-ctat genome lib [/tmp/nxf.CXw1DMFg3x/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.CXw1DMFg3x/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary
-sample contains 164779021 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.CXw1DMFg3x/ctat_genome_lib_build_dir -J /tmp/nxf.CXw1DMFg3x/659_Mt-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction -O /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.CXw1DMFg3x/659_Mt-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.CXw1DMFg3x/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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[1400000], rate=75201.43/min -building interval tree based on /tmp/nxf.CXw1DMFg3x/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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[1400000], rate=61403.51/min -building interval tree based on /tmp/nxf.CXw1DMFg3x/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes
[10000], rate=60000.00/min
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[1400000], rate=58252.43/min -building interval tree based on /tmp/nxf.CXw1DMFg3x/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
[10000], rate=120000.00/min
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[1200000], rate=48979.59/min
[1210000], rate=49220.34/min
[1220000], rate=49459.46/min
[1230000], rate=49232.82/min
[1240000], rate=48883.05/min
[1250000], rate=48606.61/min
[1260000], rate=48430.49/min
[1270000], rate=48319.59/min
[1280000], rate=48271.53/min
[1290000], rate=48254.36/min
[1300000], rate=48267.33/min
[1310000], rate=48309.77/min
[1320000], rate=48351.65/min
[1330000], rate=48422.33/min
[1340000], rate=48404.58/min
[1350000], rate=48416.02/min
[1360000], rate=48398.58/min
[1370000], rate=48409.89/min
[1380000], rate=48392.75/min
[1390000], rate=48291.84/min
[1400000], rate=48303.62/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.CXw1DMFg3x/ctat_genome_lib_build_dir --filt_file /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.
6000000.00 reads per min processed...
12000000.00 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
5000000.00 reads per min processed...
4000000.00 reads per min processed...
4200000.00 reads per min processed...
4000000.00 reads per min processed...
3857142.86 reads per min processed...
4000000.00 reads per min processed...
4125000.00 reads per min processed...
4000000.00 reads per min processed...
4105263.16 reads per min processed...
4000000.00 reads per min processed...
4090909.09 reads per min processed...
4000000.00 reads per min processed...
4080000.00 reads per min processed...
4000000.00 reads per min processed...
3931034.48 reads per min processed...
4000000.00 reads per min processed...
3937500.00 reads per min processed...
3882352.94 reads per min processed...
3942857.14 reads per min processed...
3891891.89 reads per min processed...
3947368.42 reads per min processed...
4000000.00 reads per min processed...
3951219.51 reads per min processed...
4000000.00 reads per min processed...
4046511.63 reads per min processed...
4090909.09 reads per min processed...
4133333.33 reads per min processed...
4173913.04 reads per min processed...
4125000.00 reads per min processed...
4163265.31 reads per min processed...
4117647.06 reads per min processed...
4153846.15 reads per min processed...
4111111.11 reads per min processed...
4145454.55 reads per min processed...
4105263.16 reads per min processed...
4137931.03 reads per min processed...
4100000.00 reads per min processed...
4064516.13 reads per min processed...
4095238.10 reads per min processed...
4125000.00 reads per min processed...
4090909.09 reads per min processed...
