Done.
-parsing GTF file: /tmp/nxf.u5Dl6gKIDx/aih-tih-sc-488877-R1_A23WJ53LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.u5Dl6gKIDx/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /tmp/nxf.u5Dl6gKIDx/aih-tih-sc-488877-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.u5Dl6gKIDx/aih-tih-sc-488877-R1_A23WJ53LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.u5Dl6gKIDx/fi_workdir/aih-tih-sc-488877-R1_A23WJ53LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.u5Dl6gKIDx/fi_workdir/aih-tih-sc-488877-R1_A23WJ53LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-488877-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-488877-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
11:13:34 : INFO : Done.
-parsing GTF file: /tmp/nxf.u5Dl6gKIDx/fi_workdir/aih-tih-sc-488877-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.u5Dl6gKIDx/fi_workdir/aih-tih-sc-488877-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
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[1400000] -done parsing /tmp/nxf.u5Dl6gKIDx/fi_workdir/aih-tih-sc-488877-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'per_id < 96' => 4344,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 16,
'seq-similar region overlap' => 491,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 8,
' ** passed ** ' => 16425,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 53,
'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 2,
'excessive soft clipping' => 6006,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 5,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 136,
'low complexity anchor region' => 2,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6,
'small anchor length' => 33,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8,
'num genes matched < 2' => 2
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.u5Dl6gKIDx/fi_workdir/aih-tih-sc-488877-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[89000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[29000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[23000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[89000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[26000] -fusion SPANNING read extraction for scaff: PMS2P8--CCDC146
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[43000] -fusion SPANNING read extraction for scaff: STON1--GTF2A1L
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[29000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[6000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[34000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 87284,
'lacks exon overlap' => 2209
};
EM: Starting log likelihood: -5751.281562
EM: Round [1] log likelihood: -5750.067419
EM: Round [2] log likelihood: -5749.363652
EM: Round [3] log likelihood: -5748.716035
EM: Round [4] log likelihood: -5748.116107
EM: Round [5] log likelihood: -5747.557494
EM: Round [6] log likelihood: -5747.035148
EM: Round [7] log likelihood: -5746.545057
EM: Round [8] log likelihood: -5746.084008
EM: Round [9] log likelihood: -5745.649404
EM: Round [10] log likelihood: -5745.239115
EM: Round [11] log likelihood: -5744.851364
EM: Round [12] log likelihood: -5744.484637
EM: Round [13] log likelihood: -5744.137620
EM: Round [14] log likelihood: -5743.809145
EM: Round [15] log likelihood: -5743.498150
EM: Round [16] log likelihood: -5743.203659
EM: Round [17] log likelihood: -5742.924760
EM: Round [18] log likelihood: -5742.660589
EM: Round [19] log likelihood: -5742.410329
EM: Round [20] log likelihood: -5742.173197
EM: Round [21] log likelihood: -5741.948448
