-ctat genome lib [/tmp/nxf.QWf9QWhOpP/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.QWf9QWhOpP/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary
-sample contains 45127756 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.QWf9QWhOpP/ctat_genome_lib_build_dir -J /tmp/nxf.QWf9QWhOpP/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.QWf9QWhOpP/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.QWf9QWhOpP/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
[10000], rate=100000.00/min
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[980000], rate=84848.48/min -building interval tree based on /tmp/nxf.QWf9QWhOpP/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
[10000], rate=50000.00/min
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[30000], rate=58064.52/min
[40000], rate=63157.89/min
[50000], rate=63829.79/min
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[100000], rate=53097.35/min
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[970000], rate=78436.66/min
[980000], rate=77880.79/min -building interval tree based on /tmp/nxf.QWf9QWhOpP/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
[10000], rate=40000.00/min
[20000], rate=46153.85/min
[30000], rate=45000.00/min
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[970000], rate=66438.36/min
[980000], rate=66591.17/min -building interval tree based on /tmp/nxf.QWf9QWhOpP/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes
[10000], rate=46153.85/min
[20000], rate=50000.00/min
[30000], rate=52941.18/min
[40000], rate=54545.45/min
[50000], rate=54545.45/min
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[100000], rate=60606.06/min
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[820000], rate=61500.00/min
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[840000], rate=61840.49/min
[850000], rate=62043.80/min
[860000], rate=62168.67/min
[870000], rate=62440.19/min
[880000], rate=63007.16/min
[890000], rate=63345.20/min
[900000], rate=63529.41/min
[910000], rate=63710.62/min
[920000], rate=63448.28/min
[930000], rate=63050.85/min
[940000], rate=62736.37/min
[950000], rate=62295.08/min
[960000], rate=62337.66/min
[970000], rate=62046.91/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.QWf9QWhOpP/ctat_genome_lib_build_dir --filt_file /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.QWf9QWhOpP/./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...
9000000.00 reads per min processed...
12000000.00 reads per min processed...
10000000.00 reads per min processed...
9000000.00 reads per min processed...
7000000.00 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
5500000.00 reads per min processed...
5142857.14 reads per min processed...
5200000.00 reads per min processed...
4941176.47 reads per min processed...
4736842.11 reads per min processed...
4571428.57 reads per min processed...
4636363.64 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...
4888888.89 reads per min processed...
4928571.43 reads per min processed...
4965517.24 reads per min processed...
5000000.00 reads per min processed...
5032258.06 reads per min processed...
4909090.91 reads per min processed...
4941176.47 reads per min processed...
4833333.33 reads per min processed...
4864864.86 reads per min processed...
4894736.84 reads per min processed...
4800000.00 reads per min processed...
4829268.29 reads per min processed...
4857142.86 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.QWf9QWhOpP/BreastNB_FFPE_L01_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.QWf9QWhOpP/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -64171.726154
EM: Round [1] log likelihood: -63942.802738
EM: Round [2] log likelihood: -63854.260197
EM: Round [3] log likelihood: -63811.319613
