.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (BT-20_FFPE_RNA_0001_B23LG7FLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/af227eca15d0ba3ae41d107c51f144/.command.log
Size: 69.7 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (BT-20_FFPE_RNA_0001_B23LG7FLT4_2)
Attempt
Content

  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/c0/af227eca15d0ba3ae41d107c51f144/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/eac656c045b42cd5f5b3825266dd5a/BT-20_FFPE_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/af227eca15d0ba3ae41d107c51f144/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/3e543b9fe691f4fe4913ef352c2dc8/BT-20_FFPE_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/eac656c045b42cd5f5b3825266dd5a/BT-20_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.8tOEROyOsF/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.8tOEROyOsF/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary
-sample contains 85474037 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.8tOEROyOsF/ctat_genome_lib_build_dir  -J /tmp/nxf.8tOEROyOsF/BT-20_FFPE_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction  -O /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.8tOEROyOsF/BT-20_FFPE_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction
-building interval tree based on /tmp/nxf.8tOEROyOsF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

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[2030000], rate=50061.65/min -building interval tree based on /tmp/nxf.8tOEROyOsF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

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[2040000], rate=48881.79/min -building interval tree based on /tmp/nxf.8tOEROyOsF/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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[2010000], rate=46224.61/min 
[2020000], rate=46136.28/min -building interval tree based on /tmp/nxf.8tOEROyOsF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=60000.00/min 
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[2000000], rate=43057.05/min 
[2010000], rate=43133.05/min 
[2020000], rate=43208.56/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.8tOEROyOsF/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.8tOEROyOsF/./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...  
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 10000000.00 reads per min processed...  
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 5647058.82 reads per min processed...  
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 5700000.00 reads per min processed...  
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 5023255.81 reads per min processed...  
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 5283582.09 reads per min processed...  
 5217391.30 reads per min processed...  
 5228571.43 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.8tOEROyOsF/BT-20_FFPE_RNA_0001_B23LG7FLT4_2.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.8tOEROyOsF/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -243062.690573
EM: Round [1] log likelihood: -242836.548027
EM: Round [2] log likelihood: -242741.934946
EM: Round [3] log likelihood: -242694.398587
EM: Round [4] log likelihood: -242668.440638
EM: Round [5] log likelihood: -242653.632445
EM: Round [6] log likelihood: -242644.879192
EM: Round [7] log likelihood: -242639.511234
EM: Round [8] log likelihood: -242636.092006
EM: Round [9] log likelihood: -242633.831790
EM: Round [10] log likelihood: -242632.285007
EM: Round [11] log likelihood: -242631.192585
EM: Round [12] log likelihood: -242630.399033
EM: Round [13] log likelihood: -242629.808034
EM: Round [14] log likelihood: -242629.358085
EM: Round [15] log likelihood: -242629.008776
EM: Round [16] log likelihood: -242628.732853
