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/28/f41d78578200ea95b538a8983dc8e3/EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/9b3981fd9fede9c08b406c4f731244/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/41f54a20152b67ec087fd421f9e34a/EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/9b3981fd9fede9c08b406c4f731244/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/f41d78578200ea95b538a8983dc8e3/EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.lT9KTs8yqN/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary
-sample contains 211551416 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir  -J /tmp/nxf.lT9KTs8yqN/EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction  -O /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.lT9KTs8yqN/EndoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.lT9KTs8yqN/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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-building interval tree based on /tmp/nxf.lT9KTs8yqN/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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[3300000], rate=54083.58/min 
[3310000], rate=54114.44/min -building interval tree based on /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=13636.36/min 
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[30000], rate=18947.37/min 
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[2600000], rate=41879.19/min 
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[2620000], rate=42088.35/min 
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[2680000], rate=42811.50/min 
[2690000], rate=42959.81/min 
[2700000], rate=43119.51/min 
[2710000], rate=43256.19/min 
-building interval tree based on /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes

[10000], rate=20000.00/min 
[20000], rate=21428.57/min 
[30000], rate=23684.21/min 
[40000], rate=22857.14/min 
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[1480000], rate=34687.50/min 
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[1500000], rate=34588.78/min 
[1510000], rate=34566.96/min 
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[3300000], rate=47053.23/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

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done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.lT9KTs8yqN/EndoN_FFPE_L06_RNA_01_B23LG7FLT4_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.lT9KTs8yqN/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -185535.412371
EM: Round [1] log likelihood: -185124.113175
EM: Round [2] log likelihood: -184968.838502
EM: Round [3] log likelihood: -184895.979050
EM: Round [4] log likelihood: -184858.046861
EM: Round [5] log likelihood: -184836.950656
EM: Round [6] log likelihood: -184824.558628
EM: Round [7] log likelihood: -184816.901891
EM: Round [8] log likelihood: -184811.945174
EM: Round [9] log likelihood: -184808.600339
EM: Round [10] log likelihood: -184806.260687
EM: Round [11] log likelihood: -184804.573305
EM: Round [12] log likelihood: -184803.324319
EM: Round [13] log likelihood: -184802.379098
EM: Round [14] log likelihood: -184801.649942
EM: Round [15] log likelihood: -184801.077978
EM: Round [16] log likelihood: -184800.622630
EM: Round [17] log likelihood: -184800.255294
EM: Round [18] log likelihood: -184799.955397
EM: Round [19] log likelihood: -184799.707892
EM: Round [20] log likelihood: -184799.501595
EM: Round [21] log likelihood: -184799.328085
EM: Round [22] log likelihood: -184799.180939
EM: Round [23] log likelihood: -184799.055203
EM: Round [24] log likelihood: -184798.947012
EM: Round [25] log likelihood: -184798.853324
EM: Round [26] log likelihood: -184798.771721
EM: Round [27] log likelihood: -184798.700263
EM: Round [28] log likelihood: -184798.637383
EM: Round [29] log likelihood: -184798.581800
EM: Round [30] log likelihood: -184798.532467
EM: Round [31] log likelihood: -184798.488513
EM: Round [32] log likelihood: -184798.449216
