q-value = 4.9358e-06
Finding peaks on chromosome 13
Computing background score...
Finding peaks on chromosome 14
Computing background score...
Finding peaks on chromosome 15
Computing background score...
Finding peaks on chromosome 16
Removing 24 segments from data
Removing 12 segments from data
Resolving conflicts...
Removing 9 segments from data
Computing background score...
Computing score for peak 1 of 2 on chromosome
Amplification peak at chr16:24657583-24792887(17701:17702)
q-value = 0.0069641 & residual q-value = 0.032977
Computing score for peak 2 of 2 on chromosome
Amplification peak at chr16:8621585-8859785(17585:17589)
q-value = 0.056118 & residual q-value = 0.18461
Finding peaks on chromosome 17
Removing 26 segments from data
Removing 24 segments from data
Resolving conflicts...
Removing 19 segments from data
Resolving conflicts...
Computing background score...
Computing score for peak 1 of 2 on chromosome
Amplification peak at chr17:37897401-37900661(18528:18529)
q-value = 0.00029879 & residual q-value = 0.00096428
Computing score for peak 2 of 2 on chromosome
Amplification peak at chr17:30963456-31203334(18424:18429)
q-value = 0.15748 & residual q-value = 0.19223
Finding peaks on chromosome 18
Computing background score...
Finding peaks on chromosome 19
Removing 56 segments from data
Removing 17 segments from data
Resolving conflicts...
Removing 15 segments from data
Resolving conflicts...
Computing background score...
Computing score for peak 1 of 2 on chromosome
Amplification peak at chr19:30479134-30522387(19785:19786)
q-value = 2.8274e-06 & residual q-value = 0.00018719
Computing score for peak 2 of 2 on chromosome
Amplification peak at chr19:39279384-39348459(19961:19964)
q-value = 0.00020103 & residual q-value = 0.03769
Finding peaks on chromosome 20
Removing 26 segments from data
Removing 2 segments from data
Resolving conflicts...
Computing background score...
Computing score for peak 1 of 1 on chromosome
Amplification peak at chr20:29938863-30329932(20339:20349)
q-value = 0.13122 & residual q-value = 0.13122
Finding peaks on chromosome 21
Computing background score...
Finding peaks on chromosome 22
Removing 12 segments from data
Removing 12 segments from data
Resolving conflicts...
Computing background score...
Computing score for peak 1 of 1 on chromosome
Amplification peak at chr22:25346602-26296525(20952:20961)
q-value = 0.14067 & residual q-value = 0.14067
Finding peaks on chromosome 23
Computing background score...
Finding peaks on chromosome 1
Computing background score...
Finding peaks on chromosome 2
Removing 32 segments from data
Removing 18 segments from data
Resolving conflicts...
Removing 3 segments from data
Computing background score...
Computing score for peak 1 of 2 on chromosome
Deletion peak at chr2:226228053-226330746(3203:3204)
q-value = 1.9981e-05 & residual q-value = 3.6786e-05
Computing score for peak 2 of 2 on chromosome
Deletion peak at chr2:141918802-141936476(2507:2508)
q-value = 0.0011976 & residual q-value = 0.0026783
Finding peaks on chromosome 3
Removing 16 segments from data
Removing 6 segments from data
Resolving conflicts...
Computing background score...
Computing score for peak 1 of 1 on chromosome
Deletion peak at chr3:74851549-75002284(3843:3846)
q-value = 0.11081 & residual q-value = 0.11081
Finding peaks on chromosome 4
Removing 22 segments from data
Removing 11 segments from data
Resolving conflicts...
Removing 6 segments from data
Computing background score...
Computing score for peak 1 of 2 on chromosome
Deletion peak at chr4:91795806-91872297(5623:5624)
q-value = 0.016249 & residual q-value = 0.047096
Computing score for peak 2 of 2 on chromosome
Deletion peak at chr4:180997240-181460676(6274:6283)
q-value = 0.048854 & residual q-value = 0.19938
Finding peaks on chromosome 5
Removing 18 segments from data
Removing 13 segments from data
Resolving conflicts...
Removing 4 segments from data
Resolving conflicts...
Computing background score...
Computing score for peak 1 of 2 on chromosome
Deletion peak at chr5:59114477-59132728(6818:6819)
q-value = 0.038704 & residual q-value = 0.061836
Computing score for peak 2 of 2 on chromosome
Deletion peak at chr5:166062764-166219945(7514:7517)
q-value = 0.16552 & residual q-value = 0.20292
Finding peaks on chromosome 6
Removing 16 segments from data
Removing 10 segments from data
Removing 11 segments from data
Resolving conflicts...