EM: Round [17] log likelihood: -242628.511489
EM: Round [18] log likelihood: -242628.331399
EM: Round [19] log likelihood: -242628.183024
EM: Round [20] log likelihood: -242628.059368
EM: Round [21] log likelihood: -242627.955230
EM: Round [22] log likelihood: -242627.866688
EM: Round [23] log likelihood: -242627.790749
EM: Round [24] log likelihood: -242627.725099
EM: Round [25] log likelihood: -242627.667932
EM: Round [26] log likelihood: -242627.617821
EM: Round [27] log likelihood: -242627.573630
EM: Round [28] log likelihood: -242627.534445
EM: Round [29] log likelihood: -242627.499525
EM: Round [30] log likelihood: -242627.468264
EM: Round [31] log likelihood: -242627.440163
EM: Round [32] log likelihood: -242627.414806
EM: Round [33] log likelihood: -242627.391848
EM: Round [34] log likelihood: -242627.370995
EM: Round [35] log likelihood: -242627.352001
EM: Round [36] log likelihood: -242627.334653
EM: Round [37] log likelihood: -242627.318772
EM: Round [38] log likelihood: -242627.304201
EM: Round [39] log likelihood: -242627.290805
EM: Round [40] log likelihood: -242627.278465
EM: Round [41] log likelihood: -242627.267079
EM: Round [42] log likelihood: -242627.256555
EM: Round [43] log likelihood: -242627.246814
EM: Round [44] log likelihood: -242627.237786
EM: Round [45] log likelihood: -242627.229405
EM: Round [46] log likelihood: -242627.221618
EM: Round [47] log likelihood: -242627.214372
EM: Round [48] log likelihood: -242627.207624
EM: Round [49] log likelihood: -242627.201332
EM: Round [50] log likelihood: -242627.195460
EM: Round [51] log likelihood: -242627.189974
EM: Round [52] log likelihood: -242627.184845
EM: Round [53] log likelihood: -242627.180046
EM: Round [54] log likelihood: -242627.175551
EM: Round [55] log likelihood: -242627.171338
EM: Round [56] log likelihood: -242627.167387
EM: Round [57] log likelihood: -242627.163678
EM: Round [58] log likelihood: -242627.160195
EM: Round [59] log likelihood: -242627.156921
EM: Round [60] log likelihood: -242627.153842
EM: Round [61] log likelihood: -242627.150944
EM: Round [62] log likelihood: -242627.148216
EM: Round [63] log likelihood: -242627.145646
EM: Round [64] log likelihood: -242627.143223
EM: Round [65] log likelihood: -242627.140939
EM: Round [66] log likelihood: -242627.138783
EM: Round [67] log likelihood: -242627.136747
EM: Round [68] log likelihood: -242627.134825
EM: Round [69] log likelihood: -242627.133008
EM: Round [70] log likelihood: -242627.131291
EM: Round [71] log likelihood: -242627.129666
EM: Round [72] log likelihood: -242627.128129
EM: Round [73] log likelihood: -242627.126674
EM: Round [74] log likelihood: -242627.125297
EM: Round [75] log likelihood: -242627.123992
EM: Round [76] log likelihood: -242627.122755
EM: Round [77] log likelihood: -242627.121582
EM: Round [78] log likelihood: -242627.120470
EM: Round [79] log likelihood: -242627.119416
EM: Round [80] log likelihood: -242627.118414
EM: Round [81] log likelihood: -242627.117464
EM: Round [82] log likelihood: -242627.116561
EM: Round [83] log likelihood: -242627.115704
EM: Round [84] log likelihood: -242627.114889
EM: Round [85] log likelihood: -242627.114115
EM: Round [86] log likelihood: -242627.113379
EM: Round [87] log likelihood: -242627.112678
EM: Round [88] log likelihood: -242627.112012
EM: Round [89] log likelihood: -242627.111378
EM: Round [90] log likelihood: -242627.110775
EM: Round [91] log likelihood: -242627.110200
EM: Round [92] log likelihood: -242627.109653
EM: Round [93] log likelihood: -242627.109132
EM: Round [94] log likelihood: -242627.108635
EM: Round [95] log likelihood: -242627.108162
EM: Round [96] log likelihood: -242627.107711
EM: Round [97] log likelihood: -242627.107281
EM: Round [98] log likelihood: -242627.106870
