.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/e6588b94872f862937b81285b1c2fa/.command.log
Size: 70.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/92c5ccec4f18c5aa09d0c9b3ae19ce/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/e6588b94872f862937b81285b1c2fa/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/e6588b94872f862937b81285b1c2fa/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/92c5ccec4f18c5aa09d0c9b3ae19ce/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/a60abc8bba469f1210d001de2a9373/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.KrGrv0o5KQ/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary
-sample contains 159122119 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir  -J /tmp/nxf.KrGrv0o5KQ/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Chimeric.out.junction  -O /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.KrGrv0o5KQ/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

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[1930000], rate=75587.47/min -building interval tree based on /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

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[1930000], rate=74757.91/min -building interval tree based on /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

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[1890000], rate=65360.23/min 
[1900000], rate=65404.48/min 
[1910000], rate=65410.96/min 
[1920000], rate=65454.55/min -building interval tree based on /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=100000.00/min 
[20000], rate=100000.00/min 
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[40000], rate=109090.91/min 
[50000], rate=115384.62/min 
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[80000], rate=137142.86/min 
[90000], rate=138461.54/min 
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[1820000], rate=60666.67/min 
[1830000], rate=60730.09/min 
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[1890000], rate=61231.10/min 
[1900000], rate=61389.34/min 
[1910000], rate=61513.69/min 
[1920000], rate=61670.24/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 0.00 reads per min processed...  
 12000000.00 reads per min processed...  
 18000000.00 reads per min processed...  
 12000000.00 reads per min processed...  
 7500000.00 reads per min processed...  
 7200000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 5500000.00 reads per min processed...  
 5538461.54 reads per min processed...  
 5571428.57 reads per min processed...  
 5250000.00 reads per min processed...  
 5294117.65 reads per min processed...  
 5052631.58 reads per min processed...  
 5100000.00 reads per min processed...  
 5142857.14 reads per min processed...  
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 5000000.00 reads per min processed...  
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 4888888.89 reads per min processed...  
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 4800000.00 reads per min processed...  
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 4727272.73 reads per min processed...  
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 4666666.67 reads per min processed...  
 4702702.70 reads per min processed...  
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 4666666.67 reads per min processed...  
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 4918032.79 reads per min processed...  
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 4909090.91 reads per min processed...  
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 4869565.22 reads per min processed...  
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 4909090.91 reads per min processed...  
 4860759.49 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.KrGrv0o5KQ/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Chimeric.out.junction  --tmpdir /tmp  --min_junction_reads 0  --min_sum_frags 1  --require_LDAS 0  --max_promiscuity 10  --min_pct_dom_promiscuity 20  --min_novel_junction_support 1  --min_alt_pct_junction 10  --aggregate_novel_junction_dist 5  --min_spanning_frags_only 1  --genome_lib_dir /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -240601.943935
