Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/9b240c0b91f23f1a30dd8257e792a7/659_Dl-T1-TRNA-1_B23WHTKLT4_1_1.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/9e/9b240c0b91f23f1a30dd8257e792a7/659_Dl-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/1d16eeb14e225c2a365fb869b8e5bc/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/1d16eeb14e225c2a365fb869b8e5bc/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/f19ba9cd322420929c787101d222d9/659_Dl-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)
-ctat genome lib [/tmp/nxf.MQMkj64SAp/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.MQMkj64SAp/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary
-sample contains 150357717 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.MQMkj64SAp/ctat_genome_lib_build_dir -J /tmp/nxf.MQMkj64SAp/659_Dl-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction -O /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.MQMkj64SAp/659_Dl-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.MQMkj64SAp/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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[1350000], rate=84375.00/min -building interval tree based on /tmp/nxf.MQMkj64SAp/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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[1350000], rate=83764.22/min -building interval tree based on /tmp/nxf.MQMkj64SAp/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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[1350000], rate=75913.78/min -building interval tree based on /tmp/nxf.MQMkj64SAp/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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[1030000], rate=73309.61/min
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[1050000], rate=73001.16/min
[1060000], rate=72935.78/min
[1070000], rate=72954.55/min
[1080000], rate=72972.97/min
[1090000], rate=73072.63/min
[1100000], rate=73170.73/min
[1110000], rate=73026.32/min
[1120000], rate=73043.48/min
[1130000], rate=72903.23/min
[1140000], rate=72998.93/min
[1150000], rate=73093.22/min
[1160000], rate=73263.16/min
[1170000], rate=73430.96/min
[1180000], rate=73596.67/min
[1190000], rate=73836.61/min
[1200000], rate=74074.07/min
[1210000], rate=74233.13/min
[1220000], rate=74541.75/min
[1230000], rate=74847.87/min
[1240000], rate=75075.68/min
[1250000], rate=75301.20/min
[1260000], rate=75223.88/min
[1270000], rate=74852.65/min
[1280000], rate=74563.11/min
[1290000], rate=74209.01/min
[1300000], rate=73863.64/min
[1310000], rate=73595.51/min
[1320000], rate=73333.33/min
[1330000], rate=73278.24/min
[1340000], rate=73090.91/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.MQMkj64SAp/ctat_genome_lib_build_dir --filt_file /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.MQMkj64SAp/./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...
7000000.00 reads per min processed...
6000000.00 reads per min processed...
5400000.00 reads per min processed...
5454545.45 reads per min processed...
5076923.08 reads per min processed...
5142857.14 reads per min processed...
4875000.00 reads per min processed...
4941176.47 reads per min processed...
5000000.00 reads per min processed...
4800000.00 reads per min processed...
4857142.86 reads per min processed...
4695652.17 reads per min processed...
4560000.00 reads per min processed...
4615384.62 reads per min processed...
4666666.67 reads per min processed...
4551724.14 reads per min processed...
4600000.00 reads per min processed...
4645161.29 reads per min processed...
4687500.00 reads per min processed...
4727272.73 reads per min processed...
4628571.43 reads per min processed...
4666666.67 reads per min processed...
4702702.70 reads per min processed...
4864864.86 reads per min processed...
4894736.84 reads per min processed...
4923076.92 reads per min processed...
4950000.00 reads per min processed...
4975609.76 reads per min processed...
5000000.00 reads per min processed...
5023255.81 reads per min processed...
4933333.33 reads per min processed...
4956521.74 reads per min processed...
4978723.40 reads per min processed...
5000000.00 reads per min processed...
4920000.00 reads per min processed...
4941176.47 reads per min processed...
4961538.46 reads per min processed...
4981132.08 reads per min processed...
5000000.00 reads per min processed...