Computing background score...
Computing score for peak 1 of 2 on chromosome
Deletion peak at chr6:108463916-116939576(8595:8638)
q-value = 0.048893 & residual q-value = 0.048893
Computing score for peak 2 of 2 on chromosome
Deletion peak at chr6:63814-1875640(7578:7593)
q-value = 0.21101 & residual q-value = 0.21101
Finding peaks on chromosome 7
Computing background score...
Finding peaks on chromosome 8
Removing 35 segments from data
Removing 3 segments from data
Computing background score...
Computing score for peak 1 of 1 on chromosome
Deletion peak at chr8:16715659-17786984(10049:10052)
q-value = 1.57e-05 & residual q-value = 1.57e-05
Finding peaks on chromosome 9
Removing 46 segments from data
Removing 6 segments from data
Computing background score...
Computing score for peak 1 of 1 on chromosome
Deletion peak at chr9:21973950-21998310(11786:11789)
q-value = 2.5163e-50 & residual q-value = 2.5163e-50
Finding peaks on chromosome 10
Computing background score...
Finding peaks on chromosome 11
Computing background score...
Finding peaks on chromosome 12
Removing 11 segments from data
Removing 17 segments from data
Computing background score...
Computing score for peak 1 of 1 on chromosome
Deletion peak at chr12:14209365-14667684(14666:14669)
q-value = 0.19529 & residual q-value = 0.19529
Finding peaks on chromosome 13
Removing 32 segments from data
Removing 3 segments from data
Resolving conflicts...
Computing background score...
Computing score for peak 1 of 1 on chromosome
Deletion peak at chr13:48950827-49102445(15982:15986)
q-value = 1.0263e-05 & residual q-value = 1.0263e-05
Finding peaks on chromosome 14
Computing background score...
Finding peaks on chromosome 15
Removing 16 segments from data
Removing 4 segments from data
Computing background score...
Computing score for peak 1 of 1 on chromosome
Deletion peak at chr15:25931333-27262478(17123:17135)
q-value = 0.051495 & residual q-value = 0.051495
Finding peaks on chromosome 16
Computing background score...
Finding peaks on chromosome 17
Removing 12 segments from data
Removing 4 segments from data
Computing background score...
Computing score for peak 1 of 1 on chromosome
Deletion peak at chr17:10869438-11689792(18183:18190)
q-value = 0.083417 & residual q-value = 0.083417
Finding peaks on chromosome 18
Computing background score...
Finding peaks on chromosome 19
Computing background score...
Finding peaks on chromosome 20
Computing background score...
Finding peaks on chromosome 21
Computing background score...
Finding peaks on chromosome 22
Computing background score...
Finding peaks on chromosome 23
Computing background score...
Saving peak regions...
Computing permuted score distributions...
Performing permutation 1 of 25
Performing permutation 2 of 25
Performing permutation 3 of 25
Performing permutation 4 of 25
Performing permutation 5 of 25
Performing permutation 6 of 25
Performing permutation 7 of 25
Performing permutation 8 of 25
Performing permutation 9 of 25
Performing permutation 10 of 25
Performing permutation 11 of 25
Performing permutation 12 of 25
Performing permutation 13 of 25
Performing permutation 14 of 25
Performing permutation 15 of 25
Performing permutation 16 of 25
Performing permutation 17 of 25
Performing permutation 18 of 25
Performing permutation 19 of 25
Performing permutation 20 of 25
Performing permutation 21 of 25
Performing permutation 22 of 25
Performing permutation 23 of 25
Performing permutation 24 of 25
Performing permutation 25 of 25
Performing permutation 1 of 25
Performing permutation 2 of 25
Performing permutation 3 of 25
Performing permutation 4 of 25
Performing permutation 5 of 25
Performing permutation 6 of 25
Performing permutation 7 of 25
Performing permutation 8 of 25
Performing permutation 9 of 25
Performing permutation 10 of 25
Performing permutation 11 of 25
Performing permutation 12 of 25
Performing permutation 13 of 25
Performing permutation 14 of 25
Performing permutation 15 of 25
Performing permutation 16 of 25
Performing permutation 17 of 25
Performing permutation 18 of 25
Performing permutation 19 of 25
Performing permutation 20 of 25
Performing permutation 21 of 25
Performing permutation 22 of 25
Performing permutation 23 of 25
Performing permutation 24 of 25
Performing permutation 25 of 25
Saving permuted score files...
Computing wide peak regions...
Running Regbounder at confidence level: 99%
     1