EM: Round [1] log likelihood: -240469.227743
EM: Round [2] log likelihood: -240414.099324
EM: Round [3] log likelihood: -240386.921407
EM: Round [4] log likelihood: -240372.299525
EM: Round [5] log likelihood: -240364.020384
EM: Round [6] log likelihood: -240359.148795
EM: Round [7] log likelihood: -240356.174259
EM: Round [8] log likelihood: -240354.286304
EM: Round [9] log likelihood: -240353.039751
EM: Round [10] log likelihood: -240352.184637
EM: Round [11] log likelihood: -240351.576861
EM: Round [12] log likelihood: -240351.130802
EM: Round [13] log likelihood: -240350.793944
EM: Round [14] log likelihood: -240350.533047
EM: Round [15] log likelihood: -240350.326433
EM: Round [16] log likelihood: -240350.159570
EM: Round [17] log likelihood: -240350.022463
EM: Round [18] log likelihood: -240349.908082
EM: Round [19] log likelihood: -240349.811373
EM: Round [20] log likelihood: -240349.728636
EM: Round [21] log likelihood: -240349.657111
EM: Round [22] log likelihood: -240349.594708
EM: Round [23] log likelihood: -240349.539822
EM: Round [24] log likelihood: -240349.491200
EM: Round [25] log likelihood: -240349.447853
EM: Round [26] log likelihood: -240349.408991
EM: Round [27] log likelihood: -240349.373976
EM: Round [28] log likelihood: -240349.342287
EM: Round [29] log likelihood: -240349.313494
EM: Round [30] log likelihood: -240349.287241
EM: Round [31] log likelihood: -240349.263228
EM: Round [32] log likelihood: -240349.241202
EM: Round [33] log likelihood: -240349.220948
EM: Round [34] log likelihood: -240349.202279
EM: Round [35] log likelihood: -240349.185038
EM: Round [36] log likelihood: -240349.169086
EM: Round [37] log likelihood: -240349.154301
EM: Round [38] log likelihood: -240349.140578
EM: Round [39] log likelihood: -240349.127822
EM: Round [40] log likelihood: -240349.115951
EM: Round [41] log likelihood: -240349.104891
EM: Round [42] log likelihood: -240349.094576
EM: Round [43] log likelihood: -240349.084947
EM: Round [44] log likelihood: -240349.075950
EM: Round [45] log likelihood: -240349.067537
EM: Round [46] log likelihood: -240349.059664
EM: Round [47] log likelihood: -240349.052292
EM: Round [48] log likelihood: -240349.045385
EM: Round [49] log likelihood: -240349.038910
EM: Round [50] log likelihood: -240349.032836
EM: Round [51] log likelihood: -240349.027136
EM: Round [52] log likelihood: -240349.021784
EM: Round [53] log likelihood: -240349.016757
EM: Round [54] log likelihood: -240349.012033
EM: Round [55] log likelihood: -240349.007593
EM: Round [56] log likelihood: -240349.003418
EM: Round [57] log likelihood: -240348.999490
EM: Round [58] log likelihood: -240348.995794
EM: Round [59] log likelihood: -240348.992316
EM: Round [60] log likelihood: -240348.989041
EM: Round [61] log likelihood: -240348.985957
EM: Round [62] log likelihood: -240348.983052
EM: Round [63] log likelihood: -240348.980315
EM: Round [64] log likelihood: -240348.977736
EM: Round [65] log likelihood: -240348.975304
EM: Round [66] log likelihood: -240348.973012
EM: Round [67] log likelihood: -240348.970850
EM: Round [68] log likelihood: -240348.968811
EM: Round [69] log likelihood: -240348.966887
EM: Round [70] log likelihood: -240348.965072
EM: Round [71] log likelihood: -240348.963359
EM: Round [72] log likelihood: -240348.961743
EM: Round [73] log likelihood: -240348.960216
EM: Round [74] log likelihood: -240348.958775
EM: Round [75] log likelihood: -240348.957414
EM: Round [76] log likelihood: -240348.956129
EM: Round [77] log likelihood: -240348.954914
EM: Round [78] log likelihood: -240348.953767
EM: Round [79] log likelihood: -240348.952682
EM: Round [80] log likelihood: -240348.951657
EM: Round [81] log likelihood: -240348.950688
EM: Round [82] log likelihood: -240348.949772
EM: Round [83] log likelihood: -240348.948906
