-ctat genome lib [/tmp/nxf.xNMr3uLxMe/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.xNMr3uLxMe/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary
-sample contains 51988336 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.xNMr3uLxMe/ctat_genome_lib_build_dir -J /tmp/nxf.xNMr3uLxMe/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.xNMr3uLxMe/HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.xNMr3uLxMe/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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[1230000], rate=94736.84/min -building interval tree based on /tmp/nxf.xNMr3uLxMe/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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[1220000], rate=86524.82/min -building interval tree based on /tmp/nxf.xNMr3uLxMe/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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[1220000], rate=77052.63/min -building interval tree based on /tmp/nxf.xNMr3uLxMe/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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[1210000], rate=65229.11/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.xNMr3uLxMe/ctat_genome_lib_build_dir --filt_file /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.
6000000.00 reads per min processed...
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7500000.00 reads per min processed...
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8400000.00 reads per min processed...
6857142.86 reads per min processed...
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5538461.54 reads per min processed...
5571428.57 reads per min processed...
5600000.00 reads per min processed...
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4909090.91 reads per min processed...
4750000.00 reads per min processed...
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5166666.67 reads per min processed...
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5066666.67 reads per min processed...
5086956.52 reads per min processed...
5000000.00 reads per min processed...
5020408.16 reads per min processed...
5040000.00 reads per min processed...
4961538.46 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.xNMr3uLxMe/HeadNeckN_FFPE_L04_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.xNMr3uLxMe/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -77619.789562
EM: Round [1] log likelihood: -77430.461392
EM: Round [2] log likelihood: -77356.110290
EM: Round [3] log likelihood: -77320.047110
EM: Round [4] log likelihood: -77300.730398
EM: Round [5] log likelihood: -77289.799937
EM: Round [6] log likelihood: -77283.331989
EM: Round [7] log likelihood: -77279.332290
EM: Round [8] log likelihood: -77276.750221
EM: Round [9] log likelihood: -77275.015751
EM: Round [10] log likelihood: -77273.809060
EM: Round [11] log likelihood: -77272.943911
EM: Round [12] log likelihood: -77272.307626
EM: Round [13] log likelihood: -77271.829462
EM: Round [14] log likelihood: -77271.463458
EM: Round [15] log likelihood: -77271.178819
EM: Round [16] log likelihood: -77270.954351
EM: Round [17] log likelihood: -77270.775121
EM: Round [18] log likelihood: -77270.630394
EM: Round [19] log likelihood: -77270.512319
EM: Round [20] log likelihood: -77270.415067
EM: Round [21] log likelihood: -77270.334254
EM: Round [22] log likelihood: -77270.266543
EM: Round [23] log likelihood: -77270.209367
EM: Round [24] log likelihood: -77270.160734
EM: Round [25] log likelihood: -77270.119083
EM: Round [26] log likelihood: -77270.083180
EM: Round [27] log likelihood: -77270.052043