EM: Round [33] log likelihood: -184798.413970
EM: Round [34] log likelihood: -184798.382264
EM: Round [35] log likelihood: -184798.353664
EM: Round [36] log likelihood: -184798.327801
EM: Round [37] log likelihood: -184798.304358
EM: Round [38] log likelihood: -184798.283062
EM: Round [39] log likelihood: -184798.263677
EM: Round [40] log likelihood: -184798.245999
EM: Round [41] log likelihood: -184798.229848
EM: Round [42] log likelihood: -184798.215068
EM: Round [43] log likelihood: -184798.201521
EM: Round [44] log likelihood: -184798.189086
EM: Round [45] log likelihood: -184798.177655
EM: Round [46] log likelihood: -184798.167133
EM: Round [47] log likelihood: -184798.157436
EM: Round [48] log likelihood: -184798.148487
EM: Round [49] log likelihood: -184798.140220
EM: Round [50] log likelihood: -184798.132574
EM: Round [51] log likelihood: -184798.125494
EM: Round [52] log likelihood: -184798.118932
EM: Round [53] log likelihood: -184798.112844
EM: Round [54] log likelihood: -184798.107189
EM: Round [55] log likelihood: -184798.101932
EM: Round [56] log likelihood: -184798.097041
EM: Round [57] log likelihood: -184798.092485
EM: Round [58] log likelihood: -184798.088237
EM: Round [59] log likelihood: -184798.084275
EM: Round [60] log likelihood: -184798.080574
EM: Round [61] log likelihood: -184798.077115
EM: Round [62] log likelihood: -184798.073880
EM: Round [63] log likelihood: -184798.070851
EM: Round [64] log likelihood: -184798.068013
EM: Round [65] log likelihood: -184798.065351
EM: Round [66] log likelihood: -184798.062854
EM: Round [67] log likelihood: -184798.060509
EM: Round [68] log likelihood: -184798.058304
EM: Round [69] log likelihood: -184798.056231
EM: Round [70] log likelihood: -184798.054279
EM: Round [71] log likelihood: -184798.052440
EM: Round [72] log likelihood: -184798.050707
EM: Round [73] log likelihood: -184798.049072
EM: Round [74] log likelihood: -184798.047528
EM: Round [75] log likelihood: -184798.046070
EM: Round [76] log likelihood: -184798.044692
EM: Round [77] log likelihood: -184798.043387
EM: Round [78] log likelihood: -184798.042153
EM: Round [79] log likelihood: -184798.040984
EM: Round [80] log likelihood: -184798.039875
EM: Round [81] log likelihood: -184798.038824
EM: Round [82] log likelihood: -184798.037826
EM: Round [83] log likelihood: -184798.036878
EM: Round [84] log likelihood: -184798.035977
EM: Round [85] log likelihood: -184798.035121
EM: Round [86] log likelihood: -184798.034306
EM: Round [87] log likelihood: -184798.033530
EM: Round [88] log likelihood: -184798.032791
EM: Round [89] log likelihood: -184798.032087
EM: Round [90] log likelihood: -184798.031415
EM: Round [91] log likelihood: -184798.030774
EM: Round [92] log likelihood: -184798.030162
EM: Round [93] log likelihood: -184798.029578
EM: Round [94] log likelihood: -184798.029019
EM: Round [95] log likelihood: -184798.028484
EM: Round [96] log likelihood: -184798.027973
EM: Round [97] log likelihood: -184798.027484
EM: Round [98] log likelihood: -184798.027015
EM: Round [99] log likelihood: -184798.026566
EM: Round [100] log likelihood: -184798.026135
EM: Round [101] log likelihood: -184798.025722
EM: Round [102] log likelihood: -184798.025326
EM: Round [103] log likelihood: -184798.024945
EM: Round [104] log likelihood: -184798.024580
EM: Round [105] log likelihood: -184798.024229
EM: Round [106] log likelihood: -184798.023891
EM: Round [107] log likelihood: -184798.023567
EM: Round [108] log likelihood: -184798.023255
EM: Round [109] log likelihood: -184798.022954
EM: Round [110] log likelihood: -184798.022665
EM: Round [111] log likelihood: -184798.022386
EM: Round [112] log likelihood: -184798.022118
EM: Round [113] log likelihood: -184798.021859
EM: Round [114] log likelihood: -184798.021609
EM: Round [115] log likelihood: -184798.021369
EM: Round [116] log likelihood: -184798.021136
EM: Round [117] log likelihood: -184798.020912