EM: Round [84] log likelihood: -240348.948087
EM: Round [85] log likelihood: -240348.947312
EM: Round [86] log likelihood: -240348.946578
EM: Round [87] log likelihood: -240348.945885
EM: Round [88] log likelihood: -240348.945228
EM: Round [89] log likelihood: -240348.944606
EM: Round [90] log likelihood: -240348.944018
EM: Round [91] log likelihood: -240348.943461
EM: Round [92] log likelihood: -240348.942933
EM: Round [93] log likelihood: -240348.942433
EM: Round [94] log likelihood: -240348.941960
EM: Round [95] log likelihood: -240348.941511
EM: Round [96] log likelihood: -240348.941086
EM: Round [97] log likelihood: -240348.940683
EM: Round [98] log likelihood: -240348.940301
EM: Round [99] log likelihood: -240348.939938
EM: Round [100] log likelihood: -240348.939595
EM: Round [101] log likelihood: -240348.939268
EM: Round [102] log likelihood: -240348.938959
EM: Round [103] log likelihood: -240348.938665
EM: Round [104] log likelihood: -240348.938387
EM: Round [105] log likelihood: -240348.938122
EM: Round [106] log likelihood: -240348.937871
EM: Round [107] log likelihood: -240348.937632
EM: Round [108] log likelihood: -240348.937405
EM: Round [109] log likelihood: -240348.937190
EM: Round [110] log likelihood: -240348.936985
EM: Round [111] log likelihood: -240348.936790
EM: Round [112] log likelihood: -240348.936605
EM: Round [113] log likelihood: -240348.936429
EM: Round [114] log likelihood: -240348.936261
EM: Round [115] log likelihood: -240348.936101
EM: Round [116] log likelihood: -240348.935950
EM: Round [117] log likelihood: -240348.935805
EM: Round [118] log likelihood: -240348.935667
EM: Round [119] log likelihood: -240348.935536
EM: Round [120] log likelihood: -240348.935411
EM: Round [121] log likelihood: -240348.935292
EM: Round [122] log likelihood: -240348.935178
EM: Round [123] log likelihood: -240348.935070
EM: Round [124] log likelihood: -240348.934966
EM: Round [125] log likelihood: -240348.934867
EM: Stopping iterations at round 125 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -240208.832587
EM: Round [1] log likelihood: -240086.392267
EM: Round [2] log likelihood: -240036.606650
EM: Round [3] log likelihood: -240012.704322
EM: Round [4] log likelihood: -240000.103197
EM: Round [5] log likelihood: -239993.072293
EM: Round [6] log likelihood: -239988.985760
EM: Round [7] log likelihood: -239986.519918
EM: Round [8] log likelihood: -239984.973393
EM: Round [9] log likelihood: -239983.964212
EM: Round [10] log likelihood: -239983.279489
EM: Round [11] log likelihood: -239982.797439
EM: Round [12] log likelihood: -239982.446325
EM: Round [13] log likelihood: -239982.182565
EM: Round [14] log likelihood: -239981.978868
EM: Round [15] log likelihood: -239981.817635
EM: Round [16] log likelihood: -239981.687205
EM: Round [17] log likelihood: -239981.579652
EM: Round [18] log likelihood: -239981.489465
EM: Round [19] log likelihood: -239981.412725
EM: Round [20] log likelihood: -239981.346594
EM: Round [21] log likelihood: -239981.288973
EM: Round [22] log likelihood: -239981.238286
EM: Round [23] log likelihood: -239981.193330
EM: Round [24] log likelihood: -239981.153170
EM: Round [25] log likelihood: -239981.117072
EM: Round [26] log likelihood: -239981.084450
EM: Round [27] log likelihood: -239981.054833
EM: Round [28] log likelihood: -239981.027832
EM: Round [29] log likelihood: -239981.003129
EM: Round [30] log likelihood: -239980.980458
EM: Round [31] log likelihood: -239980.959594
EM: Round [32] log likelihood: -239980.940346
EM: Round [33] log likelihood: -239980.922551
EM: Round [34] log likelihood: -239980.906068
EM: Round [35] log likelihood: -239980.890775
EM: Round [36] log likelihood: -239980.876563
EM: Round [37] log likelihood: -239980.863338
EM: Round [38] log likelihood: -239980.851018
EM: Round [39] log likelihood: -239980.839526
EM: Round [40] log likelihood: -239980.828797
EM: Round [41] log likelihood: -239980.818772
EM: Round [42] log likelihood: -239980.809396
EM: Round [43] log likelihood: -239980.800621