EM: Round [28] log likelihood: -77270.024886
EM: Round [29] log likelihood: -77270.001071
EM: Round [30] log likelihood: -77269.980081
EM: Round [31] log likelihood: -77269.961493
EM: Round [32] log likelihood: -77269.944957
EM: Round [33] log likelihood: -77269.930185
EM: Round [34] log likelihood: -77269.916935
EM: Round [35] log likelihood: -77269.905006
EM: Round [36] log likelihood: -77269.894226
EM: Round [37] log likelihood: -77269.884453
EM: Round [38] log likelihood: -77269.875564
EM: Round [39] log likelihood: -77269.867453
EM: Round [40] log likelihood: -77269.860032
EM: Round [41] log likelihood: -77269.853223
EM: Round [42] log likelihood: -77269.846959
EM: Round [43] log likelihood: -77269.841181
EM: Round [44] log likelihood: -77269.835840
EM: Round [45] log likelihood: -77269.830891
EM: Round [46] log likelihood: -77269.826295
EM: Round [47] log likelihood: -77269.822019
EM: Round [48] log likelihood: -77269.818031
EM: Round [49] log likelihood: -77269.814306
EM: Round [50] log likelihood: -77269.810819
EM: Round [51] log likelihood: -77269.807550
EM: Round [52] log likelihood: -77269.804480
EM: Round [53] log likelihood: -77269.801593
EM: Round [54] log likelihood: -77269.798873
EM: Round [55] log likelihood: -77269.796306
EM: Round [56] log likelihood: -77269.793881
EM: Round [57] log likelihood: -77269.791587
EM: Round [58] log likelihood: -77269.789414
EM: Round [59] log likelihood: -77269.787353
EM: Round [60] log likelihood: -77269.785396
EM: Round [61] log likelihood: -77269.783536
EM: Round [62] log likelihood: -77269.781765
EM: Round [63] log likelihood: -77269.780078
EM: Round [64] log likelihood: -77269.778469
EM: Round [65] log likelihood: -77269.776933
EM: Round [66] log likelihood: -77269.775465
EM: Round [67] log likelihood: -77269.774062
EM: Round [68] log likelihood: -77269.772719
EM: Round [69] log likelihood: -77269.771432
EM: Round [70] log likelihood: -77269.770198
EM: Round [71] log likelihood: -77269.769014
EM: Round [72] log likelihood: -77269.767878
EM: Round [73] log likelihood: -77269.766786
EM: Round [74] log likelihood: -77269.765736
EM: Round [75] log likelihood: -77269.764726
EM: Round [76] log likelihood: -77269.763754
EM: Round [77] log likelihood: -77269.762817
EM: Round [78] log likelihood: -77269.761914
EM: Round [79] log likelihood: -77269.761044
EM: Round [80] log likelihood: -77269.760204
EM: Round [81] log likelihood: -77269.759393
EM: Round [82] log likelihood: -77269.758610
EM: Round [83] log likelihood: -77269.757853
EM: Round [84] log likelihood: -77269.757121
EM: Round [85] log likelihood: -77269.756413
EM: Round [86] log likelihood: -77269.755729
EM: Round [87] log likelihood: -77269.755066
EM: Round [88] log likelihood: -77269.754424
EM: Round [89] log likelihood: -77269.753802
EM: Round [90] log likelihood: -77269.753199
EM: Round [91] log likelihood: -77269.752615
EM: Round [92] log likelihood: -77269.752048
EM: Round [93] log likelihood: -77269.751499
EM: Round [94] log likelihood: -77269.750965
EM: Round [95] log likelihood: -77269.750447
EM: Round [96] log likelihood: -77269.749944
EM: Round [97] log likelihood: -77269.749456
EM: Round [98] log likelihood: -77269.748981
EM: Round [99] log likelihood: -77269.748520
EM: Round [100] log likelihood: -77269.748071
EM: Round [101] log likelihood: -77269.747635
EM: Round [102] log likelihood: -77269.747211
EM: Round [103] log likelihood: -77269.746798
EM: Round [104] log likelihood: -77269.746397
EM: Round [105] log likelihood: -77269.746006
EM: Round [106] log likelihood: -77269.745626
EM: Round [107] log likelihood: -77269.745255
