-ctat genome lib [/tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.WDxxwGDlGF/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary
-sample contains 37936168 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir -J /tmp/nxf.WDxxwGDlGF/EndoN_FFPE_L08_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.WDxxwGDlGF/EndoN_FFPE_L08_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.WDxxwGDlGF/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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[790000], rate=74763.41/min -building interval tree based on /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes
[10000], rate=85714.29/min
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[30000], rate=100000.00/min
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[790000], rate=68497.11/min -building interval tree based on /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes
[10000], rate=75000.00/min
[20000], rate=70588.24/min
[30000], rate=58064.52/min
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[790000], rate=67811.16/min -building interval tree based on /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes
[10000], rate=42857.14/min
[20000], rate=44444.44/min
[30000], rate=45000.00/min
[40000], rate=46153.85/min
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[780000], rate=59016.39/min
[790000], rate=58881.99/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir --filt_file /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.
6000000.00 reads per min processed...
6000000.00 reads per min processed...
9000000.00 reads per min processed...
6000000.00 reads per min processed...
5000000.00 reads per min processed...
4500000.00 reads per min processed...
4200000.00 reads per min processed...
4000000.00 reads per min processed...
3600000.00 reads per min processed...
3529411.76 reads per min processed...
3473684.21 reads per min processed...
3272727.27 reads per min processed...
3250000.00 reads per min processed...
3230769.23 reads per min processed...
3214285.71 reads per min processed...
3200000.00 reads per min processed...
3290322.58 reads per min processed...
3375000.00 reads per min processed...
3454545.45 reads per min processed...
3529411.76 reads per min processed...
3500000.00 reads per min processed...
3473684.21 reads per min processed...
3450000.00 reads per min processed...
3512195.12 reads per min processed...
3409090.91 reads per min processed...
3391304.35 reads per min processed...
3446808.51 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.WDxxwGDlGF/EndoN_FFPE_L08_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.WDxxwGDlGF/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -58458.390367
EM: Round [1] log likelihood: -58338.710545
EM: Round [2] log likelihood: -58290.128010
EM: Round [3] log likelihood: -58266.194161
EM: Round [4] log likelihood: -58253.214656
EM: Round [5] log likelihood: -58245.810929
EM: Round [6] log likelihood: -58241.448776
EM: Round [7] log likelihood: -58238.803835
EM: Round [8] log likelihood: -58237.149147
EM: Round [9] log likelihood: -58236.077821
EM: Round [10] log likelihood: -58235.359201
EM: Round [11] log likelihood: -58234.860312
EM: Round [12] log likelihood: -58234.502734
EM: Round [13] log likelihood: -58234.238950
EM: Round [14] log likelihood: -58234.039326
EM: Round [15] log likelihood: -58233.884827
EM: Round [16] log likelihood: -58233.762878
EM: Round [17] log likelihood: -58233.664950
EM: Round [18] log likelihood: -58233.585113
EM: Round [19] log likelihood: -58233.519153
EM: Round [20] log likelihood: -58233.464014
EM: Round [21] log likelihood: -58233.417442
EM: Round [22] log likelihood: -58233.377742
EM: Round [23] log likelihood: -58233.343625
EM: Round [24] log likelihood: -58233.314093