4928571.43 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.MQMkj64SAp/659_Dl-T1-TRNA-1_B23WHTKLT4_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.MQMkj64SAp/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -96885.500865
EM: Round [1] log likelihood: -96816.480396
EM: Round [2] log likelihood: -96790.106646
EM: Round [3] log likelihood: -96777.244412
EM: Round [4] log likelihood: -96770.421501
EM: Round [5] log likelihood: -96766.665305
EM: Round [6] log likelihood: -96764.531721
EM: Round [7] log likelihood: -96763.274139
EM: Round [8] log likelihood: -96762.499841
EM: Round [9] log likelihood: -96761.999766
EM: Round [10] log likelihood: -96761.660698
EM: Round [11] log likelihood: -96761.419901
EM: Round [12] log likelihood: -96761.241636
EM: Round [13] log likelihood: -96761.104895
EM: Round [14] log likelihood: -96760.996892
EM: Round [15] log likelihood: -96760.909557
EM: Round [16] log likelihood: -96760.837598
EM: Round [17] log likelihood: -96760.777419
EM: Round [18] log likelihood: -96760.726484
EM: Round [19] log likelihood: -96760.682949
EM: Round [20] log likelihood: -96760.645436
EM: Round [21] log likelihood: -96760.612886
EM: Round [22] log likelihood: -96760.584471
EM: Round [23] log likelihood: -96760.559533
EM: Round [24] log likelihood: -96760.537538
EM: Round [25] log likelihood: -96760.518052
EM: Round [26] log likelihood: -96760.500717
EM: Round [27] log likelihood: -96760.485232
EM: Round [28] log likelihood: -96760.471347
EM: Round [29] log likelihood: -96760.458852
EM: Round [30] log likelihood: -96760.447568
EM: Round [31] log likelihood: -96760.437342
EM: Round [32] log likelihood: -96760.428045
EM: Round [33] log likelihood: -96760.419564
EM: Round [34] log likelihood: -96760.411805
EM: Round [35] log likelihood: -96760.404683
EM: Round [36] log likelihood: -96760.398128
EM: Round [37] log likelihood: -96760.392077
EM: Round [38] log likelihood: -96760.386476
EM: Round [39] log likelihood: -96760.381277
EM: Round [40] log likelihood: -96760.376440
EM: Round [41] log likelihood: -96760.371927
EM: Round [42] log likelihood: -96760.367707
EM: Round [43] log likelihood: -96760.363753
EM: Round [44] log likelihood: -96760.360039
EM: Round [45] log likelihood: -96760.356543
EM: Round [46] log likelihood: -96760.353246
EM: Round [47] log likelihood: -96760.350131
EM: Round [48] log likelihood: -96760.347182
EM: Round [49] log likelihood: -96760.344385
EM: Round [50] log likelihood: -96760.341730
EM: Round [51] log likelihood: -96760.339203
EM: Round [52] log likelihood: -96760.336796
EM: Round [53] log likelihood: -96760.334500
EM: Round [54] log likelihood: -96760.332307
EM: Round [55] log likelihood: -96760.330209
EM: Round [56] log likelihood: -96760.328200
EM: Round [57] log likelihood: -96760.326275
EM: Round [58] log likelihood: -96760.324427
EM: Round [59] log likelihood: -96760.322653
EM: Round [60] log likelihood: -96760.320947
EM: Round [61] log likelihood: -96760.319306
EM: Round [62] log likelihood: -96760.317726
EM: Round [63] log likelihood: -96760.316203
EM: Round [64] log likelihood: -96760.314734
EM: Round [65] log likelihood: -96760.313317
EM: Round [66] log likelihood: -96760.311949
EM: Round [67] log likelihood: -96760.310628
EM: Round [68] log likelihood: -96760.309350
EM: Round [69] log likelihood: -96760.308115
EM: Round [70] log likelihood: -96760.306920
EM: Round [71] log likelihood: -96760.305763
EM: Round [72] log likelihood: -96760.304643
EM: Round [73] log likelihood: -96760.303559
EM: Round [74] log likelihood: -96760.302508