EM: Round [4] log likelihood: -63788.390622
EM: Round [5] log likelihood: -63775.514365
EM: Round [6] log likelihood: -63767.976701
EM: Round [7] log likelihood: -63763.369408
EM: Round [8] log likelihood: -63760.425295
EM: Round [9] log likelihood: -63758.461434
EM: Round [10] log likelihood: -63757.098859
EM: Round [11] log likelihood: -63756.119987
EM: Round [12] log likelihood: -63755.395271
EM: Round [13] log likelihood: -63754.844732
EM: Round [14] log likelihood: -63754.417241
EM: Round [15] log likelihood: -63754.079042
EM: Round [16] log likelihood: -63753.807175
EM: Round [17] log likelihood: -63753.585607
EM: Round [18] log likelihood: -63753.402871
EM: Round [19] log likelihood: -63753.250594
EM: Round [20] log likelihood: -63753.122542
EM: Round [21] log likelihood: -63753.013998
EM: Round [22] log likelihood: -63752.921339
EM: Round [23] log likelihood: -63752.841740
EM: Round [24] log likelihood: -63752.772975
EM: Round [25] log likelihood: -63752.713267
EM: Round [26] log likelihood: -63752.661186
EM: Round [27] log likelihood: -63752.615566
EM: Round [28] log likelihood: -63752.575454
EM: Round [29] log likelihood: -63752.540059
EM: Round [30] log likelihood: -63752.508726
EM: Round [31] log likelihood: -63752.480904
EM: Round [32] log likelihood: -63752.456130
EM: Round [33] log likelihood: -63752.434010
EM: Round [34] log likelihood: -63752.414212
EM: Round [35] log likelihood: -63752.396450
EM: Round [36] log likelihood: -63752.380478
EM: Round [37] log likelihood: -63752.366085
EM: Round [38] log likelihood: -63752.353089
EM: Round [39] log likelihood: -63752.341330
EM: Round [40] log likelihood: -63752.330671
EM: Round [41] log likelihood: -63752.320991
EM: Round [42] log likelihood: -63752.312185
EM: Round [43] log likelihood: -63752.304160
EM: Round [44] log likelihood: -63752.296835
EM: Round [45] log likelihood: -63752.290136
EM: Round [46] log likelihood: -63752.284002
EM: Round [47] log likelihood: -63752.278376
EM: Round [48] log likelihood: -63752.273207
EM: Round [49] log likelihood: -63752.268451
EM: Round [50] log likelihood: -63752.264068
EM: Round [51] log likelihood: -63752.260024
EM: Round [52] log likelihood: -63752.256286
EM: Round [53] log likelihood: -63752.252827
EM: Round [54] log likelihood: -63752.249620
EM: Round [55] log likelihood: -63752.246644
EM: Round [56] log likelihood: -63752.243878
EM: Round [57] log likelihood: -63752.241303
EM: Round [58] log likelihood: -63752.238902
EM: Round [59] log likelihood: -63752.236662
EM: Round [60] log likelihood: -63752.234567
EM: Round [61] log likelihood: -63752.232607
EM: Round [62] log likelihood: -63752.230770
EM: Round [63] log likelihood: -63752.229046
EM: Round [64] log likelihood: -63752.227425
EM: Round [65] log likelihood: -63752.225900
EM: Round [66] log likelihood: -63752.224463
EM: Round [67] log likelihood: -63752.223108
EM: Round [68] log likelihood: -63752.221827
EM: Round [69] log likelihood: -63752.220616
EM: Round [70] log likelihood: -63752.219469
EM: Round [71] log likelihood: -63752.218381
EM: Round [72] log likelihood: -63752.217349
EM: Round [73] log likelihood: -63752.216368
EM: Round [74] log likelihood: -63752.215434
EM: Round [75] log likelihood: -63752.214544
EM: Round [76] log likelihood: -63752.213696
EM: Round [77] log likelihood: -63752.212886
EM: Round [78] log likelihood: -63752.212112
EM: Round [79] log likelihood: -63752.211371
EM: Round [80] log likelihood: -63752.210662
EM: Round [81] log likelihood: -63752.209982
EM: Round [82] log likelihood: -63752.209329
EM: Round [83] log likelihood: -63752.208702
EM: Round [84] log likelihood: -63752.208100
EM: Round [85] log likelihood: -63752.207520
EM: Round [86] log likelihood: -63752.206961
EM: Round [87] log likelihood: -63752.206423