EM: Round [99] log likelihood: -242627.106479
EM: Round [100] log likelihood: -242627.106105
EM: Round [101] log likelihood: -242627.105749
EM: Round [102] log likelihood: -242627.105409
EM: Round [103] log likelihood: -242627.105084
EM: Round [104] log likelihood: -242627.104774
EM: Round [105] log likelihood: -242627.104477
EM: Round [106] log likelihood: -242627.104194
EM: Round [107] log likelihood: -242627.103923
EM: Round [108] log likelihood: -242627.103665
EM: Round [109] log likelihood: -242627.103417
EM: Round [110] log likelihood: -242627.103181
EM: Round [111] log likelihood: -242627.102955
EM: Round [112] log likelihood: -242627.102738
EM: Round [113] log likelihood: -242627.102531
EM: Round [114] log likelihood: -242627.102333
EM: Round [115] log likelihood: -242627.102144
EM: Round [116] log likelihood: -242627.101962
EM: Round [117] log likelihood: -242627.101788
EM: Round [118] log likelihood: -242627.101622
EM: Round [119] log likelihood: -242627.101462
EM: Round [120] log likelihood: -242627.101310
EM: Round [121] log likelihood: -242627.101163
EM: Round [122] log likelihood: -242627.101023
EM: Round [123] log likelihood: -242627.100888
EM: Round [124] log likelihood: -242627.100759
EM: Round [125] log likelihood: -242627.100636
EM: Round [126] log likelihood: -242627.100517
EM: Round [127] log likelihood: -242627.100403
EM: Round [128] log likelihood: -242627.100294
EM: Round [129] log likelihood: -242627.100189
EM: Round [130] log likelihood: -242627.100089
EM: Round [131] log likelihood: -242627.099992
EM: Stopping iterations at round 131 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -242756.924186
EM: Round [1] log likelihood: -242565.017064
EM: Round [2] log likelihood: -242488.314562
EM: Round [3] log likelihood: -242451.129325
EM: Round [4] log likelihood: -242431.389552
EM: Round [5] log likelihood: -242420.396874
EM: Round [6] log likelihood: -242414.042926
EM: Round [7] log likelihood: -242410.230209
EM: Round [8] log likelihood: -242407.852462
EM: Round [9] log likelihood: -242406.311772
EM: Round [10] log likelihood: -242405.276174
EM: Round [11] log likelihood: -242404.555827
EM: Round [12] log likelihood: -242404.038781
EM: Round [13] log likelihood: -242403.656964
EM: Round [14] log likelihood: -242403.367730
EM: Round [15] log likelihood: -242403.143592
EM: Round [16] log likelihood: -242402.966348
EM: Round [17] log likelihood: -242402.823643
EM: Round [18] log likelihood: -242402.706893
EM: Round [19] log likelihood: -242402.610007
EM: Round [20] log likelihood: -242402.528578
EM: Round [21] log likelihood: -242402.459363
EM: Round [22] log likelihood: -242402.399934
EM: Round [23] log likelihood: -242402.348446
EM: Round [24] log likelihood: -242402.303481
EM: Round [25] log likelihood: -242402.263929
EM: Round [26] log likelihood: -242402.228915
EM: Round [27] log likelihood: -242402.197743
EM: Round [28] log likelihood: -242402.169847
EM: Round [29] log likelihood: -242402.144768
EM: Round [30] log likelihood: -242402.122128
EM: Round [31] log likelihood: -242402.101614
EM: Round [32] log likelihood: -242402.082963
EM: Round [33] log likelihood: -242402.065955
EM: Round [34] log likelihood: -242402.050401
EM: Round [35] log likelihood: -242402.036141
EM: Round [36] log likelihood: -242402.023037
EM: Round [37] log likelihood: -242402.010969
EM: Round [38] log likelihood: -242401.999835
EM: Round [39] log likelihood: -242401.989542
EM: Round [40] log likelihood: -242401.980012
EM: Round [41] log likelihood: -242401.971175
EM: Round [42] log likelihood: -242401.962967
EM: Round [43] log likelihood: -242401.955335
EM: Round [44] log likelihood: -242401.948228
EM: Round [45] log likelihood: -242401.941602
EM: Round [46] log likelihood: -242401.935419
EM: Round [47] log likelihood: -242401.929643