EM: Round [118] log likelihood: -184798.020695
EM: Round [119] log likelihood: -184798.020486
EM: Round [120] log likelihood: -184798.020284
EM: Round [121] log likelihood: -184798.020089
EM: Round [122] log likelihood: -184798.019900
EM: Round [123] log likelihood: -184798.019717
EM: Round [124] log likelihood: -184798.019541
EM: Round [125] log likelihood: -184798.019369
EM: Round [126] log likelihood: -184798.019204
EM: Round [127] log likelihood: -184798.019044
EM: Round [128] log likelihood: -184798.018888
EM: Round [129] log likelihood: -184798.018738
EM: Round [130] log likelihood: -184798.018592
EM: Round [131] log likelihood: -184798.018451
EM: Round [132] log likelihood: -184798.018314
EM: Round [133] log likelihood: -184798.018181
EM: Round [134] log likelihood: -184798.018052
EM: Round [135] log likelihood: -184798.017927
EM: Round [136] log likelihood: -184798.017805
EM: Round [137] log likelihood: -184798.017688
EM: Round [138] log likelihood: -184798.017573
EM: Round [139] log likelihood: -184798.017462
EM: Round [140] log likelihood: -184798.017354
EM: Round [141] log likelihood: -184798.017249
EM: Round [142] log likelihood: -184798.017147
EM: Round [143] log likelihood: -184798.017048
EM: Stopping iterations at round 143 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -185299.688347
EM: Round [1] log likelihood: -184940.867854
EM: Round [2] log likelihood: -184812.537424
EM: Round [3] log likelihood: -184754.082775
EM: Round [4] log likelihood: -184724.243345
EM: Round [5] log likelihood: -184707.937107
EM: Round [6] log likelihood: -184698.529548
EM: Round [7] log likelihood: -184692.823447
EM: Round [8] log likelihood: -184689.197313
EM: Round [9] log likelihood: -184686.794594
EM: Round [10] log likelihood: -184685.143905
EM: Round [11] log likelihood: -184683.974645
EM: Round [12] log likelihood: -184683.124848
EM: Round [13] log likelihood: -184682.493681
EM: Round [14] log likelihood: -184682.016100
EM: Round [15] log likelihood: -184681.648816
EM: Round [16] log likelihood: -184681.362243
EM: Round [17] log likelihood: -184681.135698
EM: Round [18] log likelihood: -184680.954441
EM: Round [19] log likelihood: -184680.807796
EM: Round [20] log likelihood: -184680.687919
EM: Round [21] log likelihood: -184680.588974
EM: Round [22] log likelihood: -184680.506568
EM: Round [23] log likelihood: -184680.437359
EM: Round [24] log likelihood: -184680.378780
EM: Round [25] log likelihood: -184680.328839
EM: Round [26] log likelihood: -184680.285975
EM: Round [27] log likelihood: -184680.248959
EM: Round [28] log likelihood: -184680.216809
EM: Round [29] log likelihood: -184680.188738
EM: Round [30] log likelihood: -184680.164108
EM: Round [31] log likelihood: -184680.142400
EM: Round [32] log likelihood: -184680.123186
EM: Round [33] log likelihood: -184680.106114
EM: Round [34] log likelihood: -184680.090891
EM: Round [35] log likelihood: -184680.077270
EM: Round [36] log likelihood: -184680.065045
EM: Round [37] log likelihood: -184680.054040
EM: Round [38] log likelihood: -184680.044107
EM: Round [39] log likelihood: -184680.035118
EM: Round [40] log likelihood: -184680.026962
EM: Round [41] log likelihood: -184680.019546
EM: Round [42] log likelihood: -184680.012788
EM: Round [43] log likelihood: -184680.006617
EM: Round [44] log likelihood: -184680.000970
EM: Round [45] log likelihood: -184679.995794
EM: Round [46] log likelihood: -184679.991039
EM: Round [47] log likelihood: -184679.986665
EM: Round [48] log likelihood: -184679.982634
EM: Round [49] log likelihood: -184679.978913
EM: Round [50] log likelihood: -184679.975473
EM: Round [51] log likelihood: -184679.972287
EM: Round [52] log likelihood: -184679.969334
EM: Round [53] log likelihood: -184679.966591
EM: Round [54] log likelihood: -184679.964040
EM: Round [55] log likelihood: -184679.961665
EM: Round [56] log likelihood: -184679.959451
EM: Round [57] log likelihood: -184679.957384
EM: Round [58] log likelihood: -184679.955452