EM: Round [22] log likelihood: -5741.735367
EM: Round [23] log likelihood: -5741.533273
EM: Round [24] log likelihood: -5741.341515
EM: Round [25] log likelihood: -5741.159476
EM: Round [26] log likelihood: -5740.986566
EM: Round [27] log likelihood: -5740.822229
EM: Round [28] log likelihood: -5740.665939
EM: Round [29] log likelihood: -5740.517200
EM: Round [30] log likelihood: -5740.375545
EM: Round [31] log likelihood: -5740.240534
EM: Round [32] log likelihood: -5740.111756
EM: Round [33] log likelihood: -5739.988827
EM: Round [34] log likelihood: -5739.871387
EM: Round [35] log likelihood: -5739.759100
EM: Round [36] log likelihood: -5739.651652
EM: Round [37] log likelihood: -5739.548752
EM: Round [38] log likelihood: -5739.450128
EM: Round [39] log likelihood: -5739.355528
EM: Round [40] log likelihood: -5739.264715
EM: Round [41] log likelihood: -5739.177472
EM: Round [42] log likelihood: -5739.093595
EM: Round [43] log likelihood: -5739.012895
EM: Round [44] log likelihood: -5738.935197
EM: Round [45] log likelihood: -5738.860337
EM: Round [46] log likelihood: -5738.788163
EM: Round [47] log likelihood: -5738.718534
EM: Round [48] log likelihood: -5738.651318
EM: Round [49] log likelihood: -5738.586392
EM: Round [50] log likelihood: -5738.523643
EM: Round [51] log likelihood: -5738.462962
EM: Round [52] log likelihood: -5738.404252
EM: Round [53] log likelihood: -5738.347418
EM: Round [54] log likelihood: -5738.292373
EM: Round [55] log likelihood: -5738.239036
EM: Round [56] log likelihood: -5738.187332
EM: Round [57] log likelihood: -5738.137187
EM: Round [58] log likelihood: -5738.088534
EM: Round [59] log likelihood: -5738.041312
EM: Round [60] log likelihood: -5737.995459
EM: Round [61] log likelihood: -5737.950920
EM: Round [62] log likelihood: -5737.907643
EM: Round [63] log likelihood: -5737.865577
EM: Round [64] log likelihood: -5737.824675
EM: Round [65] log likelihood: -5737.784893
EM: Round [66] log likelihood: -5737.746189
EM: Round [67] log likelihood: -5737.708522
EM: Round [68] log likelihood: -5737.671855
EM: Round [69] log likelihood: -5737.636152
EM: Round [70] log likelihood: -5737.601378
EM: Round [71] log likelihood: -5737.567502
EM: Round [72] log likelihood: -5737.534491
EM: Round [73] log likelihood: -5737.502317
EM: Round [74] log likelihood: -5737.470952
EM: Round [75] log likelihood: -5737.440368
EM: Round [76] log likelihood: -5737.410540
EM: Round [77] log likelihood: -5737.381443
EM: Round [78] log likelihood: -5737.353054
EM: Round [79] log likelihood: -5737.325350
EM: Round [80] log likelihood: -5737.298310
EM: Round [81] log likelihood: -5737.271913
EM: Round [82] log likelihood: -5737.246139
EM: Round [83] log likelihood: -5737.220970
EM: Round [84] log likelihood: -5737.196387
EM: Round [85] log likelihood: -5737.172373
EM: Round [86] log likelihood: -5737.148910
EM: Round [87] log likelihood: -5737.125982
EM: Round [88] log likelihood: -5737.103575
EM: Round [89] log likelihood: -5737.081672
EM: Round [90] log likelihood: -5737.060259
EM: Round [91] log likelihood: -5737.039323
EM: Round [92] log likelihood: -5737.018850
EM: Round [93] log likelihood: -5736.998826
EM: Round [94] log likelihood: -5736.979240
EM: Round [95] log likelihood: -5736.960079
EM: Round [96] log likelihood: -5736.941332
EM: Round [97] log likelihood: -5736.922987
EM: Round [98] log likelihood: -5736.905034
EM: Round [99] log likelihood: -5736.887461
EM: Round [100] log likelihood: -5736.870259
EM: Round [101] log likelihood: -5736.853418
EM: Round [102] log likelihood: -5736.836929
EM: Round [103] log likelihood: -5736.820781
