-ctat genome lib [/tmp/nxf.nLjcofNEkn/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.nLjcofNEkn/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary
-sample contains 192522058 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.nLjcofNEkn/ctat_genome_lib_build_dir -J /tmp/nxf.nLjcofNEkn/659_6i-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction -O /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.nLjcofNEkn/659_6i-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.nLjcofNEkn/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
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[1650000], rate=65003.28/min -building interval tree based on /tmp/nxf.nLjcofNEkn/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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[1650000], rate=60145.81/min -building interval tree based on /tmp/nxf.nLjcofNEkn/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
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[1650000], rate=53862.89/min -building interval tree based on /tmp/nxf.nLjcofNEkn/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
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[480000], rate=45283.02/min
[490000], rate=45440.49/min
[500000], rate=45592.71/min
[510000], rate=45739.91/min
[520000], rate=45747.80/min
[530000], rate=45821.33/min
[540000], rate=45762.71/min
[550000], rate=45961.00/min
[560000], rate=45901.64/min
[570000], rate=45906.04/min
[580000], rate=45970.94/min
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[600000], rate=46035.81/min
[610000], rate=46212.12/min
[620000], rate=46384.04/min
[630000], rate=46609.12/min
[640000], rate=46829.27/min
[650000], rate=47101.45/min
[660000], rate=47368.42/min
[670000], rate=47743.47/min
[680000], rate=48056.54/min
[690000], rate=48364.49/min
[700000], rate=48723.90/min
[710000], rate=49021.86/min
[720000], rate=49371.43/min
[730000], rate=49772.73/min
[740000], rate=49443.21/min
[750000], rate=49073.06/min
[760000], rate=48874.60/min
[770000], rate=48940.68/min
[780000], rate=48953.97/min
[790000], rate=49119.17/min
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[810000], rate=49541.28/min
[820000], rate=49646.82/min
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[840000], rate=49950.45/min
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[860000], rate=50390.62/min
[870000], rate=50581.40/min
[880000], rate=50769.23/min
[890000], rate=51051.63/min
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[910000], rate=51558.07/min
[920000], rate=51830.99/min
[930000], rate=52100.84/min
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[950000], rate=52389.71/min
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[1000000], rate=49668.87/min
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[1080000], rate=47472.53/min
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[1250000], rate=46904.32/min
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[1310000], rate=46262.51/min
[1320000], rate=45886.44/min
[1330000], rate=45470.09/min
[1340000], rate=44916.20/min
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[1620000], rate=42445.41/min
[1630000], rate=42577.27/min
[1640000], rate=42634.32/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.nLjcofNEkn/ctat_genome_lib_build_dir --filt_file /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.nLjcofNEkn/./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...
4500000.00 reads per min processed...
4000000.00 reads per min processed...
3750000.00 reads per min processed...
3600000.00 reads per min processed...
3500000.00 reads per min processed...
3692307.69 reads per min processed...
3600000.00 reads per min processed...
3529411.76 reads per min processed...
3473684.21 reads per min processed...
3428571.43 reads per min processed...
3391304.35 reads per min processed...
3360000.00 reads per min processed...
3461538.46 reads per min processed...
3428571.43 reads per min processed...
3290322.58 reads per min processed...
3272727.27 reads per min processed...
3257142.86 reads per min processed...
3243243.24 reads per min processed...
3150000.00 reads per min processed...
3142857.14 reads per min processed...
3136363.64 reads per min processed...
3130434.78 reads per min processed...
3125000.00 reads per min processed...
3120000.00 reads per min processed...
3176470.59 reads per min processed...
3230769.23 reads per min processed...
3222222.22 reads per min processed...
3214285.71 reads per min processed...
3206896.55 reads per min processed...
3200000.00 reads per min processed...
3193548.39 reads per min processed...
3238095.24 reads per min processed...
3230769.23 reads per min processed...
3272727.27 reads per min processed...
3313432.84 reads per min processed...
3304347.83 reads per min processed...
3295774.65 reads per min processed...
3287671.23 reads per min processed...
3324324.32 reads per min processed...
3315789.47 reads per min processed...
3307692.31 reads per min processed...
3341772.15 reads per min processed...