EM: Round [59] log likelihood: -184679.953643
EM: Round [60] log likelihood: -184679.951949
EM: Round [61] log likelihood: -184679.950360
EM: Round [62] log likelihood: -184679.948867
EM: Round [63] log likelihood: -184679.947464
EM: Round [64] log likelihood: -184679.946143
EM: Round [65] log likelihood: -184679.944899
EM: Round [66] log likelihood: -184679.943725
EM: Round [67] log likelihood: -184679.942617
EM: Round [68] log likelihood: -184679.941571
EM: Round [69] log likelihood: -184679.940580
EM: Round [70] log likelihood: -184679.939643
EM: Round [71] log likelihood: -184679.938754
EM: Round [72] log likelihood: -184679.937912
EM: Round [73] log likelihood: -184679.937112
EM: Round [74] log likelihood: -184679.936352
EM: Round [75] log likelihood: -184679.935630
EM: Round [76] log likelihood: -184679.934942
EM: Round [77] log likelihood: -184679.934287
EM: Round [78] log likelihood: -184679.933663
EM: Round [79] log likelihood: -184679.933068
EM: Round [80] log likelihood: -184679.932500
EM: Round [81] log likelihood: -184679.931958
EM: Round [82] log likelihood: -184679.931440
EM: Round [83] log likelihood: -184679.930944
EM: Round [84] log likelihood: -184679.930470
EM: Round [85] log likelihood: -184679.930015
EM: Round [86] log likelihood: -184679.929580
EM: Round [87] log likelihood: -184679.929163
EM: Round [88] log likelihood: -184679.928763
EM: Round [89] log likelihood: -184679.928380
EM: Round [90] log likelihood: -184679.928011
EM: Round [91] log likelihood: -184679.927657
EM: Round [92] log likelihood: -184679.927317
EM: Round [93] log likelihood: -184679.926990
EM: Round [94] log likelihood: -184679.926675
EM: Round [95] log likelihood: -184679.926372
EM: Round [96] log likelihood: -184679.926080
EM: Round [97] log likelihood: -184679.925799
EM: Round [98] log likelihood: -184679.925529
EM: Round [99] log likelihood: -184679.925268
EM: Round [100] log likelihood: -184679.925016
EM: Round [101] log likelihood: -184679.924774
EM: Round [102] log likelihood: -184679.924539
EM: Round [103] log likelihood: -184679.924313
EM: Round [104] log likelihood: -184679.924095
EM: Round [105] log likelihood: -184679.923884
EM: Round [106] log likelihood: -184679.923680
EM: Round [107] log likelihood: -184679.923483
EM: Round [108] log likelihood: -184679.923292
EM: Round [109] log likelihood: -184679.923108
EM: Round [110] log likelihood: -184679.922929
EM: Round [111] log likelihood: -184679.922757
EM: Round [112] log likelihood: -184679.922589
EM: Round [113] log likelihood: -184679.922428
EM: Round [114] log likelihood: -184679.922271
EM: Round [115] log likelihood: -184679.922119
EM: Round [116] log likelihood: -184679.921972
EM: Round [117] log likelihood: -184679.921829
EM: Round [118] log likelihood: -184679.921691
EM: Round [119] log likelihood: -184679.921557
EM: Round [120] log likelihood: -184679.921426
EM: Round [121] log likelihood: -184679.921300
EM: Round [122] log likelihood: -184679.921178
EM: Round [123] log likelihood: -184679.921059
EM: Round [124] log likelihood: -184679.920943
EM: Round [125] log likelihood: -184679.920831
EM: Round [126] log likelihood: -184679.920722
EM: Round [127] log likelihood: -184679.920616
EM: Round [128] log likelihood: -184679.920514
EM: Round [129] log likelihood: -184679.920414
EM: Stopping iterations at round 129 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.lT9KTs8yqN/./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.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.lT9KTs8yqN/./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.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 211551416 > /tmp/nxf.lT9KTs8yqN/./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.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir > /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir --annotate /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.lT9KTs8yqN/./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.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir
-done, see /tmp/nxf.lT9KTs8yqN/./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.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.lT9KTs8yqN/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 868, filtered: 7913)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.lT9KTs8yqN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.lT9KTs8yqN/./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.lT9KTs8yqN/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000239268.3]
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WARNING, no entry stored in dbm for [ENSG00000214185.3]
WARNING, no entry stored in dbm for [ENSG00000228876.4]
WARNING, no entry stored in dbm for [ENSG00000275340.1]
WARNING, no entry stored in dbm for [ENSG00000275340.1]
WARNING, no entry stored in dbm for [ENSG00000235726.7]
WARNING, no entry stored in dbm for [ENSG00000269680.1]
WARNING, no entry stored in dbm for [ENSG00000230869.1]
WARNING, no entry stored in dbm for [ENSG00000255052.5]
WARNING, no entry stored in dbm for [ENSG00000254016.3]
WARNING, no entry stored in dbm for [ENSG00000215908.10]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000249966.1]
WARNING, no entry stored in dbm for [ENSG00000179840.5]
WARNING, no entry stored in dbm for [ENSG00000269486.2]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000226688.7]
WARNING, no entry stored in dbm for [ENSG00000233098.9]
WARNING, no entry stored in dbm for [ENSG00000215016.2]
WARNING, no entry stored in dbm for [ENSG00000258980.1]
WARNING, no entry stored in dbm for [ENSG00000287891.1]
WARNING, no entry stored in dbm for [ENSG00000234984.1]
WARNING, no entry stored in dbm for [ENSG00000263278.2]
WARNING, no entry stored in dbm for [ENSG00000257550.2]
WARNING, no entry stored in dbm for [ENSG00000259660.2]
WARNING, no entry stored in dbm for [ENSG00000255470.1]
WARNING, no entry stored in dbm for [ENSG00000254275.6]
WARNING, no entry stored in dbm for [ENSG00000223750.1]
WARNING, no entry stored in dbm for [ENSG00000281344.1]
WARNING, no entry stored in dbm for [ENSG00000272321.1]
WARNING, no entry stored in dbm for [ENSG00000233937.7]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000233937.7]
WARNING, no entry stored in dbm for [ENSG00000248103.1]
WARNING, no entry stored in dbm for [ENSG00000259295.6]
WARNING, no entry stored in dbm for [ENSG00000270533.2]
WARNING, no entry stored in dbm for [ENSG00000230223.8]
WARNING, no entry stored in dbm for [ENSG00000227588.2]
WARNING, no entry stored in dbm for [ENSG00000223490.2]
WARNING, no entry stored in dbm for [ENSG00000236021.2]
WARNING, no entry stored in dbm for [ENSG00000235904.3]
WARNING, no entry stored in dbm for [ENSG00000236778.8]
WARNING, no entry stored in dbm for [ENSG00000266405.3]
WARNING, no entry stored in dbm for [ENSG00000233033.1]
WARNING, no entry stored in dbm for [ENSG00000280273.2]
WARNING, no entry stored in dbm for [ENSG00000240137.6]
WARNING, no entry stored in dbm for [ENSG00000236800.1]
WARNING, no entry stored in dbm for [ENSG00000268635.2]
WARNING, no entry stored in dbm for [ENSG00000279733.1]
WARNING, no entry stored in dbm for [ENSG00000280143.1]
WARNING, no entry stored in dbm for [ENSG00000286720.1]
WARNING, no entry stored in dbm for [ENSG00000239556.4]
WARNING, no entry stored in dbm for [ENSG00000273192.1]
WARNING, no entry stored in dbm for [ENSG00000273192.1]
WARNING, no entry stored in dbm for [ENSG00000239665.8]
WARNING, no entry stored in dbm for [ENSG00000231630.1]
WARNING, no entry stored in dbm for [ENSG00000229021.2]
WARNING, no entry stored in dbm for [ENSG00000225096.3]
WARNING, no entry stored in dbm for [ENSG00000225096.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000232499.2]
WARNING, no entry stored in dbm for [ENSG00000285812.1]
WARNING, no entry stored in dbm for [ENSG00000286610.1]
WARNING, no entry stored in dbm for [ENSG00000286782.1]
WARNING, no entry stored in dbm for [ENSG00000259994.1]