EM: Round [104] log likelihood: -5736.804966
EM: Round [105] log likelihood: -5736.789476
EM: Round [106] log likelihood: -5736.774302
EM: Round [107] log likelihood: -5736.759436
EM: Round [108] log likelihood: -5736.744871
EM: Round [109] log likelihood: -5736.730597
EM: Round [110] log likelihood: -5736.716609
EM: Round [111] log likelihood: -5736.702899
EM: Round [112] log likelihood: -5736.689460
EM: Round [113] log likelihood: -5736.676285
EM: Round [114] log likelihood: -5736.663368
EM: Round [115] log likelihood: -5736.650702
EM: Round [116] log likelihood: -5736.638282
EM: Round [117] log likelihood: -5736.626101
EM: Round [118] log likelihood: -5736.614153
EM: Round [119] log likelihood: -5736.602433
EM: Round [120] log likelihood: -5736.590935
EM: Round [121] log likelihood: -5736.579655
EM: Round [122] log likelihood: -5736.568586
EM: Round [123] log likelihood: -5736.557724
EM: Round [124] log likelihood: -5736.547064
EM: Round [125] log likelihood: -5736.536601
EM: Round [126] log likelihood: -5736.526331
EM: Round [127] log likelihood: -5736.516248
EM: Round [128] log likelihood: -5736.506350
EM: Round [129] log likelihood: -5736.496631
EM: Round [130] log likelihood: -5736.487087
EM: Round [131] log likelihood: -5736.477714
EM: Round [132] log likelihood: -5736.468509
EM: Round [133] log likelihood: -5736.459468
EM: Round [134] log likelihood: -5736.450586
EM: Round [135] log likelihood: -5736.441860
EM: Round [136] log likelihood: -5736.433288
EM: Round [137] log likelihood: -5736.424864
EM: Round [138] log likelihood: -5736.416587
EM: Round [139] log likelihood: -5736.408452
EM: Round [140] log likelihood: -5736.400457
EM: Round [141] log likelihood: -5736.392599
EM: Round [142] log likelihood: -5736.384874
EM: Round [143] log likelihood: -5736.377280
EM: Round [144] log likelihood: -5736.369813
EM: Round [145] log likelihood: -5736.362471
EM: Round [146] log likelihood: -5736.355252
EM: Round [147] log likelihood: -5736.348152
EM: Round [148] log likelihood: -5736.341169
EM: Round [149] log likelihood: -5736.334301
EM: Round [150] log likelihood: -5736.327545
EM: Round [151] log likelihood: -5736.320899
EM: Round [152] log likelihood: -5736.314360
EM: Round [153] log likelihood: -5736.307926
EM: Round [154] log likelihood: -5736.301595
EM: Round [155] log likelihood: -5736.295365
EM: Round [156] log likelihood: -5736.289233
EM: Round [157] log likelihood: -5736.283198
EM: Round [158] log likelihood: -5736.277258
EM: Round [159] log likelihood: -5736.271410
EM: Round [160] log likelihood: -5736.265653
EM: Round [161] log likelihood: -5736.259985
EM: Round [162] log likelihood: -5736.254404
EM: Round [163] log likelihood: -5736.248909
EM: Round [164] log likelihood: -5736.243497
EM: Round [165] log likelihood: -5736.238166
EM: Round [166] log likelihood: -5736.232916
EM: Round [167] log likelihood: -5736.227745
EM: Round [168] log likelihood: -5736.222651
EM: Round [169] log likelihood: -5736.217632
EM: Round [170] log likelihood: -5736.212687
EM: Round [171] log likelihood: -5736.207814
EM: Round [172] log likelihood: -5736.203013
EM: Round [173] log likelihood: -5736.198281
EM: Round [174] log likelihood: -5736.193618
EM: Round [175] log likelihood: -5736.189022
EM: Round [176] log likelihood: -5736.184491
EM: Round [177] log likelihood: -5736.180025
EM: Round [178] log likelihood: -5736.175622
EM: Round [179] log likelihood: -5736.171281
EM: Round [180] log likelihood: -5736.167000
EM: Round [181] log likelihood: -5736.162780
EM: Round [182] log likelihood: -5736.158618
EM: Round [183] log likelihood: -5736.154513