EM: Round [88] log likelihood: -63752.205903
EM: Round [89] log likelihood: -63752.205402
EM: Round [90] log likelihood: -63752.204917
EM: Round [91] log likelihood: -63752.204449
EM: Round [92] log likelihood: -63752.203995
EM: Round [93] log likelihood: -63752.203556
EM: Round [94] log likelihood: -63752.203131
EM: Round [95] log likelihood: -63752.202718
EM: Round [96] log likelihood: -63752.202318
EM: Round [97] log likelihood: -63752.201930
EM: Round [98] log likelihood: -63752.201552
EM: Round [99] log likelihood: -63752.201185
EM: Round [100] log likelihood: -63752.200829
EM: Round [101] log likelihood: -63752.200481
EM: Round [102] log likelihood: -63752.200144
EM: Round [103] log likelihood: -63752.199815
EM: Round [104] log likelihood: -63752.199494
EM: Round [105] log likelihood: -63752.199181
EM: Round [106] log likelihood: -63752.198877
EM: Round [107] log likelihood: -63752.198579
EM: Round [108] log likelihood: -63752.198289
EM: Round [109] log likelihood: -63752.198006
EM: Round [110] log likelihood: -63752.197729
EM: Round [111] log likelihood: -63752.197458
EM: Round [112] log likelihood: -63752.197194
EM: Round [113] log likelihood: -63752.196936
EM: Round [114] log likelihood: -63752.196683
EM: Round [115] log likelihood: -63752.196436
EM: Round [116] log likelihood: -63752.196194
EM: Round [117] log likelihood: -63752.195957
EM: Round [118] log likelihood: -63752.195725
EM: Round [119] log likelihood: -63752.195498
EM: Round [120] log likelihood: -63752.195275
EM: Round [121] log likelihood: -63752.195057
EM: Round [122] log likelihood: -63752.194843
EM: Round [123] log likelihood: -63752.194634
EM: Round [124] log likelihood: -63752.194428
EM: Round [125] log likelihood: -63752.194227
EM: Round [126] log likelihood: -63752.194029
EM: Round [127] log likelihood: -63752.193835
EM: Round [128] log likelihood: -63752.193645
EM: Round [129] log likelihood: -63752.193458
EM: Round [130] log likelihood: -63752.193275
EM: Round [131] log likelihood: -63752.193095
EM: Round [132] log likelihood: -63752.192919
EM: Round [133] log likelihood: -63752.192745
EM: Round [134] log likelihood: -63752.192575
EM: Round [135] log likelihood: -63752.192408
EM: Round [136] log likelihood: -63752.192243
EM: Round [137] log likelihood: -63752.192082
EM: Round [138] log likelihood: -63752.191923
EM: Round [139] log likelihood: -63752.191767
EM: Round [140] log likelihood: -63752.191614
EM: Round [141] log likelihood: -63752.191463
EM: Round [142] log likelihood: -63752.191315
EM: Round [143] log likelihood: -63752.191170
EM: Round [144] log likelihood: -63752.191027
EM: Round [145] log likelihood: -63752.190886
EM: Round [146] log likelihood: -63752.190748
EM: Round [147] log likelihood: -63752.190612
EM: Round [148] log likelihood: -63752.190478
EM: Round [149] log likelihood: -63752.190346
EM: Round [150] log likelihood: -63752.190217
EM: Round [151] log likelihood: -63752.190089
EM: Round [152] log likelihood: -63752.189964
EM: Round [153] log likelihood: -63752.189841
EM: Round [154] log likelihood: -63752.189720
EM: Round [155] log likelihood: -63752.189600
EM: Round [156] log likelihood: -63752.189483
EM: Round [157] log likelihood: -63752.189368
EM: Round [158] log likelihood: -63752.189254
EM: Round [159] log likelihood: -63752.189142
EM: Round [160] log likelihood: -63752.189032
EM: Round [161] log likelihood: -63752.188924
EM: Round [162] log likelihood: -63752.188817
EM: Round [163] log likelihood: -63752.188712
EM: Round [164] log likelihood: -63752.188609
EM: Round [165] log likelihood: -63752.188507
EM: Round [166] log likelihood: -63752.188407
EM: Round [167] log likelihood: -63752.188308
EM: Stopping iterations at round 167 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -64101.826272