EM: Round [108] log likelihood: -77269.744894
EM: Round [109] log likelihood: -77269.744543
EM: Round [110] log likelihood: -77269.744200
EM: Round [111] log likelihood: -77269.743866
EM: Round [112] log likelihood: -77269.743541
EM: Round [113] log likelihood: -77269.743224
EM: Round [114] log likelihood: -77269.742915
EM: Round [115] log likelihood: -77269.742613
EM: Round [116] log likelihood: -77269.742319
EM: Round [117] log likelihood: -77269.742032
EM: Round [118] log likelihood: -77269.741752
EM: Round [119] log likelihood: -77269.741479
EM: Round [120] log likelihood: -77269.741212
EM: Round [121] log likelihood: -77269.740952
EM: Round [122] log likelihood: -77269.740698
EM: Round [123] log likelihood: -77269.740450
EM: Round [124] log likelihood: -77269.740208
EM: Round [125] log likelihood: -77269.739971
EM: Round [126] log likelihood: -77269.739740
EM: Round [127] log likelihood: -77269.739515
EM: Round [128] log likelihood: -77269.739294
EM: Round [129] log likelihood: -77269.739079
EM: Round [130] log likelihood: -77269.738868
EM: Round [131] log likelihood: -77269.738663
EM: Round [132] log likelihood: -77269.738462
EM: Round [133] log likelihood: -77269.738265
EM: Round [134] log likelihood: -77269.738073
EM: Round [135] log likelihood: -77269.737885
EM: Round [136] log likelihood: -77269.737701
EM: Round [137] log likelihood: -77269.737522
EM: Round [138] log likelihood: -77269.737346
EM: Round [139] log likelihood: -77269.737174
EM: Round [140] log likelihood: -77269.737006
EM: Round [141] log likelihood: -77269.736842
EM: Round [142] log likelihood: -77269.736681
EM: Round [143] log likelihood: -77269.736523
EM: Round [144] log likelihood: -77269.736369
EM: Round [145] log likelihood: -77269.736219
EM: Round [146] log likelihood: -77269.736071
EM: Round [147] log likelihood: -77269.735927
EM: Round [148] log likelihood: -77269.735785
EM: Round [149] log likelihood: -77269.735647
EM: Round [150] log likelihood: -77269.735512
EM: Round [151] log likelihood: -77269.735379
EM: Round [152] log likelihood: -77269.735249
EM: Round [153] log likelihood: -77269.735122
EM: Round [154] log likelihood: -77269.734997
EM: Round [155] log likelihood: -77269.734875
EM: Round [156] log likelihood: -77269.734756
EM: Round [157] log likelihood: -77269.734639
EM: Round [158] log likelihood: -77269.734524
EM: Round [159] log likelihood: -77269.734412
EM: Round [160] log likelihood: -77269.734302
EM: Round [161] log likelihood: -77269.734194
EM: Round [162] log likelihood: -77269.734089
EM: Round [163] log likelihood: -77269.733985
EM: Round [164] log likelihood: -77269.733884
EM: Round [165] log likelihood: -77269.733784
EM: Stopping iterations at round 165 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -77556.154605
EM: Round [1] log likelihood: -77388.744313
EM: Round [2] log likelihood: -77326.995134
EM: Round [3] log likelihood: -77298.151737
EM: Round [4] log likelihood: -77283.044835
EM: Round [5] log likelihood: -77274.625060
EM: Round [6] log likelihood: -77269.699843
EM: Round [7] log likelihood: -77266.683704
EM: Round [8] log likelihood: -77264.753729
EM: Round [9] log likelihood: -77263.467778
EM: Round [10] log likelihood: -77262.579604
EM: Round [11] log likelihood: -77261.946782
EM: Round [12] log likelihood: -77261.483753
EM: Round [13] log likelihood: -77261.137202
EM: Round [14] log likelihood: -77260.872763
EM: Round [15] log likelihood: -77260.667584
EM: Round [16] log likelihood: -77260.506048
EM: Round [17] log likelihood: -77260.377223
EM: Round [18] log likelihood: -77260.273292
EM: Round [19] log likelihood: -77260.188565