EM: Round [184] log likelihood: -5736.150464
EM: Round [185] log likelihood: -5736.146471
EM: Round [186] log likelihood: -5736.142531
EM: Round [187] log likelihood: -5736.138645
EM: Round [188] log likelihood: -5736.134811
EM: Round [189] log likelihood: -5736.131028
EM: Round [190] log likelihood: -5736.127296
EM: Round [191] log likelihood: -5736.123613
EM: Round [192] log likelihood: -5736.119978
EM: Round [193] log likelihood: -5736.116391
EM: Round [194] log likelihood: -5736.112850
EM: Round [195] log likelihood: -5736.109355
EM: Round [196] log likelihood: -5736.105905
EM: Round [197] log likelihood: -5736.102500
EM: Round [198] log likelihood: -5736.099137
EM: Round [199] log likelihood: -5736.095818
EM: Round [200] log likelihood: -5736.092540
EM: Round [201] log likelihood: -5736.089303
EM: Round [202] log likelihood: -5736.086106
EM: Round [203] log likelihood: -5736.082950
EM: Round [204] log likelihood: -5736.079832
EM: Round [205] log likelihood: -5736.076752
EM: Round [206] log likelihood: -5736.073710
EM: Round [207] log likelihood: -5736.070705
EM: Round [208] log likelihood: -5736.067736
EM: Round [209] log likelihood: -5736.064803
EM: Round [210] log likelihood: -5736.061905
EM: Round [211] log likelihood: -5736.059042
EM: Round [212] log likelihood: -5736.056212
EM: Round [213] log likelihood: -5736.053416
EM: Round [214] log likelihood: -5736.050652
EM: Round [215] log likelihood: -5736.047920
EM: Round [216] log likelihood: -5736.045221
EM: Round [217] log likelihood: -5736.042552
EM: Round [218] log likelihood: -5736.039914
EM: Round [219] log likelihood: -5736.037306
EM: Round [220] log likelihood: -5736.034727
EM: Round [221] log likelihood: -5736.032178
EM: Round [222] log likelihood: -5736.029657
EM: Round [223] log likelihood: -5736.027165
EM: Round [224] log likelihood: -5736.024700
EM: Round [225] log likelihood: -5736.022262
EM: Round [226] log likelihood: -5736.019852
EM: Round [227] log likelihood: -5736.017467
EM: Round [228] log likelihood: -5736.015109
EM: Round [229] log likelihood: -5736.012776
EM: Round [230] log likelihood: -5736.010468
EM: Round [231] log likelihood: -5736.008186
EM: Round [232] log likelihood: -5736.005927
EM: Round [233] log likelihood: -5736.003692
EM: Round [234] log likelihood: -5736.001481
EM: Round [235] log likelihood: -5735.999294
EM: Round [236] log likelihood: -5735.997129
EM: Round [237] log likelihood: -5735.994987
EM: Round [238] log likelihood: -5735.992866
EM: Round [239] log likelihood: -5735.990768
EM: Round [240] log likelihood: -5735.988691
EM: Round [241] log likelihood: -5735.986636
EM: Round [242] log likelihood: -5735.984601
EM: Round [243] log likelihood: -5735.982587
EM: Round [244] log likelihood: -5735.980593
EM: Round [245] log likelihood: -5735.978619
EM: Round [246] log likelihood: -5735.976665
EM: Round [247] log likelihood: -5735.974730
EM: Round [248] log likelihood: -5735.972814
EM: Round [249] log likelihood: -5735.970917
EM: Round [250] log likelihood: -5735.969039
EM: Round [251] log likelihood: -5735.967179
EM: Round [252] log likelihood: -5735.965337
EM: Round [253] log likelihood: -5735.963512
EM: Round [254] log likelihood: -5735.961705
EM: Round [255] log likelihood: -5735.959916
EM: Round [256] log likelihood: -5735.958143
EM: Round [257] log likelihood: -5735.956387
EM: Round [258] log likelihood: -5735.954648
EM: Round [259] log likelihood: -5735.952925
EM: Round [260] log likelihood: -5735.951218
EM: Round [261] log likelihood: -5735.949527
EM: Round [262] log likelihood: -5735.947851
EM: Round [263] log likelihood: -5735.946191