EM: Round [75] log likelihood: -96760.301489
EM: Round [76] log likelihood: -96760.300501
EM: Round [77] log likelihood: -96760.299544
EM: Round [78] log likelihood: -96760.298614
EM: Round [79] log likelihood: -96760.297713
EM: Round [80] log likelihood: -96760.296838
EM: Round [81] log likelihood: -96760.295989
EM: Round [82] log likelihood: -96760.295164
EM: Round [83] log likelihood: -96760.294364
EM: Round [84] log likelihood: -96760.293586
EM: Round [85] log likelihood: -96760.292831
EM: Round [86] log likelihood: -96760.292097
EM: Round [87] log likelihood: -96760.291385
EM: Round [88] log likelihood: -96760.290692
EM: Round [89] log likelihood: -96760.290019
EM: Round [90] log likelihood: -96760.289365
EM: Round [91] log likelihood: -96760.288729
EM: Round [92] log likelihood: -96760.288111
EM: Round [93] log likelihood: -96760.287510
EM: Round [94] log likelihood: -96760.286926
EM: Round [95] log likelihood: -96760.286358
EM: Round [96] log likelihood: -96760.285806
EM: Round [97] log likelihood: -96760.285269
EM: Round [98] log likelihood: -96760.284747
EM: Round [99] log likelihood: -96760.284239
EM: Round [100] log likelihood: -96760.283746
EM: Round [101] log likelihood: -96760.283266
EM: Round [102] log likelihood: -96760.282799
EM: Round [103] log likelihood: -96760.282344
EM: Round [104] log likelihood: -96760.281903
EM: Round [105] log likelihood: -96760.281473
EM: Round [106] log likelihood: -96760.281055
EM: Round [107] log likelihood: -96760.280648
EM: Round [108] log likelihood: -96760.280253
EM: Round [109] log likelihood: -96760.279868
EM: Round [110] log likelihood: -96760.279494
EM: Round [111] log likelihood: -96760.279130
EM: Round [112] log likelihood: -96760.278776
EM: Round [113] log likelihood: -96760.278431
EM: Round [114] log likelihood: -96760.278096
EM: Round [115] log likelihood: -96760.277770
EM: Round [116] log likelihood: -96760.277453
EM: Round [117] log likelihood: -96760.277145
EM: Round [118] log likelihood: -96760.276844
EM: Round [119] log likelihood: -96760.276552
EM: Round [120] log likelihood: -96760.276268
EM: Round [121] log likelihood: -96760.275992
EM: Round [122] log likelihood: -96760.275723
EM: Round [123] log likelihood: -96760.275462
EM: Round [124] log likelihood: -96760.275207
EM: Round [125] log likelihood: -96760.274960
EM: Round [126] log likelihood: -96760.274719
EM: Round [127] log likelihood: -96760.274484
EM: Round [128] log likelihood: -96760.274256
EM: Round [129] log likelihood: -96760.274035
EM: Round [130] log likelihood: -96760.273819
EM: Round [131] log likelihood: -96760.273609
EM: Round [132] log likelihood: -96760.273405
EM: Round [133] log likelihood: -96760.273206
EM: Round [134] log likelihood: -96760.273013
EM: Round [135] log likelihood: -96760.272825
EM: Round [136] log likelihood: -96760.272642
EM: Round [137] log likelihood: -96760.272464
EM: Round [138] log likelihood: -96760.272291
EM: Round [139] log likelihood: -96760.272122
EM: Round [140] log likelihood: -96760.271958
EM: Round [141] log likelihood: -96760.271799
EM: Round [142] log likelihood: -96760.271643
EM: Round [143] log likelihood: -96760.271492
EM: Round [144] log likelihood: -96760.271345
EM: Round [145] log likelihood: -96760.271203
EM: Round [146] log likelihood: -96760.271063
EM: Round [147] log likelihood: -96760.270928
EM: Round [148] log likelihood: -96760.270796
EM: Round [149] log likelihood: -96760.270668
EM: Round [150] log likelihood: -96760.270544
EM: Round [151] log likelihood: -96760.270422
EM: Round [152] log likelihood: -96760.270304