EM: Round [1] log likelihood: -63899.525753
EM: Round [2] log likelihood: -63824.771062
EM: Round [3] log likelihood: -63789.518744
EM: Round [4] log likelihood: -63771.021082
EM: Round [5] log likelihood: -63760.754679
EM: Round [6] log likelihood: -63754.792379
EM: Round [7] log likelihood: -63751.166157
EM: Round [8] log likelihood: -63748.854991
EM: Round [9] log likelihood: -63747.314496
EM: Round [10] log likelihood: -63746.245102
EM: Round [11] log likelihood: -63745.475911
EM: Round [12] log likelihood: -63744.905630
EM: Round [13] log likelihood: -63744.471878
EM: Round [14] log likelihood: -63744.134804
EM: Round [15] log likelihood: -63743.868064
EM: Round [16] log likelihood: -63743.653698
EM: Round [17] log likelihood: -63743.479125
EM: Round [18] log likelihood: -63743.335314
EM: Round [19] log likelihood: -63743.215647
EM: Round [20] log likelihood: -63743.115184
EM: Round [21] log likelihood: -63743.030175
EM: Round [22] log likelihood: -63742.957734
EM: Round [23] log likelihood: -63742.895611
EM: Round [24] log likelihood: -63742.842030
EM: Round [25] log likelihood: -63742.795575
EM: Round [26] log likelihood: -63742.755107
EM: Round [27] log likelihood: -63742.719701
EM: Round [28] log likelihood: -63742.688598
EM: Round [29] log likelihood: -63742.661174
EM: Round [30] log likelihood: -63742.636911
EM: Round [31] log likelihood: -63742.615375
EM: Round [32] log likelihood: -63742.596202
EM: Round [33] log likelihood: -63742.579086
EM: Round [34] log likelihood: -63742.563764
EM: Round [35] log likelihood: -63742.550016
EM: Round [36] log likelihood: -63742.537649
EM: Round [37] log likelihood: -63742.526500
EM: Round [38] log likelihood: -63742.516427
EM: Round [39] log likelihood: -63742.507308
EM: Round [40] log likelihood: -63742.499036
EM: Round [41] log likelihood: -63742.491518
EM: Round [42] log likelihood: -63742.484673
EM: Round [43] log likelihood: -63742.478430
EM: Round [44] log likelihood: -63742.472725
EM: Round [45] log likelihood: -63742.467503
EM: Round [46] log likelihood: -63742.462716
EM: Round [47] log likelihood: -63742.458321
EM: Round [48] log likelihood: -63742.454278
EM: Round [49] log likelihood: -63742.450553
EM: Round [50] log likelihood: -63742.447117
EM: Round [51] log likelihood: -63742.443942
EM: Round [52] log likelihood: -63742.441004
EM: Round [53] log likelihood: -63742.438280
EM: Round [54] log likelihood: -63742.435753
EM: Round [55] log likelihood: -63742.433403
EM: Round [56] log likelihood: -63742.431216
EM: Round [57] log likelihood: -63742.429177
EM: Round [58] log likelihood: -63742.427273
EM: Round [59] log likelihood: -63742.425493
EM: Round [60] log likelihood: -63742.423827
EM: Round [61] log likelihood: -63742.422265
EM: Round [62] log likelihood: -63742.420798
EM: Round [63] log likelihood: -63742.419419
EM: Round [64] log likelihood: -63742.418121
EM: Round [65] log likelihood: -63742.416897
EM: Round [66] log likelihood: -63742.415742
EM: Round [67] log likelihood: -63742.414650
EM: Round [68] log likelihood: -63742.413617
EM: Round [69] log likelihood: -63742.412638
EM: Round [70] log likelihood: -63742.411709
EM: Round [71] log likelihood: -63742.410826
EM: Round [72] log likelihood: -63742.409987
EM: Round [73] log likelihood: -63742.409188
EM: Round [74] log likelihood: -63742.408426
EM: Round [75] log likelihood: -63742.407699
EM: Round [76] log likelihood: -63742.407004
EM: Round [77] log likelihood: -63742.406339
EM: Round [78] log likelihood: -63742.405703
EM: Round [79] log likelihood: -63742.405093
EM: Round [80] log likelihood: -63742.404507
EM: Round [81] log likelihood: -63742.403945
EM: Round [82] log likelihood: -63742.403405
EM: Round [83] log likelihood: -63742.402885