4119402.99 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.CXw1DMFg3x/659_Mt-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.CXw1DMFg3x/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -111837.198620
EM: Round [1] log likelihood: -111778.793798
EM: Round [2] log likelihood: -111755.797948
EM: Round [3] log likelihood: -111744.546504
EM: Round [4] log likelihood: -111738.392612
EM: Round [5] log likelihood: -111734.801622
EM: Round [6] log likelihood: -111732.600356
EM: Round [7] log likelihood: -111731.189043
EM: Round [8] log likelihood: -111730.245295
EM: Round [9] log likelihood: -111729.589386
EM: Round [10] log likelihood: -111729.117526
EM: Round [11] log likelihood: -111728.767598
EM: Round [12] log likelihood: -111728.501107
EM: Round [13] log likelihood: -111728.293389
EM: Round [14] log likelihood: -111728.128154
EM: Round [15] log likelihood: -111727.994331
EM: Round [16] log likelihood: -111727.884211
EM: Round [17] log likelihood: -111727.792298
EM: Round [18] log likelihood: -111727.714600
EM: Round [19] log likelihood: -111727.648162
EM: Round [20] log likelihood: -111727.590762
EM: Round [21] log likelihood: -111727.540707
EM: Round [22] log likelihood: -111727.496690
EM: Round [23] log likelihood: -111727.457688
EM: Round [24] log likelihood: -111727.422893
EM: Round [25] log likelihood: -111727.391659
EM: Round [26] log likelihood: -111727.363466
EM: Round [27] log likelihood: -111727.337890
EM: Round [28] log likelihood: -111727.314582
EM: Round [29] log likelihood: -111727.293253
EM: Round [30] log likelihood: -111727.273663
EM: Round [31] log likelihood: -111727.255609
EM: Round [32] log likelihood: -111727.238918
EM: Round [33] log likelihood: -111727.223443
EM: Round [34] log likelihood: -111727.209058
EM: Round [35] log likelihood: -111727.195654
EM: Round [36] log likelihood: -111727.183135
EM: Round [37] log likelihood: -111727.171419
EM: Round [38] log likelihood: -111727.160433
EM: Round [39] log likelihood: -111727.150111
EM: Round [40] log likelihood: -111727.140397
EM: Round [41] log likelihood: -111727.131240
EM: Round [42] log likelihood: -111727.122595
EM: Round [43] log likelihood: -111727.114421
EM: Round [44] log likelihood: -111727.106681
EM: Round [45] log likelihood: -111727.099343
EM: Round [46] log likelihood: -111727.092376
EM: Round [47] log likelihood: -111727.085755
EM: Round [48] log likelihood: -111727.079453
EM: Round [49] log likelihood: -111727.073449
EM: Round [50] log likelihood: -111727.067724
EM: Round [51] log likelihood: -111727.062257
EM: Round [52] log likelihood: -111727.057033
EM: Round [53] log likelihood: -111727.052036
EM: Round [54] log likelihood: -111727.047252
EM: Round [55] log likelihood: -111727.042667
EM: Round [56] log likelihood: -111727.038270
EM: Round [57] log likelihood: -111727.034050
EM: Round [58] log likelihood: -111727.029996
EM: Round [59] log likelihood: -111727.026099
EM: Round [60] log likelihood: -111727.022350
EM: Round [61] log likelihood: -111727.018742
EM: Round [62] log likelihood: -111727.015266
EM: Round [63] log likelihood: -111727.011916
EM: Round [64] log likelihood: -111727.008686
EM: Round [65] log likelihood: -111727.005569
EM: Round [66] log likelihood: -111727.002560
EM: Round [67] log likelihood: -111726.999654
EM: Round [68] log likelihood: -111726.996846
EM: Round [69] log likelihood: -111726.994130
EM: Round [70] log likelihood: -111726.991504
EM: Round [71] log likelihood: -111726.988963
EM: Round [72] log likelihood: -111726.986503
EM: Round [73] log likelihood: -111726.984122
EM: Round [74] log likelihood: -111726.981814
EM: Round [75] log likelihood: -111726.979578
EM: Round [76] log likelihood: -111726.977411
EM: Round [77] log likelihood: -111726.975309
EM: Round [78] log likelihood: -111726.973271
EM: Round [79] log likelihood: -111726.971293
EM: Round [80] log likelihood: -111726.969374
EM: Round [81] log likelihood: -111726.967511
EM: Round [82] log likelihood: -111726.965703
EM: Round [83] log likelihood: -111726.963946