EM: Round [20] log likelihood: -77260.118832
EM: Round [21] log likelihood: -77260.060936
EM: Round [22] log likelihood: -77260.012478
EM: Round [23] log likelihood: -77259.971614
EM: Round [24] log likelihood: -77259.936915
EM: Round [25] log likelihood: -77259.907260
EM: Round [26] log likelihood: -77259.881763
EM: Round [27] log likelihood: -77259.859716
EM: Round [28] log likelihood: -77259.840551
EM: Round [29] log likelihood: -77259.823809
EM: Round [30] log likelihood: -77259.809115
EM: Round [31] log likelihood: -77259.796160
EM: Round [32] log likelihood: -77259.784691
EM: Round [33] log likelihood: -77259.774496
EM: Round [34] log likelihood: -77259.765398
EM: Round [35] log likelihood: -77259.757250
EM: Round [36] log likelihood: -77259.749926
EM: Round [37] log likelihood: -77259.743319
EM: Round [38] log likelihood: -77259.737341
EM: Round [39] log likelihood: -77259.731912
EM: Round [40] log likelihood: -77259.726968
EM: Round [41] log likelihood: -77259.722451
EM: Round [42] log likelihood: -77259.718311
EM: Round [43] log likelihood: -77259.714507
EM: Round [44] log likelihood: -77259.711001
EM: Round [45] log likelihood: -77259.707760
EM: Round [46] log likelihood: -77259.704757
EM: Round [47] log likelihood: -77259.701967
EM: Round [48] log likelihood: -77259.699367
EM: Round [49] log likelihood: -77259.696940
EM: Round [50] log likelihood: -77259.694667
EM: Round [51] log likelihood: -77259.692536
EM: Round [52] log likelihood: -77259.690531
EM: Round [53] log likelihood: -77259.688642
EM: Round [54] log likelihood: -77259.686858
EM: Round [55] log likelihood: -77259.685170
EM: Round [56] log likelihood: -77259.683570
EM: Round [57] log likelihood: -77259.682051
EM: Round [58] log likelihood: -77259.680606
EM: Round [59] log likelihood: -77259.679228
EM: Round [60] log likelihood: -77259.677914
EM: Round [61] log likelihood: -77259.676658
EM: Round [62] log likelihood: -77259.675456
EM: Round [63] log likelihood: -77259.674304
EM: Round [64] log likelihood: -77259.673199
EM: Round [65] log likelihood: -77259.672137
EM: Round [66] log likelihood: -77259.671116
EM: Round [67] log likelihood: -77259.670133
EM: Round [68] log likelihood: -77259.669186
EM: Round [69] log likelihood: -77259.668273
EM: Round [70] log likelihood: -77259.667391
EM: Round [71] log likelihood: -77259.666539
EM: Round [72] log likelihood: -77259.665715
EM: Round [73] log likelihood: -77259.664918
EM: Round [74] log likelihood: -77259.664147
EM: Round [75] log likelihood: -77259.663399
EM: Round [76] log likelihood: -77259.662675
EM: Round [77] log likelihood: -77259.661972
EM: Round [78] log likelihood: -77259.661290
EM: Round [79] log likelihood: -77259.660628
EM: Round [80] log likelihood: -77259.659985
EM: Round [81] log likelihood: -77259.659360
EM: Round [82] log likelihood: -77259.658753
EM: Round [83] log likelihood: -77259.658162
EM: Round [84] log likelihood: -77259.657588
EM: Round [85] log likelihood: -77259.657029
EM: Round [86] log likelihood: -77259.656485
EM: Round [87] log likelihood: -77259.655955
EM: Round [88] log likelihood: -77259.655439
EM: Round [89] log likelihood: -77259.654936
EM: Round [90] log likelihood: -77259.654446
EM: Round [91] log likelihood: -77259.653969
EM: Round [92] log likelihood: -77259.653504
EM: Round [93] log likelihood: -77259.653050
EM: Round [94] log likelihood: -77259.652607
EM: Round [95] log likelihood: -77259.652176
EM: Round [96] log likelihood: -77259.651755
EM: Round [97] log likelihood: -77259.651344
EM: Round [98] log likelihood: -77259.650943
EM: Round [99] log likelihood: -77259.650552