EM: Round [264] log likelihood: -5735.944546
EM: Round [265] log likelihood: -5735.942916
EM: Round [266] log likelihood: -5735.941301
EM: Round [267] log likelihood: -5735.939701
EM: Round [268] log likelihood: -5735.938115
EM: Round [269] log likelihood: -5735.936543
EM: Round [270] log likelihood: -5735.934985
EM: Round [271] log likelihood: -5735.933442
EM: Round [272] log likelihood: -5735.931911
EM: Round [273] log likelihood: -5735.930395
EM: Round [274] log likelihood: -5735.928891
EM: Round [275] log likelihood: -5735.927401
EM: Round [276] log likelihood: -5735.925924
EM: Round [277] log likelihood: -5735.924459
EM: Round [278] log likelihood: -5735.923007
EM: Round [279] log likelihood: -5735.921568
EM: Round [280] log likelihood: -5735.920141
EM: Round [281] log likelihood: -5735.918726
EM: Round [282] log likelihood: -5735.917324
EM: Round [283] log likelihood: -5735.915933
EM: Round [284] log likelihood: -5735.914554
EM: Round [285] log likelihood: -5735.913186
EM: Round [286] log likelihood: -5735.911830
EM: Round [287] log likelihood: -5735.910485
EM: Round [288] log likelihood: -5735.909151
EM: Round [289] log likelihood: -5735.907829
EM: Round [290] log likelihood: -5735.906517
EM: Round [291] log likelihood: -5735.905216
EM: Round [292] log likelihood: -5735.903926
EM: Round [293] log likelihood: -5735.902646
EM: Round [294] log likelihood: -5735.901377
EM: Round [295] log likelihood: -5735.900118
EM: Round [296] log likelihood: -5735.898869
EM: Round [297] log likelihood: -5735.897630
EM: Round [298] log likelihood: -5735.896401
EM: Round [299] log likelihood: -5735.895182
EM: Round [300] log likelihood: -5735.893972
EM: Round [301] log likelihood: -5735.892772
EM: Round [302] log likelihood: -5735.891582
EM: Round [303] log likelihood: -5735.890401
EM: Round [304] log likelihood: -5735.889229
EM: Round [305] log likelihood: -5735.888067
EM: Round [306] log likelihood: -5735.886913
EM: Round [307] log likelihood: -5735.885768
EM: Round [308] log likelihood: -5735.884633
EM: Round [309] log likelihood: -5735.883506
EM: Round [310] log likelihood: -5735.882387
EM: Round [311] log likelihood: -5735.881278
EM: Round [312] log likelihood: -5735.880177
EM: Round [313] log likelihood: -5735.879084
EM: Round [314] log likelihood: -5735.877999
EM: Round [315] log likelihood: -5735.876923
EM: Round [316] log likelihood: -5735.875855
EM: Round [317] log likelihood: -5735.874795
EM: Round [318] log likelihood: -5735.873742
EM: Round [319] log likelihood: -5735.872698
EM: Round [320] log likelihood: -5735.871662
EM: Round [321] log likelihood: -5735.870633
EM: Round [322] log likelihood: -5735.869612
EM: Round [323] log likelihood: -5735.868598
EM: Round [324] log likelihood: -5735.867592
EM: Round [325] log likelihood: -5735.866593
EM: Round [326] log likelihood: -5735.865602
EM: Round [327] log likelihood: -5735.864618
EM: Round [328] log likelihood: -5735.863641
EM: Round [329] log likelihood: -5735.862671
EM: Round [330] log likelihood: -5735.861708
EM: Round [331] log likelihood: -5735.860753
EM: Round [332] log likelihood: -5735.859804
EM: Round [333] log likelihood: -5735.858862
EM: Round [334] log likelihood: -5735.857926
EM: Round [335] log likelihood: -5735.856998
EM: Round [336] log likelihood: -5735.856076
EM: Round [337] log likelihood: -5735.855160
EM: Round [338] log likelihood: -5735.854251
EM: Round [339] log likelihood: -5735.853349
EM: Round [340] log likelihood: -5735.852453
EM: Round [341] log likelihood: -5735.851563
EM: Round [342] log likelihood: -5735.850680
EM: Round [343] log likelihood: -5735.849803
EM: Round [344] log likelihood: -5735.848931