EM: Round [153] log likelihood: -96760.270190
EM: Round [154] log likelihood: -96760.270078
EM: Round [155] log likelihood: -96760.269969
EM: Round [156] log likelihood: -96760.269863
EM: Round [157] log likelihood: -96760.269760
EM: Round [158] log likelihood: -96760.269660
EM: Round [159] log likelihood: -96760.269563
EM: Stopping iterations at round 159 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -96795.772761
EM: Round [1] log likelihood: -96737.933943
EM: Round [2] log likelihood: -96715.706792
EM: Round [3] log likelihood: -96704.987490
EM: Round [4] log likelihood: -96699.360109
EM: Round [5] log likelihood: -96696.284616
EM: Round [6] log likelihood: -96694.545579
EM: Round [7] log likelihood: -96693.523126
EM: Round [8] log likelihood: -96692.894080
EM: Round [9] log likelihood: -96692.487301
EM: Round [10] log likelihood: -96692.210462
EM: Round [11] log likelihood: -96692.012614
EM: Round [12] log likelihood: -96691.864880
EM: Round [13] log likelihood: -96691.750389
EM: Round [14] log likelihood: -96691.658940
EM: Round [15] log likelihood: -96691.584131
EM: Round [16] log likelihood: -96691.521788
EM: Round [17] log likelihood: -96691.469075
EM: Round [18] log likelihood: -96691.423996
EM: Round [19] log likelihood: -96691.385092
EM: Round [20] log likelihood: -96691.351268
EM: Round [21] log likelihood: -96691.321674
EM: Round [22] log likelihood: -96691.295642
EM: Round [23] log likelihood: -96691.272633
EM: Round [24] log likelihood: -96691.252207
EM: Round [25] log likelihood: -96691.234003
EM: Round [26] log likelihood: -96691.217717
EM: Round [27] log likelihood: -96691.203095
EM: Round [28] log likelihood: -96691.189923
EM: Round [29] log likelihood: -96691.178017
EM: Round [30] log likelihood: -96691.167222
EM: Round [31] log likelihood: -96691.157403
EM: Round [32] log likelihood: -96691.148445
EM: Round [33] log likelihood: -96691.140249
EM: Round [34] log likelihood: -96691.132728
EM: Round [35] log likelihood: -96691.125808
EM: Round [36] log likelihood: -96691.119422
EM: Round [37] log likelihood: -96691.113514
EM: Round [38] log likelihood: -96691.108034
EM: Round [39] log likelihood: -96691.102939
EM: Round [40] log likelihood: -96691.098190
EM: Round [41] log likelihood: -96691.093753
EM: Round [42] log likelihood: -96691.089599
EM: Round [43] log likelihood: -96691.085700
EM: Round [44] log likelihood: -96691.082034
EM: Round [45] log likelihood: -96691.078580
EM: Round [46] log likelihood: -96691.075320
EM: Round [47] log likelihood: -96691.072236
EM: Round [48] log likelihood: -96691.069315
EM: Round [49] log likelihood: -96691.066543
EM: Round [50] log likelihood: -96691.063908
EM: Round [51] log likelihood: -96691.061400
EM: Round [52] log likelihood: -96691.059010
EM: Round [53] log likelihood: -96691.056729
EM: Round [54] log likelihood: -96691.054549
EM: Round [55] log likelihood: -96691.052462
EM: Round [56] log likelihood: -96691.050464
EM: Round [57] log likelihood: -96691.048548
EM: Round [58] log likelihood: -96691.046709
EM: Round [59] log likelihood: -96691.044942
EM: Round [60] log likelihood: -96691.043243
EM: Round [61] log likelihood: -96691.041608
EM: Round [62] log likelihood: -96691.040034
EM: Round [63] log likelihood: -96691.038516
EM: Round [64] log likelihood: -96691.037052
EM: Round [65] log likelihood: -96691.035639
EM: Round [66] log likelihood: -96691.034275
EM: Round [67] log likelihood: -96691.032957
EM: Round [68] log likelihood: -96691.031683
EM: Round [69] log likelihood: -96691.030451