EM: Round [25] log likelihood: -58233.288365
EM: Round [26] log likelihood: -58233.265822
EM: Round [27] log likelihood: -58233.245968
EM: Round [28] log likelihood: -58233.228401
EM: Round [29] log likelihood: -58233.212793
EM: Round [30] log likelihood: -58233.198871
EM: Round [31] log likelihood: -58233.186410
EM: Round [32] log likelihood: -58233.175221
EM: Round [33] log likelihood: -58233.165142
EM: Round [34] log likelihood: -58233.156037
EM: Round [35] log likelihood: -58233.147790
EM: Round [36] log likelihood: -58233.140300
EM: Round [37] log likelihood: -58233.133479
EM: Round [38] log likelihood: -58233.127253
EM: Round [39] log likelihood: -58233.121556
EM: Round [40] log likelihood: -58233.116330
EM: Round [41] log likelihood: -58233.111525
EM: Round [42] log likelihood: -58233.107096
EM: Round [43] log likelihood: -58233.103004
EM: Round [44] log likelihood: -58233.099214
EM: Round [45] log likelihood: -58233.095696
EM: Round [46] log likelihood: -58233.092423
EM: Round [47] log likelihood: -58233.089370
EM: Round [48] log likelihood: -58233.086516
EM: Round [49] log likelihood: -58233.083842
EM: Round [50] log likelihood: -58233.081330
EM: Round [51] log likelihood: -58233.078967
EM: Round [52] log likelihood: -58233.076737
EM: Round [53] log likelihood: -58233.074628
EM: Round [54] log likelihood: -58233.072631
EM: Round [55] log likelihood: -58233.070735
EM: Round [56] log likelihood: -58233.068931
EM: Round [57] log likelihood: -58233.067212
EM: Round [58] log likelihood: -58233.065570
EM: Round [59] log likelihood: -58233.063999
EM: Round [60] log likelihood: -58233.062494
EM: Round [61] log likelihood: -58233.061049
EM: Round [62] log likelihood: -58233.059660
EM: Round [63] log likelihood: -58233.058323
EM: Round [64] log likelihood: -58233.057033
EM: Round [65] log likelihood: -58233.055788
EM: Round [66] log likelihood: -58233.054585
EM: Round [67] log likelihood: -58233.053420
EM: Round [68] log likelihood: -58233.052291
EM: Round [69] log likelihood: -58233.051196
EM: Round [70] log likelihood: -58233.050133
EM: Round [71] log likelihood: -58233.049100
EM: Round [72] log likelihood: -58233.048096
EM: Round [73] log likelihood: -58233.047118
EM: Round [74] log likelihood: -58233.046166
EM: Round [75] log likelihood: -58233.045238
EM: Round [76] log likelihood: -58233.044333
EM: Round [77] log likelihood: -58233.043450
EM: Round [78] log likelihood: -58233.042588
EM: Round [79] log likelihood: -58233.041746
EM: Round [80] log likelihood: -58233.040923
EM: Round [81] log likelihood: -58233.040119
EM: Round [82] log likelihood: -58233.039333
EM: Round [83] log likelihood: -58233.038564
EM: Round [84] log likelihood: -58233.037812
EM: Round [85] log likelihood: -58233.037076
EM: Round [86] log likelihood: -58233.036355
EM: Round [87] log likelihood: -58233.035650
EM: Round [88] log likelihood: -58233.034959
EM: Round [89] log likelihood: -58233.034283
EM: Round [90] log likelihood: -58233.033621
EM: Round [91] log likelihood: -58233.032972
EM: Round [92] log likelihood: -58233.032337
EM: Round [93] log likelihood: -58233.031714
EM: Round [94] log likelihood: -58233.031104
EM: Round [95] log likelihood: -58233.030507
EM: Round [96] log likelihood: -58233.029921
EM: Round [97] log likelihood: -58233.029347
EM: Round [98] log likelihood: -58233.028785
EM: Round [99] log likelihood: -58233.028235
EM: Round [100] log likelihood: -58233.027695
EM: Round [101] log likelihood: -58233.027166
EM: Round [102] log likelihood: -58233.026648
EM: Round [103] log likelihood: -58233.026141
EM: Round [104] log likelihood: -58233.025644
EM: Round [105] log likelihood: -58233.025156
EM: Round [106] log likelihood: -58233.024679
EM: Round [107] log likelihood: -58233.024212
EM: Round [108] log likelihood: -58233.023754