EM: Round [100] log likelihood: -77259.650170
EM: Round [101] log likelihood: -77259.649797
EM: Round [102] log likelihood: -77259.649433
EM: Round [103] log likelihood: -77259.649077
EM: Round [104] log likelihood: -77259.648730
EM: Round [105] log likelihood: -77259.648391
EM: Round [106] log likelihood: -77259.648059
EM: Round [107] log likelihood: -77259.647736
EM: Round [108] log likelihood: -77259.647419
EM: Round [109] log likelihood: -77259.647110
EM: Round [110] log likelihood: -77259.646808
EM: Round [111] log likelihood: -77259.646513
EM: Round [112] log likelihood: -77259.646225
EM: Round [113] log likelihood: -77259.645943
EM: Round [114] log likelihood: -77259.645667
EM: Round [115] log likelihood: -77259.645398
EM: Round [116] log likelihood: -77259.645134
EM: Round [117] log likelihood: -77259.644876
EM: Round [118] log likelihood: -77259.644624
EM: Round [119] log likelihood: -77259.644378
EM: Round [120] log likelihood: -77259.644137
EM: Round [121] log likelihood: -77259.643901
EM: Round [122] log likelihood: -77259.643671
EM: Round [123] log likelihood: -77259.643445
EM: Round [124] log likelihood: -77259.643225
EM: Round [125] log likelihood: -77259.643009
EM: Round [126] log likelihood: -77259.642798
EM: Round [127] log likelihood: -77259.642591
EM: Round [128] log likelihood: -77259.642389
EM: Round [129] log likelihood: -77259.642191
EM: Round [130] log likelihood: -77259.641997
EM: Round [131] log likelihood: -77259.641808
EM: Round [132] log likelihood: -77259.641622
EM: Round [133] log likelihood: -77259.641441
EM: Round [134] log likelihood: -77259.641263
EM: Round [135] log likelihood: -77259.641089
EM: Round [136] log likelihood: -77259.640919
EM: Round [137] log likelihood: -77259.640752
EM: Round [138] log likelihood: -77259.640589
EM: Round [139] log likelihood: -77259.640429
EM: Round [140] log likelihood: -77259.640273
EM: Round [141] log likelihood: -77259.640120
EM: Round [142] log likelihood: -77259.639970
EM: Round [143] log likelihood: -77259.639823
EM: Round [144] log likelihood: -77259.639679
EM: Round [145] log likelihood: -77259.639538
EM: Round [146] log likelihood: -77259.639400
EM: Round [147] log likelihood: -77259.639265
EM: Round [148] log likelihood: -77259.639132
EM: Round [149] log likelihood: -77259.639002
EM: Round [150] log likelihood: -77259.638875
EM: Round [151] log likelihood: -77259.638751
EM: Round [152] log likelihood: -77259.638629
EM: Round [153] log likelihood: -77259.638509
EM: Round [154] log likelihood: -77259.638392
EM: Round [155] log likelihood: -77259.638277
EM: Round [156] log likelihood: -77259.638165
EM: Round [157] log likelihood: -77259.638055
EM: Round [158] log likelihood: -77259.637947
EM: Round [159] log likelihood: -77259.637841
EM: Round [160] log likelihood: -77259.637737
EM: Round [161] log likelihood: -77259.637635
EM: Round [162] log likelihood: -77259.637535
EM: Stopping iterations at round 162 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.xNMr3uLxMe/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.xNMr3uLxMe/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.xNMr3uLxMe/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.xNMr3uLxMe/./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.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.xNMr3uLxMe/./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.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 51988336 > /tmp/nxf.xNMr3uLxMe/./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.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.xNMr3uLxMe/ctat_genome_lib_build_dir > /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.xNMr3uLxMe/ctat_genome_lib_build_dir --annotate /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.xNMr3uLxMe/./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.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.xNMr3uLxMe/ctat_genome_lib_build_dir