EM: Round [70] log likelihood: -96691.029258
EM: Round [71] log likelihood: -96691.028104
EM: Round [72] log likelihood: -96691.026987
EM: Round [73] log likelihood: -96691.025904
EM: Round [74] log likelihood: -96691.024855
EM: Round [75] log likelihood: -96691.023838
EM: Round [76] log likelihood: -96691.022852
EM: Round [77] log likelihood: -96691.021896
EM: Round [78] log likelihood: -96691.020968
EM: Round [79] log likelihood: -96691.020068
EM: Round [80] log likelihood: -96691.019194
EM: Round [81] log likelihood: -96691.018346
EM: Round [82] log likelihood: -96691.017523
EM: Round [83] log likelihood: -96691.016723
EM: Round [84] log likelihood: -96691.015947
EM: Round [85] log likelihood: -96691.015192
EM: Round [86] log likelihood: -96691.014460
EM: Round [87] log likelihood: -96691.013748
EM: Round [88] log likelihood: -96691.013056
EM: Round [89] log likelihood: -96691.012383
EM: Round [90] log likelihood: -96691.011730
EM: Round [91] log likelihood: -96691.011095
EM: Round [92] log likelihood: -96691.010477
EM: Round [93] log likelihood: -96691.009877
EM: Round [94] log likelihood: -96691.009293
EM: Round [95] log likelihood: -96691.008726
EM: Round [96] log likelihood: -96691.008174
EM: Round [97] log likelihood: -96691.007637
EM: Round [98] log likelihood: -96691.007116
EM: Round [99] log likelihood: -96691.006608
EM: Round [100] log likelihood: -96691.006115
EM: Round [101] log likelihood: -96691.005635
EM: Round [102] log likelihood: -96691.005168
EM: Round [103] log likelihood: -96691.004714
EM: Round [104] log likelihood: -96691.004273
EM: Round [105] log likelihood: -96691.003843
EM: Round [106] log likelihood: -96691.003426
EM: Round [107] log likelihood: -96691.003019
EM: Round [108] log likelihood: -96691.002624
EM: Round [109] log likelihood: -96691.002239
EM: Round [110] log likelihood: -96691.001865
EM: Round [111] log likelihood: -96691.001502
EM: Round [112] log likelihood: -96691.001148
EM: Round [113] log likelihood: -96691.000803
EM: Round [114] log likelihood: -96691.000468
EM: Round [115] log likelihood: -96691.000143
EM: Round [116] log likelihood: -96690.999826
EM: Round [117] log likelihood: -96690.999517
EM: Round [118] log likelihood: -96690.999217
EM: Round [119] log likelihood: -96690.998925
EM: Round [120] log likelihood: -96690.998641
EM: Round [121] log likelihood: -96690.998365
EM: Round [122] log likelihood: -96690.998096
EM: Round [123] log likelihood: -96690.997835
EM: Round [124] log likelihood: -96690.997580
EM: Round [125] log likelihood: -96690.997333
EM: Round [126] log likelihood: -96690.997092
EM: Round [127] log likelihood: -96690.996858
EM: Round [128] log likelihood: -96690.996630
EM: Round [129] log likelihood: -96690.996408
EM: Round [130] log likelihood: -96690.996193
EM: Round [131] log likelihood: -96690.995983
EM: Round [132] log likelihood: -96690.995779
EM: Round [133] log likelihood: -96690.995580
EM: Round [134] log likelihood: -96690.995387
EM: Round [135] log likelihood: -96690.995199
EM: Round [136] log likelihood: -96690.995016
EM: Round [137] log likelihood: -96690.994838
EM: Round [138] log likelihood: -96690.994665
EM: Round [139] log likelihood: -96690.994496
EM: Round [140] log likelihood: -96690.994332
EM: Round [141] log likelihood: -96690.994173
EM: Round [142] log likelihood: -96690.994018
EM: Round [143] log likelihood: -96690.993867
EM: Round [144] log likelihood: -96690.993720
EM: Round [145] log likelihood: -96690.993577
EM: Round [146] log likelihood: -96690.993438
EM: Round [147] log likelihood: -96690.993303