EM: Round [109] log likelihood: -58233.023305
EM: Round [110] log likelihood: -58233.022866
EM: Round [111] log likelihood: -58233.022435
EM: Round [112] log likelihood: -58233.022014
EM: Round [113] log likelihood: -58233.021601
EM: Round [114] log likelihood: -58233.021197
EM: Round [115] log likelihood: -58233.020801
EM: Round [116] log likelihood: -58233.020413
EM: Round [117] log likelihood: -58233.020034
EM: Round [118] log likelihood: -58233.019662
EM: Round [119] log likelihood: -58233.019299
EM: Round [120] log likelihood: -58233.018943
EM: Round [121] log likelihood: -58233.018594
EM: Round [122] log likelihood: -58233.018253
EM: Round [123] log likelihood: -58233.017920
EM: Round [124] log likelihood: -58233.017593
EM: Round [125] log likelihood: -58233.017273
EM: Round [126] log likelihood: -58233.016961
EM: Round [127] log likelihood: -58233.016655
EM: Round [128] log likelihood: -58233.016355
EM: Round [129] log likelihood: -58233.016062
EM: Round [130] log likelihood: -58233.015776
EM: Round [131] log likelihood: -58233.015495
EM: Round [132] log likelihood: -58233.015221
EM: Round [133] log likelihood: -58233.014953
EM: Round [134] log likelihood: -58233.014691
EM: Round [135] log likelihood: -58233.014434
EM: Round [136] log likelihood: -58233.014184
EM: Round [137] log likelihood: -58233.013938
EM: Round [138] log likelihood: -58233.013699
EM: Round [139] log likelihood: -58233.013464
EM: Round [140] log likelihood: -58233.013235
EM: Round [141] log likelihood: -58233.013011
EM: Round [142] log likelihood: -58233.012792
EM: Round [143] log likelihood: -58233.012578
EM: Round [144] log likelihood: -58233.012368
EM: Round [145] log likelihood: -58233.012164
EM: Round [146] log likelihood: -58233.011964
EM: Round [147] log likelihood: -58233.011768
EM: Round [148] log likelihood: -58233.011577
EM: Round [149] log likelihood: -58233.011391
EM: Round [150] log likelihood: -58233.011208
EM: Round [151] log likelihood: -58233.011030
EM: Round [152] log likelihood: -58233.010856
EM: Round [153] log likelihood: -58233.010686
EM: Round [154] log likelihood: -58233.010519
EM: Round [155] log likelihood: -58233.010357
EM: Round [156] log likelihood: -58233.010198
EM: Round [157] log likelihood: -58233.010043
EM: Round [158] log likelihood: -58233.009892
EM: Round [159] log likelihood: -58233.009744
EM: Round [160] log likelihood: -58233.009599
EM: Round [161] log likelihood: -58233.009458
EM: Round [162] log likelihood: -58233.009320
EM: Round [163] log likelihood: -58233.009186
EM: Round [164] log likelihood: -58233.009054
EM: Round [165] log likelihood: -58233.008926
EM: Round [166] log likelihood: -58233.008800
EM: Round [167] log likelihood: -58233.008678
EM: Round [168] log likelihood: -58233.008558
EM: Round [169] log likelihood: -58233.008441
EM: Round [170] log likelihood: -58233.008327
EM: Round [171] log likelihood: -58233.008216
EM: Round [172] log likelihood: -58233.008107
EM: Round [173] log likelihood: -58233.008001
EM: Round [174] log likelihood: -58233.007897
EM: Round [175] log likelihood: -58233.007796
EM: Round [176] log likelihood: -58233.007697
EM: Stopping iterations at round 176 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -58429.992898
EM: Round [1] log likelihood: -58322.821547
EM: Round [2] log likelihood: -58280.725245
EM: Round [3] log likelihood: -58260.519805
EM: Round [4] log likelihood: -58249.731143
EM: Round [5] log likelihood: -58243.619988
EM: Round [6] log likelihood: -58240.027344
EM: Round [7] log likelihood: -58237.848351
EM: Round [8] log likelihood: -58236.482951
EM: Round [9] log likelihood: -58235.596903
EM: Round [10] log likelihood: -58235.001030
EM: Round [11] log likelihood: -58234.586239
EM: Round [12] log likelihood: -58234.288115