3333333.33 reads per min processed...
3325301.20 reads per min processed...
3317647.06 reads per min processed...
3310344.83 reads per min processed...
3340909.09 reads per min processed...
3333333.33 reads per min processed...
3326086.96 reads per min processed...
3319148.94 reads per min processed...
3312500.00 reads per min processed...
3306122.45 reads per min processed...
3300000.00 reads per min processed...
3326732.67 reads per min processed...
3320388.35 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.nLjcofNEkn/659_6i-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction --tmpdir /tmp --min_junction_reads 0 --min_sum_frags 1 --require_LDAS 0 --max_promiscuity 10 --min_pct_dom_promiscuity 20 --min_novel_junction_support 1 --min_alt_pct_junction 10 --aggregate_novel_junction_dist 5 --min_spanning_frags_only 1 --genome_lib_dir /tmp/nxf.nLjcofNEkn/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -154543.699397
EM: Round [1] log likelihood: -154465.167775
EM: Round [2] log likelihood: -154437.367375
EM: Round [3] log likelihood: -154424.048036
EM: Round [4] log likelihood: -154416.829644
EM: Round [5] log likelihood: -154412.652464
EM: Round [6] log likelihood: -154410.121445
EM: Round [7] log likelihood: -154408.522992
EM: Round [8] log likelihood: -154407.470610
EM: Round [9] log likelihood: -154406.748923
EM: Round [10] log likelihood: -154406.235054
EM: Round [11] log likelihood: -154405.856851
EM: Round [12] log likelihood: -154405.570477
EM: Round [13] log likelihood: -154405.348317
EM: Round [14] log likelihood: -154405.172350
EM: Round [15] log likelihood: -154405.030427
EM: Round [16] log likelihood: -154404.914120
EM: Round [17] log likelihood: -154404.817434
EM: Round [18] log likelihood: -154404.736016
EM: Round [19] log likelihood: -154404.666643
EM: Round [20] log likelihood: -154404.606895
EM: Round [21] log likelihood: -154404.554928
EM: Round [22] log likelihood: -154404.509319
EM: Round [23] log likelihood: -154404.468959
EM: Round [24] log likelihood: -154404.432974
EM: Round [25] log likelihood: -154404.400667
EM: Round [26] log likelihood: -154404.371481
EM: Round [27] log likelihood: -154404.344964
EM: Round [28] log likelihood: -154404.320747
EM: Round [29] log likelihood: -154404.298527
EM: Round [30] log likelihood: -154404.278053
EM: Round [31] log likelihood: -154404.259114
EM: Round [32] log likelihood: -154404.241534
EM: Round [33] log likelihood: -154404.225164
EM: Round [34] log likelihood: -154404.209876
EM: Round [35] log likelihood: -154404.195563
EM: Round [36] log likelihood: -154404.182130
EM: Round [37] log likelihood: -154404.169495
EM: Round [38] log likelihood: -154404.157587
EM: Round [39] log likelihood: -154404.146345
EM: Round [40] log likelihood: -154404.135713
EM: Round [41] log likelihood: -154404.125643
EM: Round [42] log likelihood: -154404.116092
EM: Round [43] log likelihood: -154404.107021
EM: Round [44] log likelihood: -154404.098396
EM: Round [45] log likelihood: -154404.090185
EM: Round [46] log likelihood: -154404.082360
EM: Round [47] log likelihood: -154404.074897
EM: Round [48] log likelihood: -154404.067771
EM: Round [49] log likelihood: -154404.060961
EM: Round [50] log likelihood: -154404.054449
EM: Round [51] log likelihood: -154404.048216
EM: Round [52] log likelihood: -154404.042246
EM: Round [53] log likelihood: -154404.036524
EM: Round [54] log likelihood: -154404.031037
EM: Round [55] log likelihood: -154404.025771
EM: Round [56] log likelihood: -154404.020714
EM: Round [57] log likelihood: -154404.015855
EM: Round [58] log likelihood: -154404.011185
EM: Round [59] log likelihood: -154404.006693
EM: Round [60] log likelihood: -154404.002370