Calculating on permutation 1 of 25
Calculating on permutation 2 of 25
Calculating on permutation 3 of 25
Calculating on permutation 4 of 25
Calculating on permutation 5 of 25
Calculating on permutation 6 of 25
Calculating on permutation 7 of 25
Calculating on permutation 8 of 25
Calculating on permutation 9 of 25
Calculating on permutation 10 of 25
Calculating on permutation 11 of 25
Calculating on permutation 12 of 25
Calculating on permutation 13 of 25
Calculating on permutation 14 of 25
Calculating on permutation 15 of 25
Calculating on permutation 16 of 25
Calculating on permutation 17 of 25
Calculating on permutation 18 of 25
Calculating on permutation 19 of 25
Calculating on permutation 20 of 25
Calculating on permutation 21 of 25
Calculating on permutation 22 of 25
Calculating on permutation 23 of 25
Calculating on permutation 24 of 25
Calculating on permutation 25 of 25
     2

Calculating on permutation 1 of 25
Calculating on permutation 2 of 25
Calculating on permutation 3 of 25
Calculating on permutation 4 of 25
Calculating on permutation 5 of 25
Calculating on permutation 6 of 25
Calculating on permutation 7 of 25
Calculating on permutation 8 of 25
Calculating on permutation 9 of 25
Calculating on permutation 10 of 25
Calculating on permutation 11 of 25
Calculating on permutation 12 of 25
Calculating on permutation 13 of 25
Calculating on permutation 14 of 25
Calculating on permutation 15 of 25
Calculating on permutation 16 of 25
Calculating on permutation 17 of 25
Calculating on permutation 18 of 25
Calculating on permutation 19 of 25
Calculating on permutation 20 of 25
Calculating on permutation 21 of 25
Calculating on permutation 22 of 25
Calculating on permutation 23 of 25
Calculating on permutation 24 of 25
Calculating on permutation 25 of 25
Amplification wide peak at chr1:160715526-161112063(1043:1068)
Amplification wide peak at chr1:39479426-40536420(256:281)
Amplification wide peak at chr3:11931389-12492867(3400:3417)
Amplification wide peak at chr4:68610755-78216278(5298:5440)
Amplification wide peak at chr6:17882616-23785507(7883:7924)
Amplification wide peak at chr6:19329929-24669727(7923:7948)
Amplification wide peak at chr7:54753282-55427161(9402:9425)
Amplification wide peak at chr8:100274020-103249873(11012:11085)
Amplification wide peak at chr8:37144531-37787195(10282:10325)
Amplification wide peak at chr10:4201426-10688828(12407:12458)
Amplification wide peak at chr11:70110204-70417926(13898:13917)
Amplification wide peak at chr12:69130919-70420917(15237:15272)
Amplification wide peak at chr16:23879423-27102172(17692:17730)
Amplification wide peak at chr16:6480817-13148104(17563:17639)
Amplification wide peak at chr17:37809929-38014602(18519:18537)
Amplification wide peak at chr17:20979844-34943690(18295:18465)
Amplification wide peak at chr19:30025328-30797567(19768:19799)
Amplification wide peak at chr19:38026422-41158417(19946:20001)
Amplification wide peak at chr20:25328497-30730975(20338:20356)
Amplification wide peak at chr22:17450338-27262681(20933:20978)
Deletion wide peak at chr2:213680354-243189359(3102:3310)
Deletion wide peak at chr2:141753755-141964876(2492:2515)
Deletion wide peak at chr3:41449449-85122339(3641:3955)
Deletion wide peak at chr4:91468745-92537601(5602:5644)
Deletion wide peak at chr4:155886614-188680501(6158:6327)
Deletion wide peak at chr5:45373655-78941998(6698:6936)
Deletion wide peak at chr5:163766968-180905246(7499:7577)
Deletion wide peak at chr6:91320642-122521775(8516:8675)
Deletion wide peak at chr6:63814-5190075(7578:7644)
Deletion wide peak at chr8:23379-31619595(9995:10147)
Deletion wide peak at chr9:21965768-22004311(11781:11792)
Deletion wide peak at chr12:4377550-19937178(14614:14714)
Deletion wide peak at chr13:48792454-51676610(15976:16006)
Deletion wide peak at chr15:23835793-33124920(17108:17143)
Deletion wide peak at chr17:10232869-12629622(18169:18199)
Saving final_regions...
Writing output files...
Writing all_lesions file to: /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/BLCA-TP/22507482/all_lesions.conf_99.txt
Adding gene annotations
Writing output gene table files
Writing q value, p value and amp/del score file
About to save Raw_copy_number figure file
{Warning: Large-scale algorithm does not currently solve this problem
formulation,
using medium-scale algorithm instead.} 
> In quadprog at 291
  In find_text_pos at 42
  In draw_spaced_text at 42
  In plot_snp_score at 470
  In gistic_plots at 214
  In run_focal_gistic at 359
  In run_gistic20 at 125
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: Large-scale algorithm does not currently solve this problem
formulation,
using medium-scale algorithm instead.} 
> In quadprog at 291
  In find_text_pos at 42
  In draw_spaced_text at 42
  In plot_snp_score at 470
  In gistic_plots at 214
  In run_focal_gistic at 359
  In run_gistic20 at 125
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
Focal GISTIC completed without error
Running broad analysis...
Reconstructing genome: amp
Reconstructing genome: aod
Reconstructing genome: del
Reconstructing genome: doa
Calculating median of arm values...
Finding median of arms on chromosome:
     1