EM: Round [44] log likelihood: -239980.792402
EM: Round [45] log likelihood: -239980.784701
EM: Round [46] log likelihood: -239980.777479
EM: Round [47] log likelihood: -239980.770704
EM: Round [48] log likelihood: -239980.764345
EM: Round [49] log likelihood: -239980.758374
EM: Round [50] log likelihood: -239980.752765
EM: Round [51] log likelihood: -239980.747493
EM: Round [52] log likelihood: -239980.742537
EM: Round [53] log likelihood: -239980.737877
EM: Round [54] log likelihood: -239980.733493
EM: Round [55] log likelihood: -239980.729368
EM: Round [56] log likelihood: -239980.725485
EM: Round [57] log likelihood: -239980.721829
EM: Round [58] log likelihood: -239980.718387
EM: Round [59] log likelihood: -239980.715145
EM: Round [60] log likelihood: -239980.712090
EM: Round [61] log likelihood: -239980.709211
EM: Round [62] log likelihood: -239980.706498
EM: Round [63] log likelihood: -239980.703940
EM: Round [64] log likelihood: -239980.701529
EM: Round [65] log likelihood: -239980.699255
EM: Round [66] log likelihood: -239980.697110
EM: Round [67] log likelihood: -239980.695086
EM: Round [68] log likelihood: -239980.693177
EM: Round [69] log likelihood: -239980.691376
EM: Round [70] log likelihood: -239980.689675
EM: Round [71] log likelihood: -239980.688070
EM: Round [72] log likelihood: -239980.686555
EM: Round [73] log likelihood: -239980.685125
EM: Round [74] log likelihood: -239980.683773
EM: Round [75] log likelihood: -239980.682497
EM: Round [76] log likelihood: -239980.681292
EM: Round [77] log likelihood: -239980.680153
EM: Round [78] log likelihood: -239980.679077
EM: Round [79] log likelihood: -239980.678060
EM: Round [80] log likelihood: -239980.677099
EM: Round [81] log likelihood: -239980.676190
EM: Round [82] log likelihood: -239980.675331
EM: Round [83] log likelihood: -239980.674519
EM: Round [84] log likelihood: -239980.673751
EM: Round [85] log likelihood: -239980.673025
EM: Round [86] log likelihood: -239980.672337
EM: Round [87] log likelihood: -239980.671687
EM: Round [88] log likelihood: -239980.671072
EM: Round [89] log likelihood: -239980.670489
EM: Round [90] log likelihood: -239980.669938
EM: Round [91] log likelihood: -239980.669416
EM: Round [92] log likelihood: -239980.668922
EM: Round [93] log likelihood: -239980.668455
EM: Round [94] log likelihood: -239980.668011
EM: Round [95] log likelihood: -239980.667592
EM: Round [96] log likelihood: -239980.667194
EM: Round [97] log likelihood: -239980.666817
EM: Round [98] log likelihood: -239980.666460
EM: Round [99] log likelihood: -239980.666121
EM: Round [100] log likelihood: -239980.665800
EM: Round [101] log likelihood: -239980.665495
EM: Round [102] log likelihood: -239980.665207
EM: Round [103] log likelihood: -239980.664932
EM: Round [104] log likelihood: -239980.664672
EM: Round [105] log likelihood: -239980.664426
EM: Round [106] log likelihood: -239980.664191
EM: Round [107] log likelihood: -239980.663969
EM: Round [108] log likelihood: -239980.663758
EM: Round [109] log likelihood: -239980.663557
EM: Round [110] log likelihood: -239980.663367
EM: Round [111] log likelihood: -239980.663185
EM: Round [112] log likelihood: -239980.663013
EM: Round [113] log likelihood: -239980.662849
EM: Round [114] log likelihood: -239980.662694
EM: Round [115] log likelihood: -239980.662546
EM: Round [116] log likelihood: -239980.662405
EM: Round [117] log likelihood: -239980.662271
EM: Round [118] log likelihood: -239980.662143
EM: Round [119] log likelihood: -239980.662021
EM: Round [120] log likelihood: -239980.661905
EM: Round [121] log likelihood: -239980.661795
EM: Round [122] log likelihood: -239980.661690
EM: Round [123] log likelihood: -239980.661590
EM: Round [124] log likelihood: -239980.661494
EM: Stopping iterations at round 124 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter
CMD: /usr/local/src/STAR-Fusion/util/column_exclusions.pl /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered
* Running CMD: /usr/local/src/STAR-Fusion/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 159122119 > /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM
* Running CMD: /usr/local/src/STAR-Fusion/util/append_breakpoint_junction_info.pl /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir > /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir --annotate /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot
* Running CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir
-done, see /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_likely_RT_artifacts.pl --fusions /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 1619, filtered: 11218)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.KrGrv0o5KQ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass.minFFPM.0.00001.pass star-fusion.fusion_predictions.tsv
* Running CMD: /usr/local/src/STAR-Fusion/util/column_exclusions.pl star-fusion.fusion_predictions.tsv JunctionReads,SpanningFrags > star-fusion.fusion_predictions.abridged.tsv
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/util/fusion_to_coding_region_effect.pl  --fusions star-fusion.fusion_predictions.abridged.tsv --genome_lib_dir /tmp/nxf.KrGrv0o5KQ/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [IGH-.g@-ext]
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WARNING, no entry stored in dbm for [IGH-.g@-ext]
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WARNING, no entry stored in dbm for [IGH-.g@-ext]
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WARNING, no entry stored in dbm for [IGH-.g@-ext]
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WARNING, no entry stored in dbm for [ENSG00000234722.5]
WARNING, no entry stored in dbm for [ENSG00000184106.8]
WARNING, no entry stored in dbm for [ENSG00000228271.2]
WARNING, no entry stored in dbm for [ENSG00000236546.1]
WARNING, no entry stored in dbm for [ENSG00000259375.1]
WARNING, no entry stored in dbm for [ENSG00000237604.1]
WARNING, no entry stored in dbm for [ENSG00000273149.1]
WARNING, no entry stored in dbm for [ENSG00000228340.6]
WARNING, no entry stored in dbm for [ENSG00000228340.6]
WARNING, no entry stored in dbm for [ENSG00000267532.5]
WARNING, no entry stored in dbm for [ENSG00000201315.1]
WARNING, no entry stored in dbm for [ENSG00000267519.6]
WARNING, no entry stored in dbm for [ENSG00000279393.1]
WARNING, no entry stored in dbm for [ENSG00000287332.1]
WARNING, no entry stored in dbm for [ENSG00000261556.10]
WARNING, no entry stored in dbm for [ENSG00000234199.3]
WARNING, no entry stored in dbm for [ENSG00000189238.6]
WARNING, no entry stored in dbm for [ENSG00000238045.9]
WARNING, no entry stored in dbm for [ENSG00000236318.2]
WARNING, no entry stored in dbm for [ENSG00000284237.1]
WARNING, no entry stored in dbm for [ENSG00000258884.2]
WARNING, no entry stored in dbm for [ENSG00000244215.2]
WARNING, no entry stored in dbm for [ENSG00000225548.7]
WARNING, no entry stored in dbm for [ENSG00000226476.6]
WARNING, no entry stored in dbm for [ENSG00000225518.3]
WARNING, no entry stored in dbm for [ENSG00000279579.3]
WARNING, no entry stored in dbm for [ENSG00000279579.3]
WARNING, no entry stored in dbm for [ENSG00000228262.10]
WARNING, no entry stored in dbm for [ENSG00000242512.9]
WARNING, no entry stored in dbm for [ENSG00000228794.10]
WARNING, no entry stored in dbm for [ENSG00000224582.7]
WARNING, no entry stored in dbm for [ENSG00000228393.4]
WARNING, no entry stored in dbm for [ENSG00000225269.3]
WARNING, no entry stored in dbm for [ENSG00000225269.3]
WARNING, no entry stored in dbm for [ENSG00000232677.9]
WARNING, no entry stored in dbm for [ENSG00000225179.2]
WARNING, no entry stored in dbm for [ENSG00000236790.6]
WARNING, no entry stored in dbm for [ENSG00000231535.7]
WARNING, no entry stored in dbm for [ENSG00000227354.7]
WARNING, no entry stored in dbm for [ENSG00000240770.5]
WARNING, no entry stored in dbm for [ENSG00000228791.8]
WARNING, no entry stored in dbm for [ENSG00000237978.6]
WARNING, no entry stored in dbm for [ENSG00000256663.1]
WARNING, no entry stored in dbm for [ENSG00000229656.7]