EM: Round [61] log likelihood: -154403.998209
EM: Round [62] log likelihood: -154403.994200
EM: Round [63] log likelihood: -154403.990338
EM: Round [64] log likelihood: -154403.986615
EM: Round [65] log likelihood: -154403.983024
EM: Round [66] log likelihood: -154403.979559
EM: Round [67] log likelihood: -154403.976216
EM: Round [68] log likelihood: -154403.972987
EM: Round [69] log likelihood: -154403.969869
EM: Round [70] log likelihood: -154403.966857
EM: Round [71] log likelihood: -154403.963945
EM: Round [72] log likelihood: -154403.961130
EM: Round [73] log likelihood: -154403.958407
EM: Round [74] log likelihood: -154403.955774
EM: Round [75] log likelihood: -154403.953225
EM: Round [76] log likelihood: -154403.950758
EM: Round [77] log likelihood: -154403.948370
EM: Round [78] log likelihood: -154403.946056
EM: Round [79] log likelihood: -154403.943816
EM: Round [80] log likelihood: -154403.941644
EM: Round [81] log likelihood: -154403.939540
EM: Round [82] log likelihood: -154403.937500
EM: Round [83] log likelihood: -154403.935522
EM: Round [84] log likelihood: -154403.933603
EM: Round [85] log likelihood: -154403.931743
EM: Round [86] log likelihood: -154403.929937
EM: Round [87] log likelihood: -154403.928185
EM: Round [88] log likelihood: -154403.926484
EM: Round [89] log likelihood: -154403.924833
EM: Round [90] log likelihood: -154403.923230
EM: Round [91] log likelihood: -154403.921673
EM: Round [92] log likelihood: -154403.920161
EM: Round [93] log likelihood: -154403.918692
EM: Round [94] log likelihood: -154403.917265
EM: Round [95] log likelihood: -154403.915878
EM: Round [96] log likelihood: -154403.914530
EM: Round [97] log likelihood: -154403.913219
EM: Round [98] log likelihood: -154403.911945
EM: Round [99] log likelihood: -154403.910706
EM: Round [100] log likelihood: -154403.909502
EM: Round [101] log likelihood: -154403.908330
EM: Round [102] log likelihood: -154403.907191
EM: Round [103] log likelihood: -154403.906082
EM: Round [104] log likelihood: -154403.905004
EM: Round [105] log likelihood: -154403.903955
EM: Round [106] log likelihood: -154403.902933
EM: Round [107] log likelihood: -154403.901939
EM: Round [108] log likelihood: -154403.900972
EM: Round [109] log likelihood: -154403.900031
EM: Round [110] log likelihood: -154403.899114
EM: Round [111] log likelihood: -154403.898221
EM: Round [112] log likelihood: -154403.897353
EM: Round [113] log likelihood: -154403.896506
EM: Round [114] log likelihood: -154403.895682
EM: Round [115] log likelihood: -154403.894880
EM: Round [116] log likelihood: -154403.894098
EM: Round [117] log likelihood: -154403.893337
EM: Round [118] log likelihood: -154403.892595
EM: Round [119] log likelihood: -154403.891873
EM: Round [120] log likelihood: -154403.891169
EM: Round [121] log likelihood: -154403.890483
EM: Round [122] log likelihood: -154403.889814
EM: Round [123] log likelihood: -154403.889163
EM: Round [124] log likelihood: -154403.888529
EM: Round [125] log likelihood: -154403.887910
EM: Round [126] log likelihood: -154403.887307
EM: Round [127] log likelihood: -154403.886720
EM: Round [128] log likelihood: -154403.886147
EM: Round [129] log likelihood: -154403.885589
EM: Round [130] log likelihood: -154403.885045
EM: Round [131] log likelihood: -154403.884514
EM: Round [132] log likelihood: -154403.883997
EM: Round [133] log likelihood: -154403.883493
EM: Round [134] log likelihood: -154403.883001
EM: Round [135] log likelihood: -154403.882522
EM: Round [136] log likelihood: -154403.882055
EM: Round [137] log likelihood: -154403.881599
EM: Round [138] log likelihood: -154403.881155
EM: Round [139] log likelihood: -154403.880721
EM: Round [140] log likelihood: -154403.880299