EM: Round [48] log likelihood: -242401.924241
EM: Round [49] log likelihood: -242401.919184
EM: Round [50] log likelihood: -242401.914447
EM: Round [51] log likelihood: -242401.910005
EM: Round [52] log likelihood: -242401.905836
EM: Round [53] log likelihood: -242401.901921
EM: Round [54] log likelihood: -242401.898242
EM: Round [55] log likelihood: -242401.894782
EM: Round [56] log likelihood: -242401.891526
EM: Round [57] log likelihood: -242401.888461
EM: Round [58] log likelihood: -242401.885572
EM: Round [59] log likelihood: -242401.882848
EM: Round [60] log likelihood: -242401.880279
EM: Round [61] log likelihood: -242401.877855
EM: Round [62] log likelihood: -242401.875565
EM: Round [63] log likelihood: -242401.873403
EM: Round [64] log likelihood: -242401.871359
EM: Round [65] log likelihood: -242401.869426
EM: Round [66] log likelihood: -242401.867597
EM: Round [67] log likelihood: -242401.865867
EM: Round [68] log likelihood: -242401.864229
EM: Round [69] log likelihood: -242401.862678
EM: Round [70] log likelihood: -242401.861208
EM: Round [71] log likelihood: -242401.859815
EM: Round [72] log likelihood: -242401.858494
EM: Round [73] log likelihood: -242401.857241
EM: Round [74] log likelihood: -242401.856053
EM: Round [75] log likelihood: -242401.854925
EM: Round [76] log likelihood: -242401.853854
EM: Round [77] log likelihood: -242401.852837
EM: Round [78] log likelihood: -242401.851872
EM: Round [79] log likelihood: -242401.850954
EM: Round [80] log likelihood: -242401.850082
EM: Round [81] log likelihood: -242401.849254
EM: Round [82] log likelihood: -242401.848465
EM: Round [83] log likelihood: -242401.847716
EM: Round [84] log likelihood: -242401.847003
EM: Round [85] log likelihood: -242401.846325
EM: Round [86] log likelihood: -242401.845679
EM: Round [87] log likelihood: -242401.845065
EM: Round [88] log likelihood: -242401.844480
EM: Round [89] log likelihood: -242401.843923
EM: Round [90] log likelihood: -242401.843392
EM: Round [91] log likelihood: -242401.842886
EM: Round [92] log likelihood: -242401.842405
EM: Round [93] log likelihood: -242401.841946
EM: Round [94] log likelihood: -242401.841508
EM: Round [95] log likelihood: -242401.841091
EM: Round [96] log likelihood: -242401.840693
EM: Round [97] log likelihood: -242401.840314
EM: Round [98] log likelihood: -242401.839952
EM: Round [99] log likelihood: -242401.839607
EM: Round [100] log likelihood: -242401.839277
EM: Round [101] log likelihood: -242401.838963
EM: Round [102] log likelihood: -242401.838663
EM: Round [103] log likelihood: -242401.838377
EM: Round [104] log likelihood: -242401.838103
EM: Round [105] log likelihood: -242401.837842
EM: Round [106] log likelihood: -242401.837593
EM: Round [107] log likelihood: -242401.837354
EM: Round [108] log likelihood: -242401.837127
EM: Round [109] log likelihood: -242401.836909
EM: Round [110] log likelihood: -242401.836701
EM: Round [111] log likelihood: -242401.836503
EM: Round [112] log likelihood: -242401.836313
EM: Round [113] log likelihood: -242401.836131
EM: Round [114] log likelihood: -242401.835957
EM: Round [115] log likelihood: -242401.835791
EM: Round [116] log likelihood: -242401.835633
EM: Round [117] log likelihood: -242401.835481
EM: Round [118] log likelihood: -242401.835335
EM: Round [119] log likelihood: -242401.835196
EM: Round [120] log likelihood: -242401.835063
EM: Round [121] log likelihood: -242401.834935
EM: Round [122] log likelihood: -242401.834813
EM: Round [123] log likelihood: -242401.834697
EM: Round [124] log likelihood: -242401.834585
EM: Round [125] log likelihood: -242401.834478
EM: Round [126] log likelihood: -242401.834375
EM: Round [127] log likelihood: -242401.834277