WARNING, no entry stored in dbm for [ENSG00000280409.1]
WARNING, no entry stored in dbm for [ENSG00000276988.1]
WARNING, no entry stored in dbm for [ENSG00000246662.6]
WARNING, no entry stored in dbm for [ENSG00000279965.1]
WARNING, no entry stored in dbm for [ENSG00000224609.8]
WARNING, no entry stored in dbm for [ENSG00000259905.7]
WARNING, no entry stored in dbm for [ENSG00000259905.7]
WARNING, no entry stored in dbm for [ENSG00000259905.7]
WARNING, no entry stored in dbm for [ENSG00000286263.1]
WARNING, no entry stored in dbm for [ENSG00000215492.6]
WARNING, no entry stored in dbm for [ENSG00000226188.2]
WARNING, no entry stored in dbm for [ENSG00000253774.1]
WARNING, no entry stored in dbm for [ENSG00000222037.5]
WARNING, no entry stored in dbm for [ENSG00000258667.2]
WARNING, no entry stored in dbm for [ENSG00000259845.1]
WARNING, no entry stored in dbm for [ENSG00000281344.1]
WARNING, no entry stored in dbm for [ENSG00000278041.1]
WARNING, no entry stored in dbm for [ENSG00000205885.7]
WARNING, no entry stored in dbm for [ENSG00000257287.1]
WARNING, no entry stored in dbm for [ENSG00000178458.5]
WARNING, no entry stored in dbm for [ENSG00000230111.1]
WARNING, no entry stored in dbm for [ENSG00000225083.2]
WARNING, no entry stored in dbm for [ENSG00000247498.10]
WARNING, no entry stored in dbm for [ENSG00000215386.13]
WARNING, no entry stored in dbm for [ENSG00000241621.1]
WARNING, no entry stored in dbm for [ENSG00000239533.6]
WARNING, no entry stored in dbm for [ENSG00000235590.7]
WARNING, no entry stored in dbm for [ENSG00000283041.1]
WARNING, no entry stored in dbm for [ENSG00000231523.1]
WARNING, no entry stored in dbm for [ENSG00000234741.8]
WARNING, no entry stored in dbm for [ENSG00000196295.12]
WARNING, no entry stored in dbm for [ENSG00000249839.1]
WARNING, no entry stored in dbm for [ENSG00000227128.5]
WARNING, no entry stored in dbm for [ENSG00000262408.1]
WARNING, no entry stored in dbm for [ENSG00000228055.3]
WARNING, no entry stored in dbm for [ENSG00000267254.7]
WARNING, no entry stored in dbm for [ENSG00000226571.2]
WARNING, no entry stored in dbm for [ENSG00000234709.2]
WARNING, no entry stored in dbm for [ENSG00000258527.1]
WARNING, no entry stored in dbm for [ENSG00000201744.1]
WARNING, no entry stored in dbm for [ENSG00000223814.1]
WARNING, no entry stored in dbm for [ENSG00000228251.1]
WARNING, no entry stored in dbm for [ENSG00000234152.1]
WARNING, no entry stored in dbm for [ENSG00000275154.1]
WARNING, no entry stored in dbm for [ENSG00000233912.1]
WARNING, no entry stored in dbm for [ENSG00000186704.9]
WARNING, no entry stored in dbm for [ENSG00000256381.1]
WARNING, no entry stored in dbm for [ENSG00000271162.1]
WARNING, no entry stored in dbm for [ENSG00000235244.4]
WARNING, no entry stored in dbm for [ENSG00000232034.1]
WARNING, no entry stored in dbm for [ENSG00000230936.1]
WARNING, no entry stored in dbm for [ENSG00000230630.5]
WARNING, no entry stored in dbm for [ENSG00000227195.11]
WARNING, no entry stored in dbm for [ENSG00000260139.6]
WARNING, no entry stored in dbm for [ENSG00000100058.12]
WARNING, no entry stored in dbm for [ENSG00000100058.12]
WARNING, no entry stored in dbm for [ENSG00000245694.10]
WARNING, no entry stored in dbm for [ENSG00000245768.7]
WARNING, no entry stored in dbm for [ENSG00000225172.6]
WARNING, no entry stored in dbm for [ENSG00000248307.6]
WARNING, no entry stored in dbm for [ENSG00000205890.3]
WARNING, no entry stored in dbm for [ENSG00000203930.12]
WARNING, no entry stored in dbm for [ENSG00000259755.1]
WARNING, no entry stored in dbm for [ENSG00000226688.7]
WARNING, no entry stored in dbm for [ENSG00000244306.11]
WARNING, no entry stored in dbm for [ENSG00000225401.2]
WARNING, no entry stored in dbm for [ENSG00000242593.7]
WARNING, no entry stored in dbm for [ENSG00000251264.1]
WARNING, no entry stored in dbm for [ENSG00000287845.1]
WARNING, no entry stored in dbm for [ENSG00000196796.5]
WARNING, no entry stored in dbm for [ENSG00000272168.8]
WARNING, no entry stored in dbm for [ENSG00000256594.8]