EM: Round [345] log likelihood: -5735.848066
EM: Round [346] log likelihood: -5735.847208
EM: Round [347] log likelihood: -5735.846355
EM: Round [348] log likelihood: -5735.845508
EM: Round [349] log likelihood: -5735.844666
EM: Round [350] log likelihood: -5735.843831
EM: Round [351] log likelihood: -5735.843001
EM: Round [352] log likelihood: -5735.842178
EM: Round [353] log likelihood: -5735.841359
EM: Round [354] log likelihood: -5735.840547
EM: Round [355] log likelihood: -5735.839740
EM: Round [356] log likelihood: -5735.838938
EM: Round [357] log likelihood: -5735.838142
EM: Round [358] log likelihood: -5735.837352
EM: Round [359] log likelihood: -5735.836566
EM: Round [360] log likelihood: -5735.835786
EM: Round [361] log likelihood: -5735.835012
EM: Round [362] log likelihood: -5735.834242
EM: Round [363] log likelihood: -5735.833478
EM: Round [364] log likelihood: -5735.832719
EM: Round [365] log likelihood: -5735.831965
EM: Round [366] log likelihood: -5735.831216
EM: Round [367] log likelihood: -5735.830472
EM: Round [368] log likelihood: -5735.829733
EM: Round [369] log likelihood: -5735.828999
EM: Round [370] log likelihood: -5735.828270
EM: Round [371] log likelihood: -5735.827546
EM: Round [372] log likelihood: -5735.826826
EM: Round [373] log likelihood: -5735.826111
EM: Round [374] log likelihood: -5735.825401
EM: Round [375] log likelihood: -5735.824696
EM: Round [376] log likelihood: -5735.823995
EM: Round [377] log likelihood: -5735.823299
EM: Round [378] log likelihood: -5735.822607
EM: Round [379] log likelihood: -5735.821920
EM: Round [380] log likelihood: -5735.821238
EM: Round [381] log likelihood: -5735.820560
EM: Round [382] log likelihood: -5735.819886
EM: Round [383] log likelihood: -5735.819217
EM: Round [384] log likelihood: -5735.818552
EM: Round [385] log likelihood: -5735.817892
EM: Round [386] log likelihood: -5735.817235
EM: Round [387] log likelihood: -5735.816583
EM: Round [388] log likelihood: -5735.815935
EM: Round [389] log likelihood: -5735.815292
EM: Round [390] log likelihood: -5735.814652
EM: Round [391] log likelihood: -5735.814017
EM: Round [392] log likelihood: -5735.813386
EM: Round [393] log likelihood: -5735.812758
EM: Round [394] log likelihood: -5735.812135
EM: Round [395] log likelihood: -5735.811516
EM: Round [396] log likelihood: -5735.810900
EM: Round [397] log likelihood: -5735.810289
EM: Round [398] log likelihood: -5735.809682
EM: Round [399] log likelihood: -5735.809078
EM: Round [400] log likelihood: -5735.808478
EM: Round [401] log likelihood: -5735.807882
EM: Round [402] log likelihood: -5735.807290
EM: Round [403] log likelihood: -5735.806702
EM: Round [404] log likelihood: -5735.806117
EM: Round [405] log likelihood: -5735.805536
EM: Round [406] log likelihood: -5735.804959
EM: Round [407] log likelihood: -5735.804385
EM: Round [408] log likelihood: -5735.803815
EM: Round [409] log likelihood: -5735.803248
EM: Round [410] log likelihood: -5735.802685
EM: Round [411] log likelihood: -5735.802126
EM: Round [412] log likelihood: -5735.801570
EM: Round [413] log likelihood: -5735.801018
EM: Round [414] log likelihood: -5735.800469
EM: Round [415] log likelihood: -5735.799923
EM: Round [416] log likelihood: -5735.799381
EM: Round [417] log likelihood: -5735.798842
EM: Round [418] log likelihood: -5735.798307
EM: Round [419] log likelihood: -5735.797775
EM: Round [420] log likelihood: -5735.797246
EM: Round [421] log likelihood: -5735.796720
EM: Round [422] log likelihood: -5735.796198
EM: Round [423] log likelihood: -5735.795679
EM: Round [424] log likelihood: -5735.795163