EM: Round [84] log likelihood: -63742.402384
EM: Round [85] log likelihood: -63742.401901
EM: Round [86] log likelihood: -63742.401435
EM: Round [87] log likelihood: -63742.400985
EM: Round [88] log likelihood: -63742.400550
EM: Round [89] log likelihood: -63742.400129
EM: Round [90] log likelihood: -63742.399722
EM: Round [91] log likelihood: -63742.399328
EM: Round [92] log likelihood: -63742.398946
EM: Round [93] log likelihood: -63742.398575
EM: Round [94] log likelihood: -63742.398216
EM: Round [95] log likelihood: -63742.397866
EM: Round [96] log likelihood: -63742.397527
EM: Round [97] log likelihood: -63742.397197
EM: Round [98] log likelihood: -63742.396876
EM: Round [99] log likelihood: -63742.396563
EM: Round [100] log likelihood: -63742.396259
EM: Round [101] log likelihood: -63742.395962
EM: Round [102] log likelihood: -63742.395673
EM: Round [103] log likelihood: -63742.395391
EM: Round [104] log likelihood: -63742.395116
EM: Round [105] log likelihood: -63742.394848
EM: Round [106] log likelihood: -63742.394586
EM: Round [107] log likelihood: -63742.394329
EM: Round [108] log likelihood: -63742.394079
EM: Round [109] log likelihood: -63742.393834
EM: Round [110] log likelihood: -63742.393595
EM: Round [111] log likelihood: -63742.393361
EM: Round [112] log likelihood: -63742.393132
EM: Round [113] log likelihood: -63742.392907
EM: Round [114] log likelihood: -63742.392688
EM: Round [115] log likelihood: -63742.392473
EM: Round [116] log likelihood: -63742.392262
EM: Round [117] log likelihood: -63742.392055
EM: Round [118] log likelihood: -63742.391853
EM: Round [119] log likelihood: -63742.391655
EM: Round [120] log likelihood: -63742.391460
EM: Round [121] log likelihood: -63742.391269
EM: Round [122] log likelihood: -63742.391082
EM: Round [123] log likelihood: -63742.390898
EM: Round [124] log likelihood: -63742.390718
EM: Round [125] log likelihood: -63742.390540
EM: Round [126] log likelihood: -63742.390367
EM: Round [127] log likelihood: -63742.390196
EM: Round [128] log likelihood: -63742.390028
EM: Round [129] log likelihood: -63742.389864
EM: Round [130] log likelihood: -63742.389702
EM: Round [131] log likelihood: -63742.389543
EM: Round [132] log likelihood: -63742.389387
EM: Round [133] log likelihood: -63742.389233
EM: Round [134] log likelihood: -63742.389082
EM: Round [135] log likelihood: -63742.388934
EM: Round [136] log likelihood: -63742.388788
EM: Round [137] log likelihood: -63742.388644
EM: Round [138] log likelihood: -63742.388503
EM: Round [139] log likelihood: -63742.388365
EM: Round [140] log likelihood: -63742.388228
EM: Round [141] log likelihood: -63742.388094
EM: Round [142] log likelihood: -63742.387962
EM: Round [143] log likelihood: -63742.387832
EM: Round [144] log likelihood: -63742.387705
EM: Round [145] log likelihood: -63742.387579
EM: Round [146] log likelihood: -63742.387455
EM: Round [147] log likelihood: -63742.387333
EM: Round [148] log likelihood: -63742.387214
EM: Round [149] log likelihood: -63742.387096
EM: Round [150] log likelihood: -63742.386980
EM: Round [151] log likelihood: -63742.386865
EM: Round [152] log likelihood: -63742.386753
EM: Round [153] log likelihood: -63742.386642
EM: Round [154] log likelihood: -63742.386533
EM: Round [155] log likelihood: -63742.386426
EM: Round [156] log likelihood: -63742.386321
EM: Round [157] log likelihood: -63742.386217
EM: Round [158] log likelihood: -63742.386114
EM: Round [159] log likelihood: -63742.386013
EM: Round [160] log likelihood: -63742.385914