EM: Stopping iterations at round 127 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.8tOEROyOsF/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.8tOEROyOsF/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.8tOEROyOsF/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.8tOEROyOsF/./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.8tOEROyOsF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.8tOEROyOsF/./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.8tOEROyOsF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 85474037 > /tmp/nxf.8tOEROyOsF/./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.8tOEROyOsF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.8tOEROyOsF/ctat_genome_lib_build_dir > /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.8tOEROyOsF/ctat_genome_lib_build_dir --annotate /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.8tOEROyOsF/./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.8tOEROyOsF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.8tOEROyOsF/ctat_genome_lib_build_dir
-done, see /tmp/nxf.8tOEROyOsF/./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.8tOEROyOsF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.8tOEROyOsF/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 1021, filtered: 10130)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.8tOEROyOsF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.8tOEROyOsF/./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.8tOEROyOsF/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 [ENSG00000234801.3]
WARNING, no entry stored in dbm for [ENSG00000180438.15]
WARNING, no entry stored in dbm for [ENSG00000225769.1]
WARNING, no entry stored in dbm for [ENSG00000248926.1]
WARNING, no entry stored in dbm for [ENSG00000179066.8]
WARNING, no entry stored in dbm for [ENSG00000228824.7]
WARNING, no entry stored in dbm for [ENSG00000221697.1]
WARNING, no entry stored in dbm for [ENSG00000234474.3]
WARNING, no entry stored in dbm for [ENSG00000226416.1]
WARNING, no entry stored in dbm for [ENSG00000279940.1]
WARNING, no entry stored in dbm for [ENSG00000252594.1]
WARNING, no entry stored in dbm for [ENSG00000207083.1]
WARNING, no entry stored in dbm for [ENSG00000207257.1]
WARNING, no entry stored in dbm for [ENSG00000206972.1]
WARNING, no entry stored in dbm for [ENSG00000261123.1]
WARNING, no entry stored in dbm for [ENSG00000213862.4]
WARNING, no entry stored in dbm for [ENSG00000248323.7]
WARNING, no entry stored in dbm for [ENSG00000272381.2]
WARNING, no entry stored in dbm for [ENSG00000258175.1]
WARNING, no entry stored in dbm for [ENSG00000281903.2]
WARNING, no entry stored in dbm for [ENSG00000204650.14]
WARNING, no entry stored in dbm for [ENSG00000232190.3]
WARNING, no entry stored in dbm for [ENSG00000265555.1]
WARNING, no entry stored in dbm for [ENSG00000255171.7]
WARNING, no entry stored in dbm for [ENSG00000281404.2]
WARNING, no entry stored in dbm for [ENSG00000228794.10]
WARNING, no entry stored in dbm for [ENSG00000226091.7]
WARNING, no entry stored in dbm for [ENSG00000254817.1]
WARNING, no entry stored in dbm for [ENSG00000251209.9]
WARNING, no entry stored in dbm for [ENSG00000196205.8]
WARNING, no entry stored in dbm for [ENSG00000232677.9]
WARNING, no entry stored in dbm for [ENSG00000263065.1]
WARNING, no entry stored in dbm for [ENSG00000226317.3]
WARNING, no entry stored in dbm for [ENSG00000254811.5]
WARNING, no entry stored in dbm for [ENSG00000230630.5]
WARNING, no entry stored in dbm for [ENSG00000232021.7]
WARNING, no entry stored in dbm for [ENSG00000262294.1]
WARNING, no entry stored in dbm for [ENSG00000250778.1]
WARNING, no entry stored in dbm for [ENSG00000283103.3]
WARNING, no entry stored in dbm for [ENSG00000250686.2]
WARNING, no entry stored in dbm for [ENSG00000229127.2]
WARNING, no entry stored in dbm for [ENSG00000225783.8]
WARNING, no entry stored in dbm for [ENSG00000259673.6]