EM: Round [425] log likelihood: -5735.794651
EM: Round [426] log likelihood: -5735.794141
EM: Round [427] log likelihood: -5735.793635
EM: Round [428] log likelihood: -5735.793132
EM: Round [429] log likelihood: -5735.792632
EM: Round [430] log likelihood: -5735.792135
EM: Round [431] log likelihood: -5735.791641
EM: Round [432] log likelihood: -5735.791150
EM: Round [433] log likelihood: -5735.790662
EM: Round [434] log likelihood: -5735.790177
EM: Round [435] log likelihood: -5735.789695
EM: Round [436] log likelihood: -5735.789216
EM: Round [437] log likelihood: -5735.788740
EM: Round [438] log likelihood: -5735.788267
EM: Round [439] log likelihood: -5735.787797
EM: Round [440] log likelihood: -5735.787329
EM: Round [441] log likelihood: -5735.786865
EM: Round [442] log likelihood: -5735.786403
EM: Round [443] log likelihood: -5735.785944
EM: Round [444] log likelihood: -5735.785488
EM: Round [445] log likelihood: -5735.785034
EM: Round [446] log likelihood: -5735.784584
EM: Round [447] log likelihood: -5735.784136
EM: Round [448] log likelihood: -5735.783691
EM: Round [449] log likelihood: -5735.783248
EM: Round [450] log likelihood: -5735.782808
EM: Round [451] log likelihood: -5735.782371
EM: Round [452] log likelihood: -5735.781937
EM: Round [453] log likelihood: -5735.781505
EM: Round [454] log likelihood: -5735.781076
EM: Round [455] log likelihood: -5735.780649
EM: Round [456] log likelihood: -5735.780225
EM: Round [457] log likelihood: -5735.779803
EM: Round [458] log likelihood: -5735.779384
EM: Round [459] log likelihood: -5735.778968
EM: Round [460] log likelihood: -5735.778554
EM: Round [461] log likelihood: -5735.778142
EM: Round [462] log likelihood: -5735.777733
EM: Round [463] log likelihood: -5735.777326
EM: Round [464] log likelihood: -5735.776922
EM: Round [465] log likelihood: -5735.776520
EM: Round [466] log likelihood: -5735.776121
EM: Round [467] log likelihood: -5735.775724
EM: Round [468] log likelihood: -5735.775330
EM: Round [469] log likelihood: -5735.774937
EM: Round [470] log likelihood: -5735.774547
EM: Round [471] log likelihood: -5735.774160
EM: Round [472] log likelihood: -5735.773775
EM: Round [473] log likelihood: -5735.773392
EM: Round [474] log likelihood: -5735.773011
EM: Round [475] log likelihood: -5735.772632
EM: Round [476] log likelihood: -5735.772256
EM: Round [477] log likelihood: -5735.771882
EM: Round [478] log likelihood: -5735.771511
EM: Round [479] log likelihood: -5735.771141
EM: Round [480] log likelihood: -5735.770774
EM: Round [481] log likelihood: -5735.770409
EM: Round [482] log likelihood: -5735.770046
EM: Round [483] log likelihood: -5735.769685
EM: Round [484] log likelihood: -5735.769326
EM: Round [485] log likelihood: -5735.768969
EM: Round [486] log likelihood: -5735.768615
EM: Round [487] log likelihood: -5735.768263
EM: Round [488] log likelihood: -5735.767912
EM: Round [489] log likelihood: -5735.767564
EM: Round [490] log likelihood: -5735.767218
EM: Round [491] log likelihood: -5735.766874
EM: Round [492] log likelihood: -5735.766532
EM: Round [493] log likelihood: -5735.766191
EM: Round [494] log likelihood: -5735.765853
EM: Round [495] log likelihood: -5735.765517
EM: Round [496] log likelihood: -5735.765183
EM: Round [497] log likelihood: -5735.764851
EM: Round [498] log likelihood: -5735.764521
EM: Round [499] log likelihood: -5735.764192
EM: Round [500] log likelihood: -5735.763866
EM: Round [501] log likelihood: -5735.763542
EM: Round [502] log likelihood: -5735.763219
EM: Round [503] log likelihood: -5735.762899
EM: Round [504] log likelihood: -5735.762580