     2

     3

     4

     5

     6

     7

     8

     9

    10

    11

    12

    13

    14

    15

    16

    17

    18

    19

    20

    21

    22

    23

Finding median of arms on chromosome:
     1

     2

     3

     4

     5

     6

     7

     8

     9

    10

    11

    12

    13

    14

    15

    16

    17

    18

    19

    20

    21

    22

    23

     1

     2

     3

     4

     5

     6

     7

     8

     9

    10

    11

    12

    13

    14

    15

    16

    17

    18

    19

    20

    21

    22

    23

    24

    25

    26

    27

    28

    29

    30

    31

    32

    33

    34

    35

    36

    37

    38

    39

    40

Writing arm medians file...
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp before} 
> In find_snps at 66
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
{Warning: no snp after} 
> In find_snps at 73
  In add_snps_to_rg at 26
  In run_gistic20 at 165
  In run_gistic2_from_seg at 225
  In call_gistic2 at 119
Reducing all data to genes
reduce_to_genes: defining gene 1000 of 24924
reduce_to_genes: defining gene 2000 of 24924
reduce_to_genes: defining gene 3000 of 24924
reduce_to_genes: defining gene 4000 of 24924
reduce_to_genes: defining gene 5000 of 24924
reduce_to_genes: defining gene 6000 of 24924
reduce_to_genes: defining gene 7000 of 24924
reduce_to_genes: defining gene 8000 of 24924
reduce_to_genes: defining gene 9000 of 24924
reduce_to_genes: defining gene 10000 of 24924
reduce_to_genes: defining gene 11000 of 24924
reduce_to_genes: defining gene 12000 of 24924
reduce_to_genes: defining gene 13000 of 24924
reduce_to_genes: defining gene 14000 of 24924
reduce_to_genes: defining gene 15000 of 24924
reduce_to_genes: defining gene 16000 of 24924
reduce_to_genes: defining gene 17000 of 24924
reduce_to_genes: defining gene 18000 of 24924
reduce_to_genes: defining gene 19000 of 24924
reduce_to_genes: defining gene 20000 of 24924
reduce_to_genes: defining gene 21000 of 24924
reduce_to_genes: defining gene 22000 of 24924
reduce_to_genes: defining gene 23000 of 24924
reduce_to_genes: defining gene 24000 of 24924
reduce_to_genes: reducing gene 1000 of 24776
reduce_to_genes: reducing gene 2000 of 24776
reduce_to_genes: reducing gene 3000 of 24776
reduce_to_genes: reducing gene 4000 of 24776
reduce_to_genes: reducing gene 5000 of 24776
reduce_to_genes: reducing gene 6000 of 24776
reduce_to_genes: reducing gene 7000 of 24776
reduce_to_genes: reducing gene 8000 of 24776
reduce_to_genes: reducing gene 9000 of 24776
reduce_to_genes: reducing gene 10000 of 24776
reduce_to_genes: reducing gene 11000 of 24776
reduce_to_genes: reducing gene 12000 of 24776
reduce_to_genes: reducing gene 13000 of 24776
reduce_to_genes: reducing gene 14000 of 24776
reduce_to_genes: reducing gene 15000 of 24776
reduce_to_genes: reducing gene 16000 of 24776
reduce_to_genes: reducing gene 17000 of 24776
reduce_to_genes: reducing gene 18000 of 24776
reduce_to_genes: reducing gene 19000 of 24776
reduce_to_genes: reducing gene 20000 of 24776
reduce_to_genes: reducing gene 21000 of 24776
reduce_to_genes: reducing gene 22000 of 24776
reduce_to_genes: reducing gene 23000 of 24776
reduce_to_genes: reducing gene 24000 of 24776
        1000