-done, see /tmp/nxf.xNMr3uLxMe/./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.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.xNMr3uLxMe/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 328, filtered: 3850)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.xNMr3uLxMe/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.xNMr3uLxMe/./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.xNMr3uLxMe/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000259020.3]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000203930.12]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000239899.3]
WARNING, no entry stored in dbm for [ENSG00000241175.3]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000229739.4]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000250398.1]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000204177.10]
WARNING, no entry stored in dbm for [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000259315.1]
WARNING, no entry stored in dbm for [ENSG00000273062.1]
WARNING, no entry stored in dbm for [ENSG00000230202.1]
WARNING, no entry stored in dbm for [ENSG00000279714.1]
WARNING, no entry stored in dbm for [ENSG00000279217.1]
WARNING, no entry stored in dbm for [ENSG00000230202.1]
WARNING, no entry stored in dbm for [ENSG00000278433.1]
WARNING, no entry stored in dbm for [ENSG00000237036.5]
WARNING, no entry stored in dbm for [ENSG00000226383.7]
WARNING, no entry stored in dbm for [ENSG00000235782.1]
WARNING, no entry stored in dbm for [ENSG00000184106.8]
WARNING, no entry stored in dbm for [ENSG00000274712.2]
WARNING, no entry stored in dbm for [ENSG00000250995.1]
WARNING, no entry stored in dbm for [ENSG00000228791.8]
WARNING, no entry stored in dbm for [ENSG00000287243.2]
WARNING, no entry stored in dbm for [ENSG00000232973.13]
WARNING, no entry stored in dbm for [ENSG00000272274.2]
WARNING, no entry stored in dbm for [ENSG00000254880.1]
WARNING, no entry stored in dbm for [ENSG00000239332.6]
WARNING, no entry stored in dbm for [ENSG00000235033.7]
WARNING, no entry stored in dbm for [ENSG00000215790.8]
WARNING, no entry stored in dbm for [ENSG00000228948.2]
WARNING, no entry stored in dbm for [ENSG00000235064.1]
WARNING, no entry stored in dbm for [ENSG00000231367.6]
WARNING, no entry stored in dbm for [ENSG00000249096.7]
WARNING, no entry stored in dbm for [ENSG00000196183.5]
WARNING, no entry stored in dbm for [ENSG00000230508.1]
WARNING, no entry stored in dbm for [ENSG00000230559.1]
WARNING, no entry stored in dbm for [ENSG00000222177.1]
WARNING, no entry stored in dbm for [ENSG00000200653.1]
WARNING, no entry stored in dbm for [ENSG00000222177.1]
WARNING, no entry stored in dbm for [ENSG00000201342.1]
WARNING, no entry stored in dbm for [ENSG00000239437.3]
WARNING, no entry stored in dbm for [ENSG00000240863.3]
WARNING, no entry stored in dbm for [ENSG00000276047.1]
WARNING, no entry stored in dbm for [ENSG00000241529.3]
WARNING, no entry stored in dbm for [ENSG00000239710.3]
WARNING, no entry stored in dbm for [ENSG00000241665.3]
WARNING, no entry stored in dbm for [ENSG00000239702.3]
WARNING, no entry stored in dbm for [ENSG00000241665.3]
WARNING, no entry stored in dbm for [ENSG00000275014.1]
WARNING, no entry stored in dbm for [ENSG00000248360.7]
WARNING, no entry stored in dbm for [ENSG00000272195.1]