WARNING, no entry stored in dbm for [ENSG00000280195.1]
WARNING, no entry stored in dbm for [ENSG00000233848.1]
WARNING, no entry stored in dbm for [ENSG00000255571.9]
WARNING, no entry stored in dbm for [ENSG00000186312.10]
WARNING, no entry stored in dbm for [ENSG00000200156.1]
WARNING, no entry stored in dbm for [ENSG00000199568.1]
WARNING, no entry stored in dbm for [ENSG00000242396.1]
WARNING, no entry stored in dbm for [ENSG00000285417.1]
WARNING, no entry stored in dbm for [ENSG00000285417.1]
WARNING, no entry stored in dbm for [ENSG00000215146.5]
WARNING, no entry stored in dbm for [ENSG00000204960.7]
WARNING, no entry stored in dbm for [ENSG00000282851.2]
WARNING, no entry stored in dbm for [ENSG00000279022.1]
WARNING, no entry stored in dbm for [ENSG00000233967.7]
WARNING, no entry stored in dbm for [ENSG00000254560.6]
WARNING, no entry stored in dbm for [ENSG00000214176.9]
WARNING, no entry stored in dbm for [ENSG00000226592.1]
WARNING, no entry stored in dbm for [ENSG00000251598.2]
WARNING, no entry stored in dbm for [ENSG00000251066.1]
WARNING, no entry stored in dbm for [ENSG00000242753.2]
WARNING, no entry stored in dbm for [ENSG00000256591.5]
WARNING, no entry stored in dbm for [ENSG00000255031.5]
WARNING, no entry stored in dbm for [ENSG00000247137.9]
WARNING, no entry stored in dbm for [ENSG00000287864.1]
WARNING, no entry stored in dbm for [ENSG00000242153.7]
WARNING, no entry stored in dbm for [ENSG00000235281.2]
WARNING, no entry stored in dbm for [ENSG00000236723.2]
WARNING, no entry stored in dbm for [ENSG00000218426.5]
WARNING, no entry stored in dbm for [ENSG00000237409.2]
WARNING, no entry stored in dbm for [ENSG00000217477.2]
WARNING, no entry stored in dbm for [ENSG00000213080.3]
WARNING, no entry stored in dbm for [ENSG00000278932.4]
WARNING, no entry stored in dbm for [ENSG00000231804.1]
WARNING, no entry stored in dbm for [ENSG00000243181.2]
WARNING, no entry stored in dbm for [ENSG00000260475.1]
WARNING, no entry stored in dbm for [ENSG00000285424.1]
WARNING, no entry stored in dbm for [ENSG00000279392.1]
WARNING, no entry stored in dbm for [ENSG00000258581.2]
WARNING, no entry stored in dbm for [ENSG00000220685.3]
WARNING, no entry stored in dbm for [ENSG00000286071.1]
WARNING, no entry stored in dbm for [ENSG00000233448.2]
WARNING, no entry stored in dbm for [ENSG00000216642.1]
WARNING, no entry stored in dbm for [ENSG00000258959.2]
WARNING, no entry stored in dbm for [ENSG00000231770.6]
WARNING, no entry stored in dbm for [ENSG00000183239.5]
WARNING, no entry stored in dbm for [ENSG00000243730.2]
WARNING, no entry stored in dbm for [ENSG00000286546.1]
WARNING, no entry stored in dbm for [ENSG00000240131.1]
WARNING, no entry stored in dbm for [ENSG00000224066.1]
WARNING, no entry stored in dbm for [ENSG00000250917.1]
WARNING, no entry stored in dbm for [ENSG00000267882.2]
WARNING, no entry stored in dbm for [ENSG00000276150.1]
WARNING, no entry stored in dbm for [ENSG00000226310.1]
WARNING, no entry stored in dbm for [ENSG00000285646.2]
WARNING, no entry stored in dbm for [ENSG00000230869.1]
WARNING, no entry stored in dbm for [ENSG00000272140.2]
WARNING, no entry stored in dbm for [ENSG00000225330.1]
WARNING, no entry stored in dbm for [ENSG00000273382.1]
WARNING, no entry stored in dbm for [ENSG00000234996.4]
WARNING, no entry stored in dbm for [ENSG00000214223.4]
WARNING, no entry stored in dbm for [ENSG00000276216.1]
WARNING, no entry stored in dbm for [ENSG00000262831.1]
WARNING, no entry stored in dbm for [ENSG00000233836.7]
WARNING, no entry stored in dbm for [ENSG00000215158.9]
WARNING, no entry stored in dbm for [ENSG00000278212.2]
WARNING, no entry stored in dbm for [ENSG00000278212.2]
WARNING, no entry stored in dbm for [ENSG00000260570.1]
WARNING, no entry stored in dbm for [ENSG00000240808.1]
WARNING, no entry stored in dbm for [ENSG00000231416.1]
WARNING, no entry stored in dbm for [ENSG00000259704.2]
WARNING, no entry stored in dbm for [ENSG00000268081.1]