EM: Stopping iterations at round 160 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.QWf9QWhOpP/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.QWf9QWhOpP/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.QWf9QWhOpP/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.QWf9QWhOpP/./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.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.QWf9QWhOpP/./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.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 45127756 > /tmp/nxf.QWf9QWhOpP/./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.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.QWf9QWhOpP/ctat_genome_lib_build_dir > /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.QWf9QWhOpP/ctat_genome_lib_build_dir --annotate /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.QWf9QWhOpP/./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.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.QWf9QWhOpP/ctat_genome_lib_build_dir
-done, see /tmp/nxf.QWf9QWhOpP/./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.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.QWf9QWhOpP/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 325, filtered: 3525)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.QWf9QWhOpP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.QWf9QWhOpP/./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.QWf9QWhOpP/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000234715.2]
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WARNING, no entry stored in dbm for [ENSG00000282458.1]
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WARNING, no entry stored in dbm for [ENSG00000229960.1]
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WARNING, no entry stored in dbm for [ENSG00000275014.1]
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WARNING, no entry stored in dbm for [ENSG00000224897.8]
WARNING, no entry stored in dbm for [ENSG00000275131.3]
WARNING, no entry stored in dbm for [ENSG00000254094.1]
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WARNING, no entry stored in dbm for [ENSG00000243961.2]
WARNING, no entry stored in dbm for [ENSG00000214428.3]
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WARNING, no entry stored in dbm for [ENSG00000236051.7]
WARNING, no entry stored in dbm for [ENSG00000233117.4]
WARNING, no entry stored in dbm for [ENSG00000255052.5]
WARNING, no entry stored in dbm for [ENSG00000254661.3]
WARNING, no entry stored in dbm for [ENSG00000266192.3]
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WARNING, no entry stored in dbm for [ENSG00000226287.8]
WARNING, no entry stored in dbm for [ENSG00000279464.1]
WARNING, no entry stored in dbm for [ENSG00000286328.1]
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WARNING, no entry stored in dbm for [ENSG00000204241.8]
WARNING, no entry stored in dbm for [ENSG00000255344.2]
WARNING, no entry stored in dbm for [ENSG00000275340.1]
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WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000267779.7]
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WARNING, no entry stored in dbm for [ENSG00000233930.4]
WARNING, no entry stored in dbm for [ENSG00000286948.1]
WARNING, no entry stored in dbm for [ENSG00000228666.1]
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WARNING, no entry stored in dbm for [ENSG00000234222.6]
WARNING, no entry stored in dbm for [ENSG00000285219.2]
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WARNING, no entry stored in dbm for [ENSG00000285700.1]
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WARNING, no entry stored in dbm for [ENSG00000181126.13]
WARNING, no entry stored in dbm for [ENSG00000261764.1]
WARNING, no entry stored in dbm for [ENSG00000281344.1]
WARNING, no entry stored in dbm for [ENSG00000271952.2]
WARNING, no entry stored in dbm for [ENSG00000225978.3]