EM: Round [13] log likelihood: -58234.067566
EM: Round [14] log likelihood: -58233.900170
EM: Round [15] log likelihood: -58233.770215
EM: Round [16] log likelihood: -58233.667309
EM: Round [17] log likelihood: -58233.584395
EM: Round [18] log likelihood: -58233.516563
EM: Round [19] log likelihood: -58233.460321
EM: Round [20] log likelihood: -58233.413138
EM: Round [21] log likelihood: -58233.373143
EM: Round [22] log likelihood: -58233.338932
EM: Round [23] log likelihood: -58233.309433
EM: Round [24] log likelihood: -58233.283817
EM: Round [25] log likelihood: -58233.261432
EM: Round [26] log likelihood: -58233.241764
EM: Round [27] log likelihood: -58233.224395
EM: Round [28] log likelihood: -58233.208990
EM: Round [29] log likelihood: -58233.195271
EM: Round [30] log likelihood: -58233.183008
EM: Round [31] log likelihood: -58233.172010
EM: Round [32] log likelihood: -58233.162116
EM: Round [33] log likelihood: -58233.153187
EM: Round [34] log likelihood: -58233.145108
EM: Round [35] log likelihood: -58233.137777
EM: Round [36] log likelihood: -58233.131109
EM: Round [37] log likelihood: -58233.125027
EM: Round [38] log likelihood: -58233.119466
EM: Round [39] log likelihood: -58233.114369
EM: Round [40] log likelihood: -58233.109686
EM: Round [41] log likelihood: -58233.105373
EM: Round [42] log likelihood: -58233.101391
EM: Round [43] log likelihood: -58233.097706
EM: Round [44] log likelihood: -58233.094287
EM: Round [45] log likelihood: -58233.091108
EM: Round [46] log likelihood: -58233.088145
EM: Round [47] log likelihood: -58233.085376
EM: Round [48] log likelihood: -58233.082783
EM: Round [49] log likelihood: -58233.080350
EM: Round [50] log likelihood: -58233.078060
EM: Round [51] log likelihood: -58233.075900
EM: Round [52] log likelihood: -58233.073860
EM: Round [53] log likelihood: -58233.071927
EM: Round [54] log likelihood: -58233.070093
EM: Round [55] log likelihood: -58233.068348
EM: Round [56] log likelihood: -58233.066686
EM: Round [57] log likelihood: -58233.065099
EM: Round [58] log likelihood: -58233.063581
EM: Round [59] log likelihood: -58233.062127
EM: Round [60] log likelihood: -58233.060731
EM: Round [61] log likelihood: -58233.059389
EM: Round [62] log likelihood: -58233.058097
EM: Round [63] log likelihood: -58233.056851
EM: Round [64] log likelihood: -58233.055649
EM: Round [65] log likelihood: -58233.054486
EM: Round [66] log likelihood: -58233.053361
EM: Round [67] log likelihood: -58233.052271
EM: Round [68] log likelihood: -58233.051213
EM: Round [69] log likelihood: -58233.050187
EM: Round [70] log likelihood: -58233.049189
EM: Round [71] log likelihood: -58233.048219
EM: Round [72] log likelihood: -58233.047274
EM: Round [73] log likelihood: -58233.046354
EM: Round [74] log likelihood: -58233.045457
EM: Round [75] log likelihood: -58233.044583
EM: Round [76] log likelihood: -58233.043729
EM: Round [77] log likelihood: -58233.042896
EM: Round [78] log likelihood: -58233.042082
EM: Round [79] log likelihood: -58233.041286
EM: Round [80] log likelihood: -58233.040509
EM: Round [81] log likelihood: -58233.039748
EM: Round [82] log likelihood: -58233.039004
EM: Round [83] log likelihood: -58233.038277
EM: Round [84] log likelihood: -58233.037564
EM: Round [85] log likelihood: -58233.036867
EM: Round [86] log likelihood: -58233.036184
EM: Round [87] log likelihood: -58233.035515
EM: Round [88] log likelihood: -58233.034860
EM: Round [89] log likelihood: -58233.034219
EM: Round [90] log likelihood: -58233.033590
EM: Round [91] log likelihood: -58233.032975
EM: Round [92] log likelihood: -58233.032371
EM: Round [93] log likelihood: -58233.031780
EM: Round [94] log likelihood: -58233.031201
EM: Round [95] log likelihood: -58233.030633
EM: Round [96] log likelihood: -58233.030076