        2000

        3000

        4000

        5000

        6000

        7000

        8000

        9000

       10000

       11000

       12000

       13000

       14000

       15000

       16000

       17000

       18000

       19000

       20000

       21000

       22000

       23000

       24000

Reducing focal data to genes
Reconstructing genome: amp
Reconstructing genome: aod
Reconstructing genome: del
Reconstructing genome: doa
reduce_to_genes: defining gene 1000 of 24924
reduce_to_genes: defining gene 2000 of 24924
reduce_to_genes: defining gene 3000 of 24924
reduce_to_genes: defining gene 4000 of 24924
reduce_to_genes: defining gene 5000 of 24924
reduce_to_genes: defining gene 6000 of 24924
reduce_to_genes: defining gene 7000 of 24924
reduce_to_genes: defining gene 8000 of 24924
reduce_to_genes: defining gene 9000 of 24924
reduce_to_genes: defining gene 10000 of 24924
reduce_to_genes: defining gene 11000 of 24924
reduce_to_genes: defining gene 12000 of 24924
reduce_to_genes: defining gene 13000 of 24924
reduce_to_genes: defining gene 14000 of 24924
reduce_to_genes: defining gene 15000 of 24924
reduce_to_genes: defining gene 16000 of 24924
reduce_to_genes: defining gene 17000 of 24924
reduce_to_genes: defining gene 18000 of 24924
reduce_to_genes: defining gene 19000 of 24924
reduce_to_genes: defining gene 20000 of 24924
reduce_to_genes: defining gene 21000 of 24924
reduce_to_genes: defining gene 22000 of 24924
reduce_to_genes: defining gene 23000 of 24924
reduce_to_genes: defining gene 24000 of 24924
reduce_to_genes: reducing gene 1000 of 24776
reduce_to_genes: reducing gene 2000 of 24776
reduce_to_genes: reducing gene 3000 of 24776
reduce_to_genes: reducing gene 4000 of 24776
reduce_to_genes: reducing gene 5000 of 24776
reduce_to_genes: reducing gene 6000 of 24776
reduce_to_genes: reducing gene 7000 of 24776
reduce_to_genes: reducing gene 8000 of 24776
reduce_to_genes: reducing gene 9000 of 24776
reduce_to_genes: reducing gene 10000 of 24776
reduce_to_genes: reducing gene 11000 of 24776
reduce_to_genes: reducing gene 12000 of 24776
reduce_to_genes: reducing gene 13000 of 24776
reduce_to_genes: reducing gene 14000 of 24776
reduce_to_genes: reducing gene 15000 of 24776
reduce_to_genes: reducing gene 16000 of 24776
reduce_to_genes: reducing gene 17000 of 24776
reduce_to_genes: reducing gene 18000 of 24776
reduce_to_genes: reducing gene 19000 of 24776
reduce_to_genes: reducing gene 20000 of 24776
reduce_to_genes: reducing gene 21000 of 24776
reduce_to_genes: reducing gene 22000 of 24776
reduce_to_genes: reducing gene 23000 of 24776
reduce_to_genes: reducing gene 24000 of 24776
        1000