EM: Round [141] log likelihood: -154403.879886
EM: Round [142] log likelihood: -154403.879485
EM: Round [143] log likelihood: -154403.879093
EM: Round [144] log likelihood: -154403.878710
EM: Round [145] log likelihood: -154403.878337
EM: Round [146] log likelihood: -154403.877974
EM: Round [147] log likelihood: -154403.877619
EM: Round [148] log likelihood: -154403.877273
EM: Round [149] log likelihood: -154403.876935
EM: Round [150] log likelihood: -154403.876606
EM: Round [151] log likelihood: -154403.876285
EM: Round [152] log likelihood: -154403.875971
EM: Round [153] log likelihood: -154403.875666
EM: Round [154] log likelihood: -154403.875368
EM: Round [155] log likelihood: -154403.875077
EM: Round [156] log likelihood: -154403.874793
EM: Round [157] log likelihood: -154403.874516
EM: Round [158] log likelihood: -154403.874246
EM: Round [159] log likelihood: -154403.873982
EM: Round [160] log likelihood: -154403.873725
EM: Round [161] log likelihood: -154403.873474
EM: Round [162] log likelihood: -154403.873229
EM: Round [163] log likelihood: -154403.872990
EM: Round [164] log likelihood: -154403.872757
EM: Round [165] log likelihood: -154403.872530
EM: Round [166] log likelihood: -154403.872308
EM: Round [167] log likelihood: -154403.872091
EM: Round [168] log likelihood: -154403.871880
EM: Round [169] log likelihood: -154403.871674
EM: Round [170] log likelihood: -154403.871473
EM: Round [171] log likelihood: -154403.871276
EM: Round [172] log likelihood: -154403.871085
EM: Round [173] log likelihood: -154403.870898
EM: Round [174] log likelihood: -154403.870715
EM: Round [175] log likelihood: -154403.870537
EM: Round [176] log likelihood: -154403.870364
EM: Round [177] log likelihood: -154403.870194
EM: Round [178] log likelihood: -154403.870029
EM: Round [179] log likelihood: -154403.869867
EM: Round [180] log likelihood: -154403.869709
EM: Round [181] log likelihood: -154403.869556
EM: Round [182] log likelihood: -154403.869406
EM: Round [183] log likelihood: -154403.869259
EM: Round [184] log likelihood: -154403.869116
EM: Round [185] log likelihood: -154403.868977
EM: Round [186] log likelihood: -154403.868840
EM: Round [187] log likelihood: -154403.868708
EM: Round [188] log likelihood: -154403.868578
EM: Round [189] log likelihood: -154403.868451
EM: Round [190] log likelihood: -154403.868328
EM: Round [191] log likelihood: -154403.868207
EM: Round [192] log likelihood: -154403.868089
EM: Round [193] log likelihood: -154403.867975
EM: Round [194] log likelihood: -154403.867862
EM: Round [195] log likelihood: -154403.867753
EM: Round [196] log likelihood: -154403.867646
EM: Round [197] log likelihood: -154403.867542
EM: Round [198] log likelihood: -154403.867440
EM: Round [199] log likelihood: -154403.867341
EM: Stopping iterations at round 199 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -154438.187807
EM: Round [1] log likelihood: -154374.206334
EM: Round [2] log likelihood: -154351.321919
EM: Round [3] log likelihood: -154340.392513
EM: Round [4] log likelihood: -154334.468543
EM: Round [5] log likelihood: -154331.025673
EM: Round [6] log likelihood: -154328.929588
EM: Round [7] log likelihood: -154327.601972
EM: Round [8] log likelihood: -154326.727604
EM: Round [9] log likelihood: -154326.129259
EM: Round [10] log likelihood: -154325.705022
EM: Round [11] log likelihood: -154325.394675
EM: Round [12] log likelihood: -154325.161463
EM: Round [13] log likelihood: -154324.982161
EM: Round [14] log likelihood: -154324.841583
EM: Round [15] log likelihood: -154324.729484
EM: Round [16] log likelihood: -154324.638757
EM: Round [17] log likelihood: -154324.564352
EM: Round [18] log likelihood: -154324.502604
EM: Round [19] log likelihood: -154324.450806