EM: Round [84] log likelihood: -111726.962240
EM: Round [85] log likelihood: -111726.960582
EM: Round [86] log likelihood: -111726.958972
EM: Round [87] log likelihood: -111726.957406
EM: Round [88] log likelihood: -111726.955884
EM: Round [89] log likelihood: -111726.954405
EM: Round [90] log likelihood: -111726.952966
EM: Round [91] log likelihood: -111726.951567
EM: Round [92] log likelihood: -111726.950206
EM: Round [93] log likelihood: -111726.948882
EM: Round [94] log likelihood: -111726.947594
EM: Round [95] log likelihood: -111726.946341
EM: Round [96] log likelihood: -111726.945121
EM: Round [97] log likelihood: -111726.943934
EM: Round [98] log likelihood: -111726.942779
EM: Round [99] log likelihood: -111726.941654
EM: Round [100] log likelihood: -111726.940559
EM: Round [101] log likelihood: -111726.939493
EM: Round [102] log likelihood: -111726.938455
EM: Round [103] log likelihood: -111726.937444
EM: Round [104] log likelihood: -111726.936459
EM: Round [105] log likelihood: -111726.935501
EM: Round [106] log likelihood: -111726.934567
EM: Round [107] log likelihood: -111726.933657
EM: Round [108] log likelihood: -111726.932771
EM: Round [109] log likelihood: -111726.931908
EM: Round [110] log likelihood: -111726.931067
EM: Round [111] log likelihood: -111726.930247
EM: Round [112] log likelihood: -111726.929449
EM: Round [113] log likelihood: -111726.928671
EM: Round [114] log likelihood: -111726.927913
EM: Round [115] log likelihood: -111726.927174
EM: Round [116] log likelihood: -111726.926454
EM: Round [117] log likelihood: -111726.925753
EM: Round [118] log likelihood: -111726.925069
EM: Round [119] log likelihood: -111726.924402
EM: Round [120] log likelihood: -111726.923753
EM: Round [121] log likelihood: -111726.923120
EM: Round [122] log likelihood: -111726.922503
EM: Round [123] log likelihood: -111726.921901
EM: Round [124] log likelihood: -111726.921315
EM: Round [125] log likelihood: -111726.920743
EM: Round [126] log likelihood: -111726.920186
EM: Round [127] log likelihood: -111726.919642
EM: Round [128] log likelihood: -111726.919113
EM: Round [129] log likelihood: -111726.918596
EM: Round [130] log likelihood: -111726.918093
EM: Round [131] log likelihood: -111726.917602
EM: Round [132] log likelihood: -111726.917123
EM: Round [133] log likelihood: -111726.916657
EM: Round [134] log likelihood: -111726.916202
EM: Round [135] log likelihood: -111726.915758
EM: Round [136] log likelihood: -111726.915326
EM: Round [137] log likelihood: -111726.914904
EM: Round [138] log likelihood: -111726.914493
EM: Round [139] log likelihood: -111726.914092
EM: Round [140] log likelihood: -111726.913700
EM: Round [141] log likelihood: -111726.913319
EM: Round [142] log likelihood: -111726.912947
EM: Round [143] log likelihood: -111726.912584
EM: Round [144] log likelihood: -111726.912231
EM: Round [145] log likelihood: -111726.911886
EM: Round [146] log likelihood: -111726.911550
EM: Round [147] log likelihood: -111726.911222
EM: Round [148] log likelihood: -111726.910902
EM: Round [149] log likelihood: -111726.910590
EM: Round [150] log likelihood: -111726.910285
EM: Round [151] log likelihood: -111726.909989
EM: Round [152] log likelihood: -111726.909699
EM: Round [153] log likelihood: -111726.909417
EM: Round [154] log likelihood: -111726.909142
EM: Round [155] log likelihood: -111726.908873
EM: Round [156] log likelihood: -111726.908611
EM: Round [157] log likelihood: -111726.908356
EM: Round [158] log likelihood: -111726.908107
EM: Round [159] log likelihood: -111726.907864
EM: Round [160] log likelihood: -111726.907627
EM: Round [161] log likelihood: -111726.907396
EM: Round [162] log likelihood: -111726.907170
EM: Round [163] log likelihood: -111726.906950
EM: Round [164] log likelihood: -111726.906736
EM: Round [165] log likelihood: -111726.906527
EM: Round [166] log likelihood: -111726.906323
EM: Round [167] log likelihood: -111726.906124
EM: Round [168] log likelihood: -111726.905930
EM: Round [169] log likelihood: -111726.905740