        2000

        3000

        4000

        5000

        6000

        7000

        8000

        9000

       10000

       11000

       12000

       13000

       14000

       15000

       16000

       17000

       18000

       19000

       20000

       21000

       22000

       23000

       24000

Reducing broad data to genes
Reconstructing genome: amp
Reconstructing genome: aod
Reconstructing genome: del
Reconstructing genome: doa
reduce_to_genes: defining gene 1000 of 24924
reduce_to_genes: defining gene 2000 of 24924
reduce_to_genes: defining gene 3000 of 24924
reduce_to_genes: defining gene 4000 of 24924
reduce_to_genes: defining gene 5000 of 24924
reduce_to_genes: defining gene 6000 of 24924
reduce_to_genes: defining gene 7000 of 24924
reduce_to_genes: defining gene 8000 of 24924
reduce_to_genes: defining gene 9000 of 24924
reduce_to_genes: defining gene 10000 of 24924
reduce_to_genes: defining gene 11000 of 24924
reduce_to_genes: defining gene 12000 of 24924
reduce_to_genes: defining gene 13000 of 24924
reduce_to_genes: defining gene 14000 of 24924
reduce_to_genes: defining gene 15000 of 24924
reduce_to_genes: defining gene 16000 of 24924
reduce_to_genes: defining gene 17000 of 24924
reduce_to_genes: defining gene 18000 of 24924
reduce_to_genes: defining gene 19000 of 24924
reduce_to_genes: defining gene 20000 of 24924
reduce_to_genes: defining gene 21000 of 24924
reduce_to_genes: defining gene 22000 of 24924
reduce_to_genes: defining gene 23000 of 24924
reduce_to_genes: defining gene 24000 of 24924
reduce_to_genes: reducing gene 1000 of 24776
reduce_to_genes: reducing gene 2000 of 24776
reduce_to_genes: reducing gene 3000 of 24776
reduce_to_genes: reducing gene 4000 of 24776
reduce_to_genes: reducing gene 5000 of 24776
reduce_to_genes: reducing gene 6000 of 24776
reduce_to_genes: reducing gene 7000 of 24776
reduce_to_genes: reducing gene 8000 of 24776
reduce_to_genes: reducing gene 9000 of 24776
reduce_to_genes: reducing gene 10000 of 24776
reduce_to_genes: reducing gene 11000 of 24776
reduce_to_genes: reducing gene 12000 of 24776
reduce_to_genes: reducing gene 13000 of 24776
reduce_to_genes: reducing gene 14000 of 24776
reduce_to_genes: reducing gene 15000 of 24776
reduce_to_genes: reducing gene 16000 of 24776
reduce_to_genes: reducing gene 17000 of 24776
reduce_to_genes: reducing gene 18000 of 24776
reduce_to_genes: reducing gene 19000 of 24776
reduce_to_genes: reducing gene 20000 of 24776
reduce_to_genes: reducing gene 21000 of 24776
reduce_to_genes: reducing gene 22000 of 24776
reduce_to_genes: reducing gene 23000 of 24776
reduce_to_genes: reducing gene 24000 of 24776
        1000