EM: Round [20] log likelihood: -154324.406928
EM: Round [21] log likelihood: -154324.369427
EM: Round [22] log likelihood: -154324.337114
EM: Round [23] log likelihood: -154324.309064
EM: Round [24] log likelihood: -154324.284549
EM: Round [25] log likelihood: -154324.262991
EM: Round [26] log likelihood: -154324.243926
EM: Round [27] log likelihood: -154324.226981
EM: Round [28] log likelihood: -154324.211849
EM: Round [29] log likelihood: -154324.198281
EM: Round [30] log likelihood: -154324.186067
EM: Round [31] log likelihood: -154324.175035
EM: Round [32] log likelihood: -154324.165039
EM: Round [33] log likelihood: -154324.155957
EM: Round [34] log likelihood: -154324.147683
EM: Round [35] log likelihood: -154324.140128
EM: Round [36] log likelihood: -154324.133216
EM: Round [37] log likelihood: -154324.126878
EM: Round [38] log likelihood: -154324.121058
EM: Round [39] log likelihood: -154324.115704
EM: Round [40] log likelihood: -154324.110772
EM: Round [41] log likelihood: -154324.106223
EM: Round [42] log likelihood: -154324.102022
EM: Round [43] log likelihood: -154324.098137
EM: Round [44] log likelihood: -154324.094543
EM: Round [45] log likelihood: -154324.091213
EM: Round [46] log likelihood: -154324.088126
EM: Round [47] log likelihood: -154324.085261
EM: Round [48] log likelihood: -154324.082601
EM: Round [49] log likelihood: -154324.080130
EM: Round [50] log likelihood: -154324.077833
EM: Round [51] log likelihood: -154324.075695
EM: Round [52] log likelihood: -154324.073706
EM: Round [53] log likelihood: -154324.071854
EM: Round [54] log likelihood: -154324.070129
EM: Round [55] log likelihood: -154324.068520
EM: Round [56] log likelihood: -154324.067021
EM: Round [57] log likelihood: -154324.065622
EM: Round [58] log likelihood: -154324.064318
EM: Round [59] log likelihood: -154324.063100
EM: Round [60] log likelihood: -154324.061963
EM: Round [61] log likelihood: -154324.060902
EM: Round [62] log likelihood: -154324.059910
EM: Round [63] log likelihood: -154324.058983
EM: Round [64] log likelihood: -154324.058118
EM: Round [65] log likelihood: -154324.057309
EM: Round [66] log likelihood: -154324.056552
EM: Round [67] log likelihood: -154324.055845
EM: Round [68] log likelihood: -154324.055183
EM: Round [69] log likelihood: -154324.054564
EM: Round [70] log likelihood: -154324.053985
EM: Round [71] log likelihood: -154324.053444
EM: Round [72] log likelihood: -154324.052937
EM: Round [73] log likelihood: -154324.052463
EM: Round [74] log likelihood: -154324.052019
EM: Round [75] log likelihood: -154324.051603
EM: Round [76] log likelihood: -154324.051214
EM: Round [77] log likelihood: -154324.050850
EM: Round [78] log likelihood: -154324.050508
EM: Round [79] log likelihood: -154324.050189
EM: Round [80] log likelihood: -154324.049890
EM: Round [81] log likelihood: -154324.049609
EM: Round [82] log likelihood: -154324.049347
EM: Round [83] log likelihood: -154324.049101
EM: Round [84] log likelihood: -154324.048870
EM: Round [85] log likelihood: -154324.048655
EM: Round [86] log likelihood: -154324.048452
EM: Round [87] log likelihood: -154324.048263
EM: Round [88] log likelihood: -154324.048085
EM: Round [89] log likelihood: -154324.047919
EM: Round [90] log likelihood: -154324.047763
EM: Round [91] log likelihood: -154324.047617
EM: Round [92] log likelihood: -154324.047480
EM: Round [93] log likelihood: -154324.047351
EM: Round [94] log likelihood: -154324.047231
EM: Round [95] log likelihood: -154324.047118
EM: Round [96] log likelihood: -154324.047012
EM: Round [97] log likelihood: -154324.046913