EM: Round [148] log likelihood: -96690.993171
EM: Round [149] log likelihood: -96690.993043
EM: Round [150] log likelihood: -96690.992918
EM: Round [151] log likelihood: -96690.992797
EM: Round [152] log likelihood: -96690.992679
EM: Round [153] log likelihood: -96690.992564
EM: Round [154] log likelihood: -96690.992453
EM: Round [155] log likelihood: -96690.992344
EM: Round [156] log likelihood: -96690.992238
EM: Round [157] log likelihood: -96690.992135
EM: Round [158] log likelihood: -96690.992035
EM: Round [159] log likelihood: -96690.991938
EM: Stopping iterations at round 159 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.MQMkj64SAp/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.MQMkj64SAp/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.MQMkj64SAp/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.MQMkj64SAp/./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.MQMkj64SAp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.MQMkj64SAp/./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.MQMkj64SAp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 150357717 > /tmp/nxf.MQMkj64SAp/./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.MQMkj64SAp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.MQMkj64SAp/ctat_genome_lib_build_dir > /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.MQMkj64SAp/ctat_genome_lib_build_dir --annotate /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.MQMkj64SAp/./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.MQMkj64SAp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.MQMkj64SAp/ctat_genome_lib_build_dir
-done, see /tmp/nxf.MQMkj64SAp/./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.MQMkj64SAp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.MQMkj64SAp/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 1016, filtered: 6827)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.MQMkj64SAp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.MQMkj64SAp/./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.MQMkj64SAp/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
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WARNING, no entry stored in dbm for [ENSG00000267723.1]
WARNING, no entry stored in dbm for [ENSG00000229738.1]
WARNING, no entry stored in dbm for [ENSG00000253133.2]
WARNING, no entry stored in dbm for [ENSG00000260198.1]
WARNING, no entry stored in dbm for [ENSG00000278912.1]
WARNING, no entry stored in dbm for [ENSG00000253155.1]
WARNING, no entry stored in dbm for [ENSG00000283041.1]
WARNING, no entry stored in dbm for [ENSG00000283041.1]
WARNING, no entry stored in dbm for [ENSG00000280392.1]
WARNING, no entry stored in dbm for [ENSG00000280392.1]
WARNING, no entry stored in dbm for [ENSG00000204929.13]
WARNING, no entry stored in dbm for [ENSG00000278156.2]
WARNING, no entry stored in dbm for [ENSG00000258587.1]
WARNING, no entry stored in dbm for [ENSG00000269968.1]
WARNING, no entry stored in dbm for [ENSG00000226824.7]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000286480.1]
WARNING, no entry stored in dbm for [ENSG00000243554.1]
WARNING, no entry stored in dbm for [ENSG00000258423.1]
WARNING, no entry stored in dbm for [ENSG00000230137.1]
WARNING, no entry stored in dbm for [ENSG00000263272.1]
WARNING, no entry stored in dbm for [ENSG00000281376.1]
WARNING, no entry stored in dbm for [ENSG00000281376.1]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
* STAR-Fusion complete. See output: /tmp/nxf.MQMkj64SAp/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)