        2000

        3000

        4000

        5000

        6000

        7000

        8000

        9000

       10000

       11000

       12000

       13000

       14000

       15000

       16000

       17000

       18000

       19000

       20000

       21000

       22000

       23000

       24000

Calculating sample cutoffs...
Reading file using format:%s%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f
Writing sample cutoff file...
Thresholding data...
Reading file using format:%s%f%f
Reading file using format:%s%s%s%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f%f
Writing thresholded gene calls...
   100

   200

   300

   400

   500

   600

   700

   800

   900

        1000

        1100

        1200

        1300

        1400

        1500

        1600

        1700

        1800

        1900

        2000

        2100

        2200

        2300

        2400

        2500

        2600

        2700

        2800

        2900

        3000

        3100

        3200

        3300

        3400

        3500

        3600

        3700

        3800

        3900

        4000

        4100

        4200

        4300

        4400

        4500

        4600

        4700

        4800

        4900

        5000

        5100

        5200

        5300

        5400

        5500

        5600

        5700

        5800

        5900

        6000

        6100

        6200

        6300

        6400

        6500

        6600

        6700

        6800

        6900

        7000

        7100

        7200

        7300

        7400

        7500

        7600

        7700

        7800

        7900

        8000

        8100

        8200

        8300

        8400

        8500

        8600

        8700

        8800

        8900

        9000

        9100

        9200

        9300

        9400

        9500

        9600

        9700

        9800

        9900

       10000

       10100

       10200

       10300

       10400

       10500

       10600

       10700

       10800

       10900

       11000

       11100

       11200

       11300

       11400

       11500

       11600

       11700

       11800

       11900

       12000

       12100

       12200

       12300

       12400

       12500

       12600

       12700

       12800

       12900

       13000

       13100

       13200

       13300

       13400

       13500

       13600

       13700

       13800

       13900

       14000

       14100

       14200

       14300

       14400

       14500

       14600

       14700

       14800

       14900

       15000

       15100

       15200

       15300

       15400

       15500

       15600

       15700

       15800

       15900

       16000

       16100

       16200

       16300

       16400

       16500

       16600

       16700

       16800

       16900

       17000

       17100

       17200

       17300

       17400

       17500

       17600

       17700

       17800

       17900

       18000

       18100

       18200

       18300

       18400

       18500

       18600

       18700

       18800

       18900

       19000

       19100

       19200

       19300

       19400

       19500

       19600

       19700

       19800

       19900

       20000

       20100

       20200

       20300

       20400

       20500

       20600

       20700

       20800

       20900

       21000

       21100

       21200

       21300

       21400

       21500

       21600

       21700

       21800

       21900

       22000

       22100

       22200

       22300

       22400

       22500

       22600

       22700

       22800

       22900

       23000

       23100

       23200

       23300

       23400

       23500

       23600

       23700

       23800

       23900

       24000

       24100

       24200

       24300

       24400

       24500

       24600

       24700

Finished writing gene tables.
GISTIC2 run completed!
Reconstructing genome: amp
Reconstructing genome: aod
Reconstructing genome: del
Reconstructing genome: doa
Reconstructing genome: amp
Reconstructing genome: aod
Reconstructing genome: del
Reconstructing genome: doa