EM: Stopping iterations at round 97 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.nLjcofNEkn/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.nLjcofNEkn/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.nLjcofNEkn/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.nLjcofNEkn/./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.nLjcofNEkn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.nLjcofNEkn/./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.nLjcofNEkn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 192522058 > /tmp/nxf.nLjcofNEkn/./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.nLjcofNEkn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.nLjcofNEkn/ctat_genome_lib_build_dir > /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.nLjcofNEkn/ctat_genome_lib_build_dir --annotate /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.nLjcofNEkn/./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.nLjcofNEkn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.nLjcofNEkn/ctat_genome_lib_build_dir
-done, see /tmp/nxf.nLjcofNEkn/./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.nLjcofNEkn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.nLjcofNEkn/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 1439, filtered: 10171)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.nLjcofNEkn/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.nLjcofNEkn/./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.nLjcofNEkn/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
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WARNING, no entry stored in dbm for [ENSG00000227456.9]
WARNING, no entry stored in dbm for [ENSG00000225200.2]
WARNING, no entry stored in dbm for [ENSG00000225393.1]
WARNING, no entry stored in dbm for [ENSG00000272888.7]
WARNING, no entry stored in dbm for [ENSG00000272888.7]
WARNING, no entry stored in dbm for [ENSG00000246082.2]
WARNING, no entry stored in dbm for [ENSG00000288393.1]
WARNING, no entry stored in dbm for [ENSG00000236830.7]
WARNING, no entry stored in dbm for [ENSG00000204623.9]
WARNING, no entry stored in dbm for [ENSG00000224750.6]
WARNING, no entry stored in dbm for [ENSG00000249082.2]
WARNING, no entry stored in dbm for [ENSG00000231424.3]
WARNING, no entry stored in dbm for [ENSG00000237263.1]
WARNING, no entry stored in dbm for [ENSG00000239300.6]
WARNING, no entry stored in dbm for [ENSG00000275374.1]
WARNING, no entry stored in dbm for [ENSG00000234028.3]
WARNING, no entry stored in dbm for [ENSG00000219507.4]
WARNING, no entry stored in dbm for [ENSG00000273679.1]
WARNING, no entry stored in dbm for [ENSG00000213033.4]
WARNING, no entry stored in dbm for [ENSG00000229498.1]
WARNING, no entry stored in dbm for [ENSG00000226835.3]
WARNING, no entry stored in dbm for [ENSG00000268812.3]
WARNING, no entry stored in dbm for [ENSG00000235050.6]
WARNING, no entry stored in dbm for [ENSG00000279491.1]
WARNING, no entry stored in dbm for [ENSG00000249936.3]
WARNING, no entry stored in dbm for [ENSG00000227615.1]
WARNING, no entry stored in dbm for [ENSG00000240494.2]
WARNING, no entry stored in dbm for [ENSG00000227615.1]
WARNING, no entry stored in dbm for [ENSG00000240752.1]
WARNING, no entry stored in dbm for [ENSG00000264449.6]
WARNING, no entry stored in dbm for [ENSG00000225906.1]
WARNING, no entry stored in dbm for [ENSG00000255045.1]
WARNING, no entry stored in dbm for [ENSG00000246889.2]
WARNING, no entry stored in dbm for [ENSG00000229956.11]
WARNING, no entry stored in dbm for [ENSG00000224431.1]
WARNING, no entry stored in dbm for [ENSG00000231259.5]
WARNING, no entry stored in dbm for [ENSG00000266931.2]
WARNING, no entry stored in dbm for [ENSG00000286724.1]
WARNING, no entry stored in dbm for [ENSG00000285799.1]