EM: Round [170] log likelihood: -111726.905556
EM: Round [171] log likelihood: -111726.905375
EM: Round [172] log likelihood: -111726.905200
EM: Round [173] log likelihood: -111726.905028
EM: Round [174] log likelihood: -111726.904861
EM: Round [175] log likelihood: -111726.904698
EM: Round [176] log likelihood: -111726.904539
EM: Round [177] log likelihood: -111726.904384
EM: Round [178] log likelihood: -111726.904232
EM: Round [179] log likelihood: -111726.904085
EM: Round [180] log likelihood: -111726.903941
EM: Round [181] log likelihood: -111726.903800
EM: Round [182] log likelihood: -111726.903663
EM: Round [183] log likelihood: -111726.903529
EM: Round [184] log likelihood: -111726.903399
EM: Round [185] log likelihood: -111726.903272
EM: Round [186] log likelihood: -111726.903148
EM: Round [187] log likelihood: -111726.903027
EM: Round [188] log likelihood: -111726.902908
EM: Round [189] log likelihood: -111726.902793
EM: Round [190] log likelihood: -111726.902681
EM: Round [191] log likelihood: -111726.902571
EM: Round [192] log likelihood: -111726.902464
EM: Round [193] log likelihood: -111726.902360
EM: Round [194] log likelihood: -111726.902258
EM: Round [195] log likelihood: -111726.902159
EM: Stopping iterations at round 195 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -111759.794539
EM: Round [1] log likelihood: -111709.741462
EM: Round [2] log likelihood: -111690.125332
EM: Round [3] log likelihood: -111680.610593
EM: Round [4] log likelihood: -111675.453296
EM: Round [5] log likelihood: -111672.468387
EM: Round [6] log likelihood: -111670.651801
EM: Round [7] log likelihood: -111669.493418
EM: Round [8] log likelihood: -111668.720805
EM: Round [9] log likelihood: -111668.183353
EM: Round [10] log likelihood: -111667.794992
EM: Round [11] log likelihood: -111667.504807
EM: Round [12] log likelihood: -111667.281602
EM: Round [13] log likelihood: -111667.105593
EM: Round [14] log likelihood: -111666.963811
EM: Round [15] log likelihood: -111666.847488
EM: Round [16] log likelihood: -111666.750528
EM: Round [17] log likelihood: -111666.668588
EM: Round [18] log likelihood: -111666.598498
EM: Round [19] log likelihood: -111666.537903
EM: Round [20] log likelihood: -111666.485021
EM: Round [21] log likelihood: -111666.438482
EM: Round [22] log likelihood: -111666.397218
EM: Round [23] log likelihood: -111666.360386
EM: Round [24] log likelihood: -111666.327313
EM: Round [25] log likelihood: -111666.297456
EM: Round [26] log likelihood: -111666.270370
EM: Round [27] log likelihood: -111666.245691
EM: Round [28] log likelihood: -111666.223116
EM: Round [29] log likelihood: -111666.202390
EM: Round [30] log likelihood: -111666.183300
EM: Round [31] log likelihood: -111666.165664
EM: Round [32] log likelihood: -111666.149324
EM: Round [33] log likelihood: -111666.134148
EM: Round [34] log likelihood: -111666.120018
EM: Round [35] log likelihood: -111666.106833
EM: Round [36] log likelihood: -111666.094505
EM: Round [37] log likelihood: -111666.082954
EM: Round [38] log likelihood: -111666.072113
EM: Round [39] log likelihood: -111666.061919
EM: Round [40] log likelihood: -111666.052318
EM: Round [41] log likelihood: -111666.043262
EM: Round [42] log likelihood: -111666.034707
EM: Round [43] log likelihood: -111666.026613
EM: Round [44] log likelihood: -111666.018945
EM: Round [45] log likelihood: -111666.011672
EM: Round [46] log likelihood: -111666.004763
EM: Round [47] log likelihood: -111665.998194
EM: Round [48] log likelihood: -111665.991941
EM: Round [49] log likelihood: -111665.985981
EM: Round [50] log likelihood: -111665.980294
EM: Round [51] log likelihood: -111665.974864
EM: Round [52] log likelihood: -111665.969672
EM: Round [53] log likelihood: -111665.964705
EM: Round [54] log likelihood: -111665.959947
EM: Round [55] log likelihood: -111665.955387
EM: Round [56] log likelihood: -111665.951013
EM: Round [57] log likelihood: -111665.946813
EM: Round [58] log likelihood: -111665.942777