EM: Round [97] log likelihood: -58233.029531
EM: Round [98] log likelihood: -58233.028997
EM: Round [99] log likelihood: -58233.028473
EM: Round [100] log likelihood: -58233.027960
EM: Round [101] log likelihood: -58233.027457
EM: Round [102] log likelihood: -58233.026964
EM: Round [103] log likelihood: -58233.026481
EM: Round [104] log likelihood: -58233.026008
EM: Round [105] log likelihood: -58233.025544
EM: Round [106] log likelihood: -58233.025090
EM: Round [107] log likelihood: -58233.024644
EM: Round [108] log likelihood: -58233.024208
EM: Round [109] log likelihood: -58233.023781
EM: Round [110] log likelihood: -58233.023362
EM: Round [111] log likelihood: -58233.022952
EM: Round [112] log likelihood: -58233.022551
EM: Round [113] log likelihood: -58233.022157
EM: Round [114] log likelihood: -58233.021772
EM: Round [115] log likelihood: -58233.021395
EM: Round [116] log likelihood: -58233.021025
EM: Round [117] log likelihood: -58233.020663
EM: Round [118] log likelihood: -58233.020309
EM: Round [119] log likelihood: -58233.019962
EM: Round [120] log likelihood: -58233.019623
EM: Round [121] log likelihood: -58233.019290
EM: Round [122] log likelihood: -58233.018965
EM: Round [123] log likelihood: -58233.018647
EM: Round [124] log likelihood: -58233.018335
EM: Round [125] log likelihood: -58233.018030
EM: Round [126] log likelihood: -58233.017732
EM: Round [127] log likelihood: -58233.017439
EM: Round [128] log likelihood: -58233.017154
EM: Round [129] log likelihood: -58233.016874
EM: Round [130] log likelihood: -58233.016600
EM: Round [131] log likelihood: -58233.016333
EM: Round [132] log likelihood: -58233.016071
EM: Round [133] log likelihood: -58233.015815
EM: Round [134] log likelihood: -58233.015564
EM: Round [135] log likelihood: -58233.015319
EM: Round [136] log likelihood: -58233.015080
EM: Round [137] log likelihood: -58233.014846
EM: Round [138] log likelihood: -58233.014616
EM: Round [139] log likelihood: -58233.014392
EM: Round [140] log likelihood: -58233.014173
EM: Round [141] log likelihood: -58233.013959
EM: Round [142] log likelihood: -58233.013750
EM: Round [143] log likelihood: -58233.013545
EM: Round [144] log likelihood: -58233.013345
EM: Round [145] log likelihood: -58233.013149
EM: Round [146] log likelihood: -58233.012958
EM: Round [147] log likelihood: -58233.012771
EM: Round [148] log likelihood: -58233.012589
EM: Round [149] log likelihood: -58233.012410
EM: Round [150] log likelihood: -58233.012236
EM: Round [151] log likelihood: -58233.012065
EM: Round [152] log likelihood: -58233.011898
EM: Round [153] log likelihood: -58233.011736
EM: Round [154] log likelihood: -58233.011577
EM: Round [155] log likelihood: -58233.011421
EM: Round [156] log likelihood: -58233.011269
EM: Round [157] log likelihood: -58233.011121
EM: Round [158] log likelihood: -58233.010976
EM: Round [159] log likelihood: -58233.010834
EM: Round [160] log likelihood: -58233.010696
EM: Round [161] log likelihood: -58233.010561
EM: Round [162] log likelihood: -58233.010429
EM: Round [163] log likelihood: -58233.010300
EM: Round [164] log likelihood: -58233.010174
EM: Round [165] log likelihood: -58233.010051
EM: Round [166] log likelihood: -58233.009931
EM: Round [167] log likelihood: -58233.009813
EM: Round [168] log likelihood: -58233.009699
EM: Round [169] log likelihood: -58233.009587
EM: Round [170] log likelihood: -58233.009478
EM: Round [171] log likelihood: -58233.009371
EM: Round [172] log likelihood: -58233.009267
EM: Round [173] log likelihood: -58233.009165
EM: Round [174] log likelihood: -58233.009065