WARNING, no entry stored in dbm for [ENSG00000254741.1]
WARNING, no entry stored in dbm for [ENSG00000241326.1]
WARNING, no entry stored in dbm for [ENSG00000270780.1]
WARNING, no entry stored in dbm for [ENSG00000271806.1]
WARNING, no entry stored in dbm for [ENSG00000225096.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000235020.5]
WARNING, no entry stored in dbm for [ENSG00000285100.1]
WARNING, no entry stored in dbm for [ENSG00000230001.1]
WARNING, no entry stored in dbm for [ENSG00000286215.1]
WARNING, no entry stored in dbm for [ENSG00000248503.2]
WARNING, no entry stored in dbm for [ENSG00000237875.1]
WARNING, no entry stored in dbm for [ENSG00000244427.1]
WARNING, no entry stored in dbm for [ENSG00000227138.1]
WARNING, no entry stored in dbm for [ENSG00000226987.1]
WARNING, no entry stored in dbm for [ENSG00000136149.6]
WARNING, no entry stored in dbm for [ENSG00000230490.3]
WARNING, no entry stored in dbm for [ENSG00000273149.1]
WARNING, no entry stored in dbm for [ENSG00000226798.1]
WARNING, no entry stored in dbm for [ENSG00000257285.6]
WARNING, no entry stored in dbm for [ENSG00000277425.1]
WARNING, no entry stored in dbm for [ENSG00000203900.2]
WARNING, no entry stored in dbm for [ENSG00000231881.2]
WARNING, no entry stored in dbm for [ENSG00000272356.1]
WARNING, no entry stored in dbm for [ENSG00000227486.2]
WARNING, no entry stored in dbm for [ENSG00000230869.1]
WARNING, no entry stored in dbm for [ENSG00000230869.1]
WARNING, no entry stored in dbm for [ENSG00000204177.10]
WARNING, no entry stored in dbm for [ENSG00000179818.14]
WARNING, no entry stored in dbm for [ENSG00000231965.4]
WARNING, no entry stored in dbm for [ENSG00000212664.5]
WARNING, no entry stored in dbm for [ENSG00000203876.10]
WARNING, no entry stored in dbm for [ENSG00000251226.1]
WARNING, no entry stored in dbm for [ENSG00000283041.1]
WARNING, no entry stored in dbm for [ENSG00000274993.1]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000261499.2]
WARNING, no entry stored in dbm for [ENSG00000188755.10]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000286830.1]
WARNING, no entry stored in dbm for [ENSG00000260628.5]
WARNING, no entry stored in dbm for [ENSG00000215158.9]
WARNING, no entry stored in dbm for [ENSG00000283345.1]
WARNING, no entry stored in dbm for [ENSG00000215302.8]
WARNING, no entry stored in dbm for [ENSG00000266490.1]
WARNING, no entry stored in dbm for [ENSG00000264538.6]
WARNING, no entry stored in dbm for [ENSG00000257169.1]
WARNING, no entry stored in dbm for [ENSG00000279738.1]
WARNING, no entry stored in dbm for [ENSG00000257252.6]
WARNING, no entry stored in dbm for [ENSG00000268081.1]
WARNING, no entry stored in dbm for [ENSG00000250461.1]
WARNING, no entry stored in dbm for [ENSG00000279391.1]
WARNING, no entry stored in dbm for [ENSG00000270911.1]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000282572.2]
WARNING, no entry stored in dbm for [ENSG00000242586.1]
WARNING, no entry stored in dbm for [ENSG00000227733.10]
WARNING, no entry stored in dbm for [ENSG00000277332.1]
WARNING, no entry stored in dbm for [ENSG00000282375.1]
WARNING, no entry stored in dbm for [ENSG00000260236.1]
WARNING, no entry stored in dbm for [ENSG00000287129.1]
WARNING, no entry stored in dbm for [ENSG00000231646.6]
WARNING, no entry stored in dbm for [ENSG00000250860.1]
WARNING, no entry stored in dbm for [ENSG00000276538.1]
WARNING, no entry stored in dbm for [ENSG00000224016.2]
WARNING, no entry stored in dbm for [ENSG00000266931.2]
WARNING, no entry stored in dbm for [ENSG00000240519.1]
WARNING, no entry stored in dbm for [ENSG00000218175.2]
WARNING, no entry stored in dbm for [ENSG00000267198.1]
WARNING, no entry stored in dbm for [ENSG00000131484.4]