EM: Round [59] log likelihood: -111665.938897
EM: Round [60] log likelihood: -111665.935164
EM: Round [61] log likelihood: -111665.931570
EM: Round [62] log likelihood: -111665.928107
EM: Round [63] log likelihood: -111665.924770
EM: Round [64] log likelihood: -111665.921550
EM: Round [65] log likelihood: -111665.918443
EM: Round [66] log likelihood: -111665.915443
EM: Round [67] log likelihood: -111665.912545
EM: Round [68] log likelihood: -111665.909744
EM: Round [69] log likelihood: -111665.907036
EM: Round [70] log likelihood: -111665.904416
EM: Round [71] log likelihood: -111665.901881
EM: Round [72] log likelihood: -111665.899426
EM: Round [73] log likelihood: -111665.897049
EM: Round [74] log likelihood: -111665.894746
EM: Round [75] log likelihood: -111665.892514
EM: Round [76] log likelihood: -111665.890350
EM: Round [77] log likelihood: -111665.888252
EM: Round [78] log likelihood: -111665.886217
EM: Round [79] log likelihood: -111665.884242
EM: Round [80] log likelihood: -111665.882325
EM: Round [81] log likelihood: -111665.880465
EM: Round [82] log likelihood: -111665.878658
EM: Round [83] log likelihood: -111665.876903
EM: Round [84] log likelihood: -111665.875199
EM: Round [85] log likelihood: -111665.873543
EM: Round [86] log likelihood: -111665.871934
EM: Round [87] log likelihood: -111665.870370
EM: Round [88] log likelihood: -111665.868849
EM: Round [89] log likelihood: -111665.867371
EM: Round [90] log likelihood: -111665.865933
EM: Round [91] log likelihood: -111665.864535
EM: Round [92] log likelihood: -111665.863175
EM: Round [93] log likelihood: -111665.861852
EM: Round [94] log likelihood: -111665.860564
EM: Round [95] log likelihood: -111665.859312
EM: Round [96] log likelihood: -111665.858093
EM: Round [97] log likelihood: -111665.856906
EM: Round [98] log likelihood: -111665.855751
EM: Round [99] log likelihood: -111665.854627
EM: Round [100] log likelihood: -111665.853532
EM: Round [101] log likelihood: -111665.852467
EM: Round [102] log likelihood: -111665.851429
EM: Round [103] log likelihood: -111665.850418
EM: Round [104] log likelihood: -111665.849434
EM: Round [105] log likelihood: -111665.848476
EM: Round [106] log likelihood: -111665.847542
EM: Round [107] log likelihood: -111665.846633
EM: Round [108] log likelihood: -111665.845747
EM: Round [109] log likelihood: -111665.844884
EM: Round [110] log likelihood: -111665.844043
EM: Round [111] log likelihood: -111665.843223
EM: Round [112] log likelihood: -111665.842425
EM: Round [113] log likelihood: -111665.841647
EM: Round [114] log likelihood: -111665.840889
EM: Round [115] log likelihood: -111665.840151
EM: Round [116] log likelihood: -111665.839431
EM: Round [117] log likelihood: -111665.838730
EM: Round [118] log likelihood: -111665.838046
EM: Round [119] log likelihood: -111665.837379
EM: Round [120] log likelihood: -111665.836730
EM: Round [121] log likelihood: -111665.836097
EM: Round [122] log likelihood: -111665.835480
EM: Round [123] log likelihood: -111665.834878
EM: Round [124] log likelihood: -111665.834292
EM: Round [125] log likelihood: -111665.833720
EM: Round [126] log likelihood: -111665.833163
EM: Round [127] log likelihood: -111665.832620
EM: Round [128] log likelihood: -111665.832090
EM: Round [129] log likelihood: -111665.831574
EM: Round [130] log likelihood: -111665.831070
EM: Round [131] log likelihood: -111665.830580
EM: Round [132] log likelihood: -111665.830101
EM: Round [133] log likelihood: -111665.829634
EM: Round [134] log likelihood: -111665.829179
EM: Round [135] log likelihood: -111665.828736
EM: Round [136] log likelihood: -111665.828303
EM: Round [137] log likelihood: -111665.827882
EM: Round [138] log likelihood: -111665.827470
EM: Round [139] log likelihood: -111665.827069
EM: Round [140] log likelihood: -111665.826678
EM: Round [141] log likelihood: -111665.826297
EM: Round [142] log likelihood: -111665.825925
EM: Round [143] log likelihood: -111665.825562
EM: Round [144] log likelihood: -111665.825209
EM: Round [145] log likelihood: -111665.824864