EM: Stopping iterations at round 174 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.WDxxwGDlGF/./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.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.WDxxwGDlGF/./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.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 37936168 > /tmp/nxf.WDxxwGDlGF/./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.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir > /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir --annotate /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.WDxxwGDlGF/./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.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir
-done, see /tmp/nxf.WDxxwGDlGF/./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.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 377, filtered: 4374)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.WDxxwGDlGF/./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.WDxxwGDlGF/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 [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 [ENSG00000181577.16]
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 [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000258853.1]
WARNING, no entry stored in dbm for [ENSG00000229739.4]
WARNING, no entry stored in dbm for [ENSG00000267573.1]
WARNING, no entry stored in dbm for [ENSG00000214433.4]
WARNING, no entry stored in dbm for [ENSG00000225092.2]
WARNING, no entry stored in dbm for [ENSG00000260236.1]
WARNING, no entry stored in dbm for [ENSG00000225840.2]
WARNING, no entry stored in dbm for [ENSG00000268189.2]
WARNING, no entry stored in dbm for [ENSG00000263072.8]
WARNING, no entry stored in dbm for [ENSG00000286211.1]
WARNING, no entry stored in dbm for [ENSG00000243771.1]
WARNING, no entry stored in dbm for [ENSG00000241743.4]
WARNING, no entry stored in dbm for [ENSG00000272848.2]
WARNING, no entry stored in dbm for [ENSG00000211513.5]
WARNING, no entry stored in dbm for [ENSG00000259393.2]
WARNING, no entry stored in dbm for [ENSG00000279625.1]
WARNING, no entry stored in dbm for [ENSG00000273344.1]
WARNING, no entry stored in dbm for [ENSG00000247828.8]
WARNING, no entry stored in dbm for [ENSG00000231721.7]
WARNING, no entry stored in dbm for [ENSG00000272368.2]
WARNING, no entry stored in dbm for [ENSG00000188004.11]
WARNING, no entry stored in dbm for [ENSG00000286813.1]
WARNING, no entry stored in dbm for [ENSG00000281207.1]
WARNING, no entry stored in dbm for [ENSG00000215241.4]
WARNING, no entry stored in dbm for [ENSG00000286176.2]
WARNING, no entry stored in dbm for [ENSG00000214389.2]
WARNING, no entry stored in dbm for [ENSG00000231022.1]
WARNING, no entry stored in dbm for [ENSG00000234637.1]
WARNING, no entry stored in dbm for [ENSG00000213880.3]
WARNING, no entry stored in dbm for [ENSG00000213862.4]
WARNING, no entry stored in dbm for [ENSG00000200296.1]
WARNING, no entry stored in dbm for [ENSG00000229828.2]
WARNING, no entry stored in dbm for [ENSG00000240606.3]
WARNING, no entry stored in dbm for [ENSG00000275014.1]
WARNING, no entry stored in dbm for [ENSG00000222974.1]
WARNING, no entry stored in dbm for [ENSG00000222386.1]
WARNING, no entry stored in dbm for [ENSG00000222974.1]
WARNING, no entry stored in dbm for [ENSG00000201010.1]
WARNING, no entry stored in dbm for [ENSG00000248223.1]
WARNING, no entry stored in dbm for [ENSG00000283907.1]
WARNING, no entry stored in dbm for [ENSG00000250072.6]
WARNING, no entry stored in dbm for [ENSG00000224729.6]
WARNING, no entry stored in dbm for [ENSG00000236778.8]
WARNING, no entry stored in dbm for [ENSG00000255875.2]
WARNING, no entry stored in dbm for [ENSG00000223991.1]
WARNING, no entry stored in dbm for [ENSG00000236051.7]
WARNING, no entry stored in dbm for [ENSG00000198886.2]
WARNING, no entry stored in dbm for [ENSG00000227584.2]
WARNING, no entry stored in dbm for [ENSG00000239586.1]