WARNING, no entry stored in dbm for [ENSG00000244627.5]
WARNING, no entry stored in dbm for [ENSG00000258352.1]
WARNING, no entry stored in dbm for [ENSG00000203914.4]
WARNING, no entry stored in dbm for [ENSG00000243014.1]
WARNING, no entry stored in dbm for [ENSG00000240477.1]
WARNING, no entry stored in dbm for [ENSG00000233714.1]
WARNING, no entry stored in dbm for [ENSG00000181126.13]
WARNING, no entry stored in dbm for [ENSG00000225851.1]
WARNING, no entry stored in dbm for [ENSG00000273077.1]
WARNING, no entry stored in dbm for [ENSG00000100181.22]
WARNING, no entry stored in dbm for [ENSG00000206149.10]
WARNING, no entry stored in dbm for [ENSG00000274471.2]
WARNING, no entry stored in dbm for [ENSG00000280927.1]
WARNING, no entry stored in dbm for [ENSG00000206337.12]
WARNING, no entry stored in dbm for [ENSG00000261716.2]
WARNING, no entry stored in dbm for [ENSG00000220323.4]
WARNING, no entry stored in dbm for [ENSG00000181201.3]
WARNING, no entry stored in dbm for [ENSG00000183666.17]
WARNING, no entry stored in dbm for [ENSG00000286695.1]
WARNING, no entry stored in dbm for [ENSG00000228564.2]
WARNING, no entry stored in dbm for [ENSG00000261659.2]
WARNING, no entry stored in dbm for [ENSG00000241621.1]
WARNING, no entry stored in dbm for [ENSG00000269332.5]
WARNING, no entry stored in dbm for [ENSG00000238105.7]
WARNING, no entry stored in dbm for [ENSG00000250903.9]
WARNING, no entry stored in dbm for [ENSG00000250903.9]
WARNING, no entry stored in dbm for [ENSG00000231367.6]
WARNING, no entry stored in dbm for [ENSG00000270538.1]
WARNING, no entry stored in dbm for [ENSG00000213338.3]
WARNING, no entry stored in dbm for [ENSG00000213935.3]
WARNING, no entry stored in dbm for [ENSG00000088340.17]
WARNING, no entry stored in dbm for [ENSG00000260536.1]
WARNING, no entry stored in dbm for [ENSG00000224032.7]
WARNING, no entry stored in dbm for [ENSG00000100068.14]
WARNING, no entry stored in dbm for [ENSG00000227906.8]
WARNING, no entry stored in dbm for [ENSG00000261557.1]
WARNING, no entry stored in dbm for [ENSG00000215160.3]
WARNING, no entry stored in dbm for [ENSG00000261795.1]
WARNING, no entry stored in dbm for [ENSG00000270938.1]
WARNING, no entry stored in dbm for [ENSG00000254291.1]
WARNING, no entry stored in dbm for [ENSG00000240216.7]
WARNING, no entry stored in dbm for [ENSG00000286724.1]
WARNING, no entry stored in dbm for [ENSG00000257279.1]
WARNING, no entry stored in dbm for [ENSG00000225005.1]
WARNING, no entry stored in dbm for [ENSG00000279182.1]
WARNING, no entry stored in dbm for [ENSG00000224918.1]
WARNING, no entry stored in dbm for [ENSG00000243389.1]
WARNING, no entry stored in dbm for [ENSG00000226312.7]
WARNING, no entry stored in dbm for [ENSG00000261103.3]
WARNING, no entry stored in dbm for [ENSG00000251264.1]
WARNING, no entry stored in dbm for [ENSG00000248709.3]
WARNING, no entry stored in dbm for [ENSG00000215039.7]
WARNING, no entry stored in dbm for [ENSG00000249392.1]
WARNING, no entry stored in dbm for [ENSG00000247556.6]
WARNING, no entry stored in dbm for [ENSG00000189348.6]
WARNING, no entry stored in dbm for [ENSG00000269486.2]
WARNING, no entry stored in dbm for [ENSG00000234312.1]
WARNING, no entry stored in dbm for [ENSG00000287352.1]
WARNING, no entry stored in dbm for [ENSG00000177335.11]
WARNING, no entry stored in dbm for [ENSG00000205885.7]
WARNING, no entry stored in dbm for [ENSG00000226445.2]
WARNING, no entry stored in dbm for [ENSG00000226445.2]
WARNING, no entry stored in dbm for [ENSG00000256075.1]
WARNING, no entry stored in dbm for [ENSG00000259165.1]
WARNING, no entry stored in dbm for [ENSG00000255248.9]
WARNING, no entry stored in dbm for [ENSG00000228748.2]
WARNING, no entry stored in dbm for [ENSG00000286563.1]
WARNING, no entry stored in dbm for [ENSG00000286128.1]