EM: Round [146] log likelihood: -111665.824527
EM: Round [147] log likelihood: -111665.824199
EM: Round [148] log likelihood: -111665.823879
EM: Round [149] log likelihood: -111665.823567
EM: Round [150] log likelihood: -111665.823263
EM: Round [151] log likelihood: -111665.822966
EM: Round [152] log likelihood: -111665.822677
EM: Round [153] log likelihood: -111665.822395
EM: Round [154] log likelihood: -111665.822119
EM: Round [155] log likelihood: -111665.821851
EM: Round [156] log likelihood: -111665.821589
EM: Round [157] log likelihood: -111665.821334
EM: Round [158] log likelihood: -111665.821085
EM: Round [159] log likelihood: -111665.820842
EM: Round [160] log likelihood: -111665.820605
EM: Round [161] log likelihood: -111665.820374
EM: Round [162] log likelihood: -111665.820148
EM: Round [163] log likelihood: -111665.819928
EM: Round [164] log likelihood: -111665.819714
EM: Round [165] log likelihood: -111665.819505
EM: Round [166] log likelihood: -111665.819301
EM: Round [167] log likelihood: -111665.819102
EM: Round [168] log likelihood: -111665.818907
EM: Round [169] log likelihood: -111665.818718
EM: Round [170] log likelihood: -111665.818533
EM: Round [171] log likelihood: -111665.818353
EM: Round [172] log likelihood: -111665.818177
EM: Round [173] log likelihood: -111665.818006
EM: Round [174] log likelihood: -111665.817839
EM: Round [175] log likelihood: -111665.817676
EM: Round [176] log likelihood: -111665.817517
EM: Round [177] log likelihood: -111665.817361
EM: Round [178] log likelihood: -111665.817210
EM: Round [179] log likelihood: -111665.817062
EM: Round [180] log likelihood: -111665.816918
EM: Round [181] log likelihood: -111665.816778
EM: Round [182] log likelihood: -111665.816641
EM: Round [183] log likelihood: -111665.816507
EM: Round [184] log likelihood: -111665.816377
EM: Round [185] log likelihood: -111665.816250
EM: Round [186] log likelihood: -111665.816125
EM: Round [187] log likelihood: -111665.816004
EM: Round [188] log likelihood: -111665.815886
EM: Round [189] log likelihood: -111665.815771
EM: Round [190] log likelihood: -111665.815659
EM: Round [191] log likelihood: -111665.815549
EM: Round [192] log likelihood: -111665.815442
EM: Round [193] log likelihood: -111665.815338
EM: Round [194] log likelihood: -111665.815236
EM: Round [195] log likelihood: -111665.815137
EM: Stopping iterations at round 195 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.CXw1DMFg3x/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.CXw1DMFg3x/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.CXw1DMFg3x/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.CXw1DMFg3x/./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.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.CXw1DMFg3x/./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.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 164779021 > /tmp/nxf.CXw1DMFg3x/./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.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.CXw1DMFg3x/ctat_genome_lib_build_dir > /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.CXw1DMFg3x/ctat_genome_lib_build_dir --annotate /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.CXw1DMFg3x/./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.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.CXw1DMFg3x/ctat_genome_lib_build_dir
-done, see /tmp/nxf.CXw1DMFg3x/./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.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.CXw1DMFg3x/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 1262, filtered: 7454)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.CXw1DMFg3x/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.CXw1DMFg3x/./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.CXw1DMFg3x/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000237296.9]
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WARNING, no entry stored in dbm for [IGH.g@-ext]