WARNING, no entry stored in dbm for [ENSG00000254541.1]
WARNING, no entry stored in dbm for [ENSG00000278913.1]
WARNING, no entry stored in dbm for [ENSG00000275449.1]
WARNING, no entry stored in dbm for [ENSG00000234769.7]
WARNING, no entry stored in dbm for [ENSG00000284419.1]
WARNING, no entry stored in dbm for [ENSG00000267472.1]
WARNING, no entry stored in dbm for [ENSG00000259134.7]
WARNING, no entry stored in dbm for [ENSG00000251372.6]
WARNING, no entry stored in dbm for [ENSG00000227128.5]
WARNING, no entry stored in dbm for [ENSG00000243438.1]
WARNING, no entry stored in dbm for [ENSG00000201113.1]
WARNING, no entry stored in dbm for [ENSG00000200814.1]
WARNING, no entry stored in dbm for [ENSG00000207029.1]
WARNING, no entry stored in dbm for [ENSG00000200153.1]
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 [ENSG00000258232.2]
WARNING, no entry stored in dbm for [ENSG00000231160.10]
WARNING, no entry stored in dbm for [ENSG00000241286.2]
WARNING, no entry stored in dbm for [ENSG00000251562.8]
WARNING, no entry stored in dbm for [ENSG00000240875.6]
WARNING, no entry stored in dbm for [ENSG00000231419.6]
WARNING, no entry stored in dbm for [ENSG00000281344.1]
WARNING, no entry stored in dbm for [ENSG00000229212.8]
WARNING, no entry stored in dbm for [ENSG00000239533.6]
WARNING, no entry stored in dbm for [ENSG00000284209.2]
WARNING, no entry stored in dbm for [ENSG00000244265.2]
WARNING, no entry stored in dbm for [ENSG00000224032.7]
WARNING, no entry stored in dbm for [ENSG00000259762.1]
WARNING, no entry stored in dbm for [ENSG00000263883.1]
WARNING, no entry stored in dbm for [ENSG00000230447.2]
WARNING, no entry stored in dbm for [ENSG00000233937.7]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000233937.7]
WARNING, no entry stored in dbm for [ENSG00000248103.1]
WARNING, no entry stored in dbm for [ENSG00000260913.1]
WARNING, no entry stored in dbm for [ENSG00000203993.6]
WARNING, no entry stored in dbm for [ENSG00000255248.9]
WARNING, no entry stored in dbm for [ENSG00000237357.2]
WARNING, no entry stored in dbm for [ENSG00000259663.2]
WARNING, no entry stored in dbm for [ENSG00000243069.8]
WARNING, no entry stored in dbm for [ENSG00000275598.1]
WARNING, no entry stored in dbm for [ENSG00000270780.1]
WARNING, no entry stored in dbm for [ENSG00000234589.4]
WARNING, no entry stored in dbm for [ENSG00000232121.1]
WARNING, no entry stored in dbm for [ENSG00000287029.1]
WARNING, no entry stored in dbm for [ENSG00000220685.3]
WARNING, no entry stored in dbm for [ENSG00000235119.1]
WARNING, no entry stored in dbm for [ENSG00000266680.1]
WARNING, no entry stored in dbm for [ENSG00000288543.1]
WARNING, no entry stored in dbm for [ENSG00000229700.1]
WARNING, no entry stored in dbm for [ENSG00000243744.2]
WARNING, no entry stored in dbm for [ENSG00000215057.4]
WARNING, no entry stored in dbm for [ENSG00000261499.2]
WARNING, no entry stored in dbm for [ENSG00000263826.1]
WARNING, no entry stored in dbm for [ENSG00000261167.1]
WARNING, no entry stored in dbm for [ENSG00000242474.3]
WARNING, no entry stored in dbm for [ENSG00000256625.1]
WARNING, no entry stored in dbm for [ENSG00000185485.14]
WARNING, no entry stored in dbm for [ENSG00000280828.1]
WARNING, no entry stored in dbm for [ENSG00000283050.2]
WARNING, no entry stored in dbm for [ENSG00000253361.3]
WARNING, no entry stored in dbm for [ENSG00000244604.1]
WARNING, no entry stored in dbm for [ENSG00000248515.2]
WARNING, no entry stored in dbm for [ENSG00000231721.7]
WARNING, no entry stored in dbm for [ENSG00000268120.1]
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000248560.1]
WARNING, no entry stored in dbm for [ENSG00000278915.1]
* STAR-Fusion complete. See output: /tmp/nxf.WDxxwGDlGF/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)