WARNING, no entry stored in dbm for [ENSG00000287315.1]
WARNING, no entry stored in dbm for [ENSG00000264080.1]
WARNING, no entry stored in dbm for [ENSG00000235023.1]
WARNING, no entry stored in dbm for [ENSG00000239861.1]
WARNING, no entry stored in dbm for [ENSG00000240898.1]
WARNING, no entry stored in dbm for [ENSG00000233536.2]
WARNING, no entry stored in dbm for [ENSG00000254758.1]
WARNING, no entry stored in dbm for [ENSG00000224790.3]
WARNING, no entry stored in dbm for [ENSG00000284128.1]
WARNING, no entry stored in dbm for [ENSG00000286643.1]
WARNING, no entry stored in dbm for [ENSG00000224660.2]
WARNING, no entry stored in dbm for [ENSG00000288694.1]
WARNING, no entry stored in dbm for [ENSG00000237251.2]
WARNING, no entry stored in dbm for [ENSG00000262585.1]
WARNING, no entry stored in dbm for [ENSG00000242894.3]
WARNING, no entry stored in dbm for [ENSG00000237550.5]
WARNING, no entry stored in dbm for [ENSG00000232573.1]
WARNING, no entry stored in dbm for [ENSG00000287338.1]
WARNING, no entry stored in dbm for [ENSG00000284740.1]
WARNING, no entry stored in dbm for [ENSG00000235226.1]
WARNING, no entry stored in dbm for [ENSG00000234488.1]
WARNING, no entry stored in dbm for [ENSG00000284618.1]
WARNING, no entry stored in dbm for [ENSG00000285280.2]
WARNING, no entry stored in dbm for [ENSG00000286215.1]
WARNING, no entry stored in dbm for [ENSG00000259162.1]
WARNING, no entry stored in dbm for [ENSG00000231616.9]
WARNING, no entry stored in dbm for [ENSG00000278390.5]
WARNING, no entry stored in dbm for [ENSG00000287410.1]
WARNING, no entry stored in dbm for [ENSG00000233178.7]
WARNING, no entry stored in dbm for [ENSG00000272078.1]
WARNING, no entry stored in dbm for [ENSG00000238098.9]
WARNING, no entry stored in dbm for [ENSG00000273783.1]
WARNING, no entry stored in dbm for [ENSG00000280355.1]
WARNING, no entry stored in dbm for [ENSG00000246308.2]
WARNING, no entry stored in dbm for [ENSG00000236673.5]
WARNING, no entry stored in dbm for [ENSG00000234282.1]
WARNING, no entry stored in dbm for [ENSG00000271857.1]
WARNING, no entry stored in dbm for [ENSG00000270792.6]
WARNING, no entry stored in dbm for [ENSG00000233558.1]
WARNING, no entry stored in dbm for [ENSG00000280011.1]
WARNING, no entry stored in dbm for [ENSG00000226310.1]
WARNING, no entry stored in dbm for [ENSG00000230912.1]
WARNING, no entry stored in dbm for [ENSG00000288540.1]
WARNING, no entry stored in dbm for [ENSG00000213107.2]
WARNING, no entry stored in dbm for [ENSG00000233406.5]
WARNING, no entry stored in dbm for [ENSG00000258730.1]
WARNING, no entry stored in dbm for [ENSG00000224016.2]
WARNING, no entry stored in dbm for [ENSG00000180139.11]
WARNING, no entry stored in dbm for [ENSG00000180139.11]
WARNING, no entry stored in dbm for [ENSG00000254452.1]
WARNING, no entry stored in dbm for [ENSG00000236936.1]
WARNING, no entry stored in dbm for [ENSG00000287970.1]
WARNING, no entry stored in dbm for [ENSG00000285062.1]
WARNING, no entry stored in dbm for [ENSG00000275140.1]
WARNING, no entry stored in dbm for [ENSG00000279047.4]
WARNING, no entry stored in dbm for [ENSG00000286118.1]
WARNING, no entry stored in dbm for [ENSG00000261499.2]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000254701.3]
WARNING, no entry stored in dbm for [ENSG00000230590.11]
WARNING, no entry stored in dbm for [ENSG00000260017.1]
WARNING, no entry stored in dbm for [ENSG00000215158.9]
WARNING, no entry stored in dbm for [ENSG00000266865.6]
WARNING, no entry stored in dbm for [ENSG00000271158.1]
WARNING, no entry stored in dbm for [ENSG00000224888.4]
WARNING, no entry stored in dbm for [ENSG00000226268.3]
WARNING, no entry stored in dbm for [ENSG00000198555.7]
WARNING, no entry stored in dbm for [ENSG00000257253.2]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000280828.1]