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WARNING, no entry stored in dbm for [IGH.g@-ext]
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WARNING, no entry stored in dbm for [ENSG00000236456.1]
WARNING, no entry stored in dbm for [ENSG00000279968.3]
WARNING, no entry stored in dbm for [ENSG00000261432.1]
WARNING, no entry stored in dbm for [ENSG00000249237.5]
WARNING, no entry stored in dbm for [ENSG00000284240.1]
WARNING, no entry stored in dbm for [ENSG00000239482.6]
WARNING, no entry stored in dbm for [ENSG00000188511.12]
WARNING, no entry stored in dbm for [ENSG00000188511.12]
WARNING, no entry stored in dbm for [ENSG00000280424.1]
WARNING, no entry stored in dbm for [ENSG00000216657.1]
WARNING, no entry stored in dbm for [ENSG00000228549.4]
WARNING, no entry stored in dbm for [ENSG00000249072.1]
WARNING, no entry stored in dbm for [ENSG00000232466.1]
WARNING, no entry stored in dbm for [ENSG00000237238.3]
WARNING, no entry stored in dbm for [ENSG00000237238.3]
WARNING, no entry stored in dbm for [ENSG00000204960.7]
WARNING, no entry stored in dbm for [ENSG00000204960.7]
WARNING, no entry stored in dbm for [ENSG00000238153.1]
WARNING, no entry stored in dbm for [ENSG00000275110.1]
WARNING, no entry stored in dbm for [ENSG00000158482.10]
WARNING, no entry stored in dbm for [ENSG00000265927.1]
WARNING, no entry stored in dbm for [ENSG00000272578.5]
WARNING, no entry stored in dbm for [ENSG00000253816.3]
WARNING, no entry stored in dbm for [ENSG00000234353.2]
WARNING, no entry stored in dbm for [ENSG00000284428.1]
WARNING, no entry stored in dbm for [ENSG00000196796.5]
WARNING, no entry stored in dbm for [ENSG00000259516.2]
WARNING, no entry stored in dbm for [ENSG00000249493.1]
WARNING, no entry stored in dbm for [ENSG00000206192.7]
WARNING, no entry stored in dbm for [ENSG00000280128.1]
WARNING, no entry stored in dbm for [ENSG00000284999.1]
WARNING, no entry stored in dbm for [ENSG00000225087.2]
WARNING, no entry stored in dbm for [ENSG00000238260.1]
WARNING, no entry stored in dbm for [ENSG00000261641.2]
WARNING, no entry stored in dbm for [ENSG00000204049.1]
WARNING, no entry stored in dbm for [ENSG00000259078.2]
WARNING, no entry stored in dbm for [ENSG00000286215.1]
WARNING, no entry stored in dbm for [ENSG00000237480.3]
WARNING, no entry stored in dbm for [ENSG00000259723.1]
WARNING, no entry stored in dbm for [ENSG00000250979.1]
WARNING, no entry stored in dbm for [ENSG00000285671.1]
WARNING, no entry stored in dbm for [ENSG00000283384.1]
WARNING, no entry stored in dbm for [ENSG00000225956.1]
WARNING, no entry stored in dbm for [ENSG00000236740.6]
WARNING, no entry stored in dbm for [ENSG00000230912.1]
WARNING, no entry stored in dbm for [ENSG00000215022.7]
WARNING, no entry stored in dbm for [ENSG00000272109.2]
WARNING, no entry stored in dbm for [ENSG00000251441.3]
WARNING, no entry stored in dbm for [ENSG00000223745.8]
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 [ENSG00000286502.1]
WARNING, no entry stored in dbm for [ENSG00000223804.5]
WARNING, no entry stored in dbm for [ENSG00000223779.6]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000281741.2]
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 [ENSG00000261273.1]
WARNING, no entry stored in dbm for [ENSG00000260413.1]
WARNING, no entry stored in dbm for [ENSG00000278212.2]
WARNING, no entry stored in dbm for [ENSG00000278212.2]
WARNING, no entry stored in dbm for [ENSG00000278212.2]
WARNING, no entry stored in dbm for [ENSG00000283345.1]
WARNING, no entry stored in dbm for [ENSG00000215302.8]
WARNING, no entry stored in dbm for [ENSG00000215302.8]
WARNING, no entry stored in dbm for [ENSG00000280033.1]
WARNING, no entry stored in dbm for [ENSG00000266145.1]
WARNING, no entry stored in dbm for [ENSG00000287126.1]
WARNING, no entry stored in dbm for [ENSG00000277332.1]
WARNING, no entry stored in dbm for [ENSG00000251600.8]
WARNING, no entry stored in dbm for [ENSG00000251600.8]
WARNING, no entry stored in dbm for [ENSG00000245768.7]
WARNING, no entry stored in dbm for [ENSG00000250159.7]