WARNING, no entry stored in dbm for [ENSG00000248587.8]
WARNING, no entry stored in dbm for [ENSG00000233695.2]
WARNING, no entry stored in dbm for [ENSG00000214353.8]
WARNING, no entry stored in dbm for [ENSG00000230937.12]
WARNING, no entry stored in dbm for [ENSG00000227288.3]
WARNING, no entry stored in dbm for [ENSG00000281383.1]
WARNING, no entry stored in dbm for [ENSG00000280800.1]
WARNING, no entry stored in dbm for [ENSG00000281181.1]
WARNING, no entry stored in dbm for [ENSG00000280614.1]
WARNING, no entry stored in dbm for [ENSG00000227220.1]
WARNING, no entry stored in dbm for [ENSG00000232944.1]
WARNING, no entry stored in dbm for [ENSG00000228184.1]
WARNING, no entry stored in dbm for [ENSG00000237870.6]
WARNING, no entry stored in dbm for [ENSG00000283103.3]
WARNING, no entry stored in dbm for [ENSG00000270938.1]
WARNING, no entry stored in dbm for [ENSG00000264589.4]
WARNING, no entry stored in dbm for [ENSG00000279954.1]
WARNING, no entry stored in dbm for [ENSG00000205534.6]
WARNING, no entry stored in dbm for [ENSG00000206585.1]
WARNING, no entry stored in dbm for [ENSG00000270722.1]
WARNING, no entry stored in dbm for [ENSG00000273768.1]
WARNING, no entry stored in dbm for [ENSG00000206737.1]
WARNING, no entry stored in dbm for [ENSG00000207389.1]
WARNING, no entry stored in dbm for [ENSG00000207513.1]
WARNING, no entry stored in dbm for [ENSG00000206588.1]
WARNING, no entry stored in dbm for [ENSG00000206596.1]
WARNING, no entry stored in dbm for [ENSG00000207005.1]
WARNING, no entry stored in dbm for [ENSG00000206652.1]
WARNING, no entry stored in dbm for [ENSG00000257252.6]
WARNING, no entry stored in dbm for [ENSG00000231188.1]
WARNING, no entry stored in dbm for [ENSG00000260896.6]
WARNING, no entry stored in dbm for [ENSG00000284639.1]
WARNING, no entry stored in dbm for [ENSG00000248618.1]
WARNING, no entry stored in dbm for [ENSG00000277878.1]
WARNING, no entry stored in dbm for [ENSG00000274502.1]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000226149.6]
WARNING, no entry stored in dbm for [ENSG00000280281.1]
WARNING, no entry stored in dbm for [ENSG00000260532.1]
WARNING, no entry stored in dbm for [ENSG00000229124.7]
WARNING, no entry stored in dbm for [ENSG00000287619.1]
WARNING, no entry stored in dbm for [ENSG00000260081.2]
WARNING, no entry stored in dbm for [ENSG00000231713.2]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
WARNING, no entry stored in dbm for [ENSG00000240197.1]
WARNING, no entry stored in dbm for [ENSG00000261499.2]
WARNING, no entry stored in dbm for [ENSG00000215158.9]
WARNING, no entry stored in dbm for [ENSG00000259993.1]
WARNING, no entry stored in dbm for [ENSG00000261012.2]
WARNING, no entry stored in dbm for [ENSG00000247193.3]
WARNING, no entry stored in dbm for [ENSG00000244184.1]
WARNING, no entry stored in dbm for [ENSG00000213280.2]
WARNING, no entry stored in dbm for [ENSG00000267408.1]
WARNING, no entry stored in dbm for [ENSG00000229212.8]
WARNING, no entry stored in dbm for [ENSG00000259540.1]
WARNING, no entry stored in dbm for [ENSG00000266313.2]
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 [ENSG00000205682.2]
WARNING, no entry stored in dbm for [ENSG00000205682.2]
WARNING, no entry stored in dbm for [ENSG00000286970.1]
WARNING, no entry stored in dbm for [ENSG00000287381.1]
WARNING, no entry stored in dbm for [ENSG00000225840.2]
WARNING, no entry stored in dbm for [ENSG00000285608.1]
WARNING, no entry stored in dbm for [ENSG00000224629.1]
WARNING, no entry stored in dbm for [ENSG00000244398.1]
WARNING, no entry stored in dbm for [ENSG00000179571.10]
WARNING, no entry stored in dbm for [ENSG00000179571.10]
* STAR-Fusion complete. See output: /tmp/nxf.QWf9QWhOpP/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)