WARNING, no entry stored in dbm for [ENSG00000259418.1]
WARNING, no entry stored in dbm for [ENSG00000265936.1]
WARNING, no entry stored in dbm for [ENSG00000214259.3]
WARNING, no entry stored in dbm for [ENSG00000259363.6]
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 [ENSG00000280828.1]
WARNING, no entry stored in dbm for [ENSG00000277654.6]
WARNING, no entry stored in dbm for [ENSG00000286348.1]
WARNING, no entry stored in dbm for [ENSG00000204745.4]
WARNING, no entry stored in dbm for [ENSG00000287733.1]
WARNING, no entry stored in dbm for [ENSG00000266599.1]
WARNING, no entry stored in dbm for [ENSG00000183199.6]
WARNING, no entry stored in dbm for [ENSG00000259605.3]
WARNING, no entry stored in dbm for [ENSG00000283355.1]
WARNING, no entry stored in dbm for [ENSG00000287188.1]
WARNING, no entry stored in dbm for [ENSG00000284663.1]
WARNING, no entry stored in dbm for [ENSG00000284610.1]
WARNING, no entry stored in dbm for [ENSG00000229212.8]
WARNING, no entry stored in dbm for [ENSG00000229212.8]
WARNING, no entry stored in dbm for [ENSG00000253200.1]
WARNING, no entry stored in dbm for [ENSG00000259475.1]
WARNING, no entry stored in dbm for [ENSG00000185641.6]
WARNING, no entry stored in dbm for [ENSG00000188002.10]
WARNING, no entry stored in dbm for [ENSG00000254485.5]
WARNING, no entry stored in dbm for [ENSG00000257454.1]
WARNING, no entry stored in dbm for [ENSG00000272140.2]
WARNING, no entry stored in dbm for [ENSG00000279058.2]
WARNING, no entry stored in dbm for [ENSG00000248898.3]
WARNING, no entry stored in dbm for [ENSG00000279619.1]
WARNING, no entry stored in dbm for [ENSG00000234241.1]
WARNING, no entry stored in dbm for [ENSG00000232377.1]
WARNING, no entry stored in dbm for [ENSG00000181577.16]
WARNING, no entry stored in dbm for [ENSG00000261329.6]
WARNING, no entry stored in dbm for [ENSG00000196796.5]
WARNING, no entry stored in dbm for [ENSG00000258454.1]
WARNING, no entry stored in dbm for [ENSG00000267707.2]
WARNING, no entry stored in dbm for [ENSG00000228835.1]
WARNING, no entry stored in dbm for [ENSG00000228835.1]
WARNING, no entry stored in dbm for [ENSG00000227252.2]
WARNING, no entry stored in dbm for [ENSG00000249839.1]
WARNING, no entry stored in dbm for [ENSG00000272702.1]
WARNING, no entry stored in dbm for [ENSG00000287866.1]
WARNING, no entry stored in dbm for [ENSG00000260905.1]
WARNING, no entry stored in dbm for [ENSG00000284671.1]
WARNING, no entry stored in dbm for [ENSG00000276548.1]
WARNING, no entry stored in dbm for [ENSG00000189149.12]
WARNING, no entry stored in dbm for [ENSG00000257403.2]
WARNING, no entry stored in dbm for [ENSG00000189149.12]
WARNING, no entry stored in dbm for [ENSG00000257403.2]
WARNING, no entry stored in dbm for [ENSG00000189149.12]
WARNING, no entry stored in dbm for [ENSG00000233175.2]
WARNING, no entry stored in dbm for [ENSG00000287867.1]
WARNING, no entry stored in dbm for [ENSG00000268460.2]
WARNING, no entry stored in dbm for [ENSG00000262879.6]
WARNING, no entry stored in dbm for [ENSG00000265489.1]
WARNING, no entry stored in dbm for [ENSG00000214243.3]
WARNING, no entry stored in dbm for [ENSG00000205485.13]
WARNING, no entry stored in dbm for [ENSG00000241057.2]
WARNING, no entry stored in dbm for [ENSG00000272655.2]
WARNING, no entry stored in dbm for [ENSG00000288546.1]
WARNING, no entry stored in dbm for [ENSG00000268163.1]
WARNING, no entry stored in dbm for [ENSG00000279159.1]
WARNING, no entry stored in dbm for [ENSG00000245750.10]
WARNING, no entry stored in dbm for [ENSG00000275927.1]
WARNING, no entry stored in dbm for [ENSG00000251595.7]
* STAR-Fusion complete. See output: /tmp/nxf.nLjcofNEkn/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)