WARNING, no entry stored in dbm for [ENSG00000232555.2]
WARNING, no entry stored in dbm for [ENSG00000259692.6]
WARNING, no entry stored in dbm for [ENSG00000250979.1]
WARNING, no entry stored in dbm for [ENSG00000259692.6]
WARNING, no entry stored in dbm for [ENSG00000250979.1]
WARNING, no entry stored in dbm for [ENSG00000228999.4]
WARNING, no entry stored in dbm for [ENSG00000249001.5]
WARNING, no entry stored in dbm for [ENSG00000245059.2]
WARNING, no entry stored in dbm for [ENSG00000224016.2]
WARNING, no entry stored in dbm for [ENSG00000276538.1]
WARNING, no entry stored in dbm for [ENSG00000288002.1]
WARNING, no entry stored in dbm for [ENSG00000240519.1]
WARNING, no entry stored in dbm for [ENSG00000218175.2]
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 [ENSG00000267198.1]
WARNING, no entry stored in dbm for [ENSG00000264164.1]
WARNING, no entry stored in dbm for [ENSG00000257410.1]
WARNING, no entry stored in dbm for [ENSG00000273329.1]
WARNING, no entry stored in dbm for [ENSG00000283537.2]
WARNING, no entry stored in dbm for [ENSG00000259589.2]
WARNING, no entry stored in dbm for [ENSG00000204814.5]
WARNING, no entry stored in dbm for [ENSG00000259433.2]
WARNING, no entry stored in dbm for [ENSG00000254951.7]
WARNING, no entry stored in dbm for [ENSG00000260018.1]
WARNING, no entry stored in dbm for [ENSG00000261528.2]
WARNING, no entry stored in dbm for [ENSG00000257817.2]
WARNING, no entry stored in dbm for [ENSG00000258732.1]
WARNING, no entry stored in dbm for [ENSG00000180229.12]
WARNING, no entry stored in dbm for [ENSG00000251131.2]
WARNING, no entry stored in dbm for [ENSG00000259429.5]
WARNING, no entry stored in dbm for [ENSG00000288082.1]
WARNING, no entry stored in dbm for [ENSG00000225885.7]
WARNING, no entry stored in dbm for [ENSG00000240669.1]
WARNING, no entry stored in dbm for [ENSG00000272140.2]
WARNING, no entry stored in dbm for [ENSG00000272140.2]
WARNING, no entry stored in dbm for [ENSG00000272140.2]
WARNING, no entry stored in dbm for [ENSG00000251079.6]
WARNING, no entry stored in dbm for [ENSG00000240418.1]
WARNING, no entry stored in dbm for [ENSG00000174171.6]
WARNING, no entry stored in dbm for [ENSG00000253792.1]
WARNING, no entry stored in dbm for [ENSG00000213963.6]
WARNING, no entry stored in dbm for [ENSG00000279069.1]
WARNING, no entry stored in dbm for [ENSG00000245532.9]
WARNING, no entry stored in dbm for [ENSG00000271018.1]
WARNING, no entry stored in dbm for [ENSG00000224237.1]
WARNING, no entry stored in dbm for [ENSG00000222017.1]
WARNING, no entry stored in dbm for [ENSG00000250979.1]
WARNING, no entry stored in dbm for [ENSG00000274895.1]
WARNING, no entry stored in dbm for [ENSG00000253706.5]
WARNING, no entry stored in dbm for [ENSG00000257890.1]
WARNING, no entry stored in dbm for [ENSG00000249839.1]
WARNING, no entry stored in dbm for [ENSG00000249839.1]
WARNING, no entry stored in dbm for [ENSG00000286481.1]
WARNING, no entry stored in dbm for [ENSG00000287741.1]
WARNING, no entry stored in dbm for [ENSG00000272372.1]
WARNING, no entry stored in dbm for [ENSG00000251441.3]
WARNING, no entry stored in dbm for [ENSG00000176593.8]
WARNING, no entry stored in dbm for [ENSG00000257403.2]
WARNING, no entry stored in dbm for [ENSG00000189149.12]
WARNING, no entry stored in dbm for [ENSG00000248560.1]
WARNING, no entry stored in dbm for [ENSG00000230189.7]
WARNING, no entry stored in dbm for [ENSG00000236886.2]
WARNING, no entry stored in dbm for [ENSG00000233143.2]
WARNING, no entry stored in dbm for [ENSG00000229180.7]
WARNING, no entry stored in dbm for [ENSG00000274712.2]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000262298.1]
WARNING, no entry stored in dbm for [ENSG00000179978.11]
WARNING, no entry stored in dbm for [ENSG00000287093.1]
WARNING, no entry stored in dbm for [ENSG00000256069.7]
WARNING, no entry stored in dbm for [ENSG00000225292.2]
* STAR-Fusion complete. See output: /tmp/nxf.CXw1DMFg3x/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)