WARNING, no entry stored in dbm for [ENSG00000287356.1]
WARNING, no entry stored in dbm for [ENSG00000286599.1]
WARNING, no entry stored in dbm for [ENSG00000249655.1]
WARNING, no entry stored in dbm for [ENSG00000257634.1]
WARNING, no entry stored in dbm for [ENSG00000183242.12]
WARNING, no entry stored in dbm for [ENSG00000184669.9]
WARNING, no entry stored in dbm for [ENSG00000232728.1]
WARNING, no entry stored in dbm for [ENSG00000281903.2]
WARNING, no entry stored in dbm for [ENSG00000225271.1]
WARNING, no entry stored in dbm for [ENSG00000259192.1]
WARNING, no entry stored in dbm for [ENSG00000230202.1]
WARNING, no entry stored in dbm for [ENSG00000283907.1]
WARNING, no entry stored in dbm for [ENSG00000227765.4]
WARNING, no entry stored in dbm for [ENSG00000078319.10]
WARNING, no entry stored in dbm for [ENSG00000251562.8]
WARNING, no entry stored in dbm for [ENSG00000214141.4]
WARNING, no entry stored in dbm for [ENSG00000251513.2]
WARNING, no entry stored in dbm for [ENSG00000250331.2]
WARNING, no entry stored in dbm for [ENSG00000205056.8]
WARNING, no entry stored in dbm for [ENSG00000249655.1]
WARNING, no entry stored in dbm for [ENSG00000258819.2]
WARNING, no entry stored in dbm for [ENSG00000237222.4]
WARNING, no entry stored in dbm for [ENSG00000267308.3]
WARNING, no entry stored in dbm for [ENSG00000275807.1]
WARNING, no entry stored in dbm for [ENSG00000232100.1]
WARNING, no entry stored in dbm for [ENSG00000237491.10]
WARNING, no entry stored in dbm for [ENSG00000228812.7]
WARNING, no entry stored in dbm for [ENSG00000251562.8]
WARNING, no entry stored in dbm for [ENSG00000224791.1]
WARNING, no entry stored in dbm for [ENSG00000254034.2]
WARNING, no entry stored in dbm for [ENSG00000240137.6]
WARNING, no entry stored in dbm for [ENSG00000207441.1]
WARNING, no entry stored in dbm for [ENSG00000272767.1]
WARNING, no entry stored in dbm for [ENSG00000237872.4]
WARNING, no entry stored in dbm for [ENSG00000244097.1]
WARNING, no entry stored in dbm for [ENSG00000230461.9]
WARNING, no entry stored in dbm for [ENSG00000223715.3]
WARNING, no entry stored in dbm for [ENSG00000259683.1]
WARNING, no entry stored in dbm for [ENSG00000255308.1]
WARNING, no entry stored in dbm for [ENSG00000232807.2]
WARNING, no entry stored in dbm for [ENSG00000203993.6]
WARNING, no entry stored in dbm for [ENSG00000088340.17]
WARNING, no entry stored in dbm for [ENSG00000254055.2]
WARNING, no entry stored in dbm for [ENSG00000257252.6]
WARNING, no entry stored in dbm for [ENSG00000286975.1]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000235749.3]
WARNING, no entry stored in dbm for [ENSG00000228685.1]
WARNING, no entry stored in dbm for [ENSG00000234851.4]
WARNING, no entry stored in dbm for [ENSG00000228830.1]
WARNING, no entry stored in dbm for [ENSG00000237422.2]
WARNING, no entry stored in dbm for [ENSG00000287562.1]
WARNING, no entry stored in dbm for [ENSG00000260236.1]
WARNING, no entry stored in dbm for [ENSG00000260236.1]
WARNING, no entry stored in dbm for [ENSG00000267127.7]
WARNING, no entry stored in dbm for [ENSG00000272693.4]
WARNING, no entry stored in dbm for [ENSG00000257817.2]
WARNING, no entry stored in dbm for [ENSG00000257681.1]
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 [ENSG00000214331.8]
WARNING, no entry stored in dbm for [ENSG00000267433.1]
WARNING, no entry stored in dbm for [ENSG00000236531.2]
WARNING, no entry stored in dbm for [ENSG00000268189.2]
WARNING, no entry stored in dbm for [ENSG00000228204.2]
* STAR-Fusion complete. See output: /tmp/nxf.xNMr3uLxMe/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)