WARNING, no entry stored in dbm for [ENSG00000230628.1]
WARNING, no entry stored in dbm for [ENSG00000230537.2]
WARNING, no entry stored in dbm for [ENSG00000272078.1]
WARNING, no entry stored in dbm for [ENSG00000230490.3]
WARNING, no entry stored in dbm for [ENSG00000232098.3]
WARNING, no entry stored in dbm for [ENSG00000227220.1]
WARNING, no entry stored in dbm for [ENSG00000236166.1]
WARNING, no entry stored in dbm for [ENSG00000227220.1]
WARNING, no entry stored in dbm for [ENSG00000236166.1]
WARNING, no entry stored in dbm for [ENSG00000276805.2]
WARNING, no entry stored in dbm for [ENSG00000233332.1]
WARNING, no entry stored in dbm for [ENSG00000231113.2]
WARNING, no entry stored in dbm for [ENSG00000204929.13]
WARNING, no entry stored in dbm for [ENSG00000280734.3]
WARNING, no entry stored in dbm for [ENSG00000253853.3]
WARNING, no entry stored in dbm for [ENSG00000254319.6]
WARNING, no entry stored in dbm for [ENSG00000277526.5]
WARNING, no entry stored in dbm for [ENSG00000223804.5]
WARNING, no entry stored in dbm for [ENSG00000263590.2]
WARNING, no entry stored in dbm for [ENSG00000287374.1]
WARNING, no entry stored in dbm for [ENSG00000227733.10]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000166104.15]
WARNING, no entry stored in dbm for [ENSG00000241991.1]
WARNING, no entry stored in dbm for [ENSG00000230837.1]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000254497.1]
WARNING, no entry stored in dbm for [ENSG00000249056.1]
WARNING, no entry stored in dbm for [ENSG00000250910.8]
WARNING, no entry stored in dbm for [ENSG00000251411.1]
WARNING, no entry stored in dbm for [ENSG00000255468.7]
WARNING, no entry stored in dbm for [ENSG00000284687.1]
WARNING, no entry stored in dbm for [ENSG00000287860.1]
WARNING, no entry stored in dbm for [ENSG00000270978.1]
WARNING, no entry stored in dbm for [ENSG00000254102.2]
WARNING, no entry stored in dbm for [ENSG00000280828.1]
WARNING, no entry stored in dbm for [ENSG00000259275.4]
WARNING, no entry stored in dbm for [ENSG00000232633.4]
WARNING, no entry stored in dbm for [ENSG00000259605.3]
WARNING, no entry stored in dbm for [ENSG00000253377.2]
WARNING, no entry stored in dbm for [ENSG00000287576.1]
WARNING, no entry stored in dbm for [ENSG00000222826.1]
WARNING, no entry stored in dbm for [ENSG00000261054.1]
WARNING, no entry stored in dbm for [ENSG00000244313.3]
WARNING, no entry stored in dbm for [ENSG00000248898.3]
WARNING, no entry stored in dbm for [ENSG00000228351.3]
WARNING, no entry stored in dbm for [ENSG00000257094.1]
WARNING, no entry stored in dbm for [ENSG00000258134.1]
WARNING, no entry stored in dbm for [ENSG00000269032.1]
WARNING, no entry stored in dbm for [ENSG00000233084.2]
WARNING, no entry stored in dbm for [ENSG00000267605.7]
WARNING, no entry stored in dbm for [ENSG00000267605.7]
WARNING, no entry stored in dbm for [ENSG00000268543.1]
WARNING, no entry stored in dbm for [ENSG00000232098.3]
WARNING, no entry stored in dbm for [ENSG00000286201.1]
WARNING, no entry stored in dbm for [ENSG00000274282.1]
WARNING, no entry stored in dbm for [ENSG00000226063.1]
WARNING, no entry stored in dbm for [ENSG00000286797.1]
WARNING, no entry stored in dbm for [ENSG00000259106.1]
WARNING, no entry stored in dbm for [ENSG00000284052.1]
WARNING, no entry stored in dbm for [ENSG00000263159.1]
WARNING, no entry stored in dbm for [ENSG00000268205.1]
WARNING, no entry stored in dbm for [ENSG00000241529.3]
WARNING, no entry stored in dbm for [ENSG00000268205.1]
WARNING, no entry stored in dbm for [ENSG00000239899.3]
WARNING, no entry stored in dbm for [ENSG00000282943.1]
WARNING, no entry stored in dbm for [ENSG00000280054.1]
WARNING, no entry stored in dbm for [ENSG00000241764.4]
WARNING, no entry stored in dbm for [ENSG00000267328.1]
WARNING, no entry stored in dbm for [ENSG00000239791.2]


	* STAR-Fusion complete.  See output: /tmp/nxf.lT9KTs8yqN/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)