WARNING, no entry stored in dbm for [ENSG00000279759.1]
WARNING, no entry stored in dbm for [ENSG00000287862.1]
WARNING, no entry stored in dbm for [ENSG00000248708.2]
WARNING, no entry stored in dbm for [ENSG00000235421.1]
WARNING, no entry stored in dbm for [ENSG00000278791.1]
WARNING, no entry stored in dbm for [ENSG00000251523.1]
WARNING, no entry stored in dbm for [ENSG00000286830.1]
WARNING, no entry stored in dbm for [ENSG00000269292.1]
WARNING, no entry stored in dbm for [ENSG00000239268.3]
WARNING, no entry stored in dbm for [ENSG00000276791.1]
WARNING, no entry stored in dbm for [ENSG00000271763.1]
WARNING, no entry stored in dbm for [ENSG00000267198.1]
WARNING, no entry stored in dbm for [ENSG00000259655.1]
WARNING, no entry stored in dbm for [ENSG00000265750.1]
WARNING, no entry stored in dbm for [ENSG00000272076.1]
WARNING, no entry stored in dbm for [ENSG00000280828.1]
WARNING, no entry stored in dbm for [ENSG00000261879.7]
WARNING, no entry stored in dbm for [ENSG00000261628.1]
WARNING, no entry stored in dbm for [ENSG00000243181.2]
WARNING, no entry stored in dbm for [ENSG00000213985.4]
WARNING, no entry stored in dbm for [ENSG00000223812.8]
WARNING, no entry stored in dbm for [ENSG00000239985.2]
WARNING, no entry stored in dbm for [ENSG00000287388.1]
WARNING, no entry stored in dbm for [ENSG00000260035.1]
WARNING, no entry stored in dbm for [ENSG00000259932.1]
WARNING, no entry stored in dbm for [ENSG00000253897.2]
WARNING, no entry stored in dbm for [ENSG00000260413.1]
WARNING, no entry stored in dbm for [ENSG00000254444.1]
WARNING, no entry stored in dbm for [ENSG00000272140.2]
WARNING, no entry stored in dbm for [ENSG00000186019.11]
WARNING, no entry stored in dbm for [ENSG00000271049.1]
WARNING, no entry stored in dbm for [ENSG00000279569.1]
WARNING, no entry stored in dbm for [ENSG00000221849.2]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000268573.1]
WARNING, no entry stored in dbm for [ENSG00000241281.1]
WARNING, no entry stored in dbm for [ENSG00000269839.1]
WARNING, no entry stored in dbm for [ENSG00000213976.4]
WARNING, no entry stored in dbm for [ENSG00000270277.1]
WARNING, no entry stored in dbm for [ENSG00000254027.1]
WARNING, no entry stored in dbm for [ENSG00000267327.2]
WARNING, no entry stored in dbm for [ENSG00000267057.6]
WARNING, no entry stored in dbm for [ENSG00000260228.6]
WARNING, no entry stored in dbm for [ENSG00000284649.1]
WARNING, no entry stored in dbm for [ENSG00000260447.1]
WARNING, no entry stored in dbm for [ENSG00000214331.8]
WARNING, no entry stored in dbm for [ENSG00000287739.1]
WARNING, no entry stored in dbm for [ENSG00000257403.2]
WARNING, no entry stored in dbm for [ENSG00000189149.12]
WARNING, no entry stored in dbm for [ENSG00000267273.1]
WARNING, no entry stored in dbm for [ENSG00000226472.8]
WARNING, no entry stored in dbm for [ENSG00000262202.4]
WARNING, no entry stored in dbm for [ENSG00000262202.4]
WARNING, no entry stored in dbm for [ENSG00000241352.3]
WARNING, no entry stored in dbm for [ENSG00000233143.2]
WARNING, no entry stored in dbm for [ENSG00000256682.2]
WARNING, no entry stored in dbm for [ENSG00000227545.1]
WARNING, no entry stored in dbm for [ENSG00000251412.1]
WARNING, no entry stored in dbm for [ENSG00000263235.1]
WARNING, no entry stored in dbm for [ENSG00000237251.2]
WARNING, no entry stored in dbm for [ENSG00000214243.3]
WARNING, no entry stored in dbm for [ENSG00000205485.13]
WARNING, no entry stored in dbm for [ENSG00000205485.13]
WARNING, no entry stored in dbm for [ENSG00000241057.2]
WARNING, no entry stored in dbm for [ENSG00000228434.1]
WARNING, no entry stored in dbm for [ENSG00000272854.1]
WARNING, no entry stored in dbm for [ENSG00000277283.1]
WARNING, no entry stored in dbm for [ENSG00000257433.6]
WARNING, no entry stored in dbm for [ENSG00000267698.1]
WARNING, no entry stored in dbm for [ENSG00000233420.2]
WARNING, no entry stored in dbm for [ENSG00000251595.7]


	* STAR-Fusion complete.  See output: /tmp/nxf.KrGrv0o5KQ/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)