WARNING, no entry stored in dbm for [ENSG00000287552.1]
WARNING, no entry stored in dbm for [ENSG00000213486.3]
WARNING, no entry stored in dbm for [ENSG00000224987.1]
WARNING, no entry stored in dbm for [ENSG00000228141.7]
WARNING, no entry stored in dbm for [ENSG00000213222.3]
WARNING, no entry stored in dbm for [ENSG00000251314.2]
WARNING, no entry stored in dbm for [ENSG00000279333.1]
WARNING, no entry stored in dbm for [ENSG00000251378.1]
WARNING, no entry stored in dbm for [ENSG00000288031.1]
WARNING, no entry stored in dbm for [ENSG00000224016.2]
WARNING, no entry stored in dbm for [ENSG00000286912.1]
WARNING, no entry stored in dbm for [ENSG00000261118.1]
WARNING, no entry stored in dbm for [ENSG00000278734.1]
WARNING, no entry stored in dbm for [ENSG00000239969.5]
WARNING, no entry stored in dbm for [ENSG00000267198.1]
WARNING, no entry stored in dbm for [ENSG00000131484.4]
WARNING, no entry stored in dbm for [ENSG00000280118.3]
WARNING, no entry stored in dbm for [ENSG00000258320.1]
WARNING, no entry stored in dbm for [ENSG00000264151.6]
WARNING, no entry stored in dbm for [ENSG00000264151.6]
WARNING, no entry stored in dbm for [ENSG00000240877.3]
WARNING, no entry stored in dbm for [ENSG00000287005.1]
WARNING, no entry stored in dbm for [ENSG00000261879.7]
WARNING, no entry stored in dbm for [ENSG00000285573.1]
WARNING, no entry stored in dbm for [ENSG00000278346.1]
WARNING, no entry stored in dbm for [ENSG00000196205.8]
WARNING, no entry stored in dbm for [ENSG00000266208.1]
WARNING, no entry stored in dbm for [ENSG00000249685.1]
WARNING, no entry stored in dbm for [ENSG00000268955.2]
WARNING, no entry stored in dbm for [ENSG00000267787.7]
WARNING, no entry stored in dbm for [ENSG00000254485.5]
WARNING, no entry stored in dbm for [ENSG00000260693.1]
WARNING, no entry stored in dbm for [ENSG00000268729.1]
WARNING, no entry stored in dbm for [ENSG00000205682.2]
WARNING, no entry stored in dbm for [ENSG00000214259.3]
WARNING, no entry stored in dbm for [ENSG00000232386.9]
WARNING, no entry stored in dbm for [ENSG00000261526.2]
WARNING, no entry stored in dbm for [ENSG00000286201.1]
WARNING, no entry stored in dbm for [ENSG00000269444.1]
WARNING, no entry stored in dbm for [ENSG00000249839.1]
WARNING, no entry stored in dbm for [ENSG00000231731.7]
WARNING, no entry stored in dbm for [ENSG00000258108.2]
WARNING, no entry stored in dbm for [ENSG00000233287.1]
WARNING, no entry stored in dbm for [ENSG00000260252.1]
WARNING, no entry stored in dbm for [ENSG00000214331.8]
WARNING, no entry stored in dbm for [ENSG00000244198.7]
WARNING, no entry stored in dbm for [ENSG00000226472.8]
WARNING, no entry stored in dbm for [ENSG00000235583.2]
WARNING, no entry stored in dbm for [ENSG00000267575.7]
WARNING, no entry stored in dbm for [ENSG00000235852.1]
WARNING, no entry stored in dbm for [ENSG00000273314.1]
WARNING, no entry stored in dbm for [ENSG00000283662.1]
WARNING, no entry stored in dbm for [ENSG00000241057.2]
WARNING, no entry stored in dbm for [ENSG00000254610.3]
WARNING, no entry stored in dbm for [ENSG00000235623.2]
WARNING, no entry stored in dbm for [ENSG00000250132.6]
WARNING, no entry stored in dbm for [ENSG00000244230.3]
WARNING, no entry stored in dbm for [ENSG00000269972.1]
WARNING, no entry stored in dbm for [ENSG00000228113.7]
WARNING, no entry stored in dbm for [ENSG00000286724.1]
WARNING, no entry stored in dbm for [ENSG00000270812.1]
WARNING, no entry stored in dbm for [ENSG00000273300.1]
WARNING, no entry stored in dbm for [ENSG00000251595.7]
WARNING, no entry stored in dbm for [ENSG00000283544.1]
WARNING, no entry stored in dbm for [ENSG00000247199.5]


	* STAR-Fusion complete.  See output: /tmp/nxf.8tOEROyOsF/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)