EM: Round [505] log likelihood: -5735.762263
EM: Round [506] log likelihood: -5735.761948
EM: Round [507] log likelihood: -5735.761635
EM: Round [508] log likelihood: -5735.761323
EM: Round [509] log likelihood: -5735.761014
EM: Round [510] log likelihood: -5735.760706
EM: Round [511] log likelihood: -5735.760400
EM: Round [512] log likelihood: -5735.760096
EM: Round [513] log likelihood: -5735.759793
EM: Round [514] log likelihood: -5735.759493
EM: Round [515] log likelihood: -5735.759194
EM: Round [516] log likelihood: -5735.758897
EM: Round [517] log likelihood: -5735.758601
EM: Round [518] log likelihood: -5735.758308
EM: Round [519] log likelihood: -5735.758016
EM: Round [520] log likelihood: -5735.757726
EM: Round [521] log likelihood: -5735.757437
EM: Round [522] log likelihood: -5735.757150
EM: Round [523] log likelihood: -5735.756865
EM: Round [524] log likelihood: -5735.756581
EM: Round [525] log likelihood: -5735.756299
EM: Round [526] log likelihood: -5735.756019
EM: Round [527] log likelihood: -5735.755740
EM: Round [528] log likelihood: -5735.755463
EM: Round [529] log likelihood: -5735.755188
EM: Round [530] log likelihood: -5735.754914
EM: Round [531] log likelihood: -5735.754642
EM: Round [532] log likelihood: -5735.754371
EM: Round [533] log likelihood: -5735.754102
EM: Round [534] log likelihood: -5735.753834
EM: Round [535] log likelihood: -5735.753568
EM: Round [536] log likelihood: -5735.753304
EM: Round [537] log likelihood: -5735.753041
EM: Round [538] log likelihood: -5735.752780
EM: Round [539] log likelihood: -5735.752520
EM: Round [540] log likelihood: -5735.752261
EM: Round [541] log likelihood: -5735.752004
EM: Round [542] log likelihood: -5735.751749
EM: Round [543] log likelihood: -5735.751495
EM: Round [544] log likelihood: -5735.751242
EM: Round [545] log likelihood: -5735.750991
EM: Round [546] log likelihood: -5735.750742
EM: Round [547] log likelihood: -5735.750494
EM: Round [548] log likelihood: -5735.750247
EM: Round [549] log likelihood: -5735.750002
EM: Round [550] log likelihood: -5735.749758
EM: Round [551] log likelihood: -5735.749515
EM: Round [552] log likelihood: -5735.749274
EM: Round [553] log likelihood: -5735.749035
EM: Round [554] log likelihood: -5735.748796
EM: Round [555] log likelihood: -5735.748559
EM: Round [556] log likelihood: -5735.748324
EM: Round [557] log likelihood: -5735.748089
EM: Round [558] log likelihood: -5735.747857
EM: Round [559] log likelihood: -5735.747625
EM: Round [560] log likelihood: -5735.747395
EM: Round [561] log likelihood: -5735.747166
EM: Round [562] log likelihood: -5735.746938
EM: Round [563] log likelihood: -5735.746712
EM: Round [564] log likelihood: -5735.746487
EM: Round [565] log likelihood: -5735.746263
EM: Round [566] log likelihood: -5735.746041
EM: Round [567] log likelihood: -5735.745820
EM: Round [568] log likelihood: -5735.745600
EM: Round [569] log likelihood: -5735.745381
EM: Round [570] log likelihood: -5735.745164
EM: Round [571] log likelihood: -5735.744948
EM: Round [572] log likelihood: -5735.744733
EM: Round [573] log likelihood: -5735.744519
EM: Round [574] log likelihood: -5735.744307
EM: Round [575] log likelihood: -5735.744096
EM: Round [576] log likelihood: -5735.743886
EM: Round [577] log likelihood: -5735.743677
EM: Round [578] log likelihood: -5735.743469
EM: Round [579] log likelihood: -5735.743263
EM: Round [580] log likelihood: -5735.743058
EM: Round [581] log likelihood: -5735.742854
EM: Round [582] log likelihood: -5735.742651
EM: Round [583] log likelihood: -5735.742449
EM: Round [584] log likelihood: -5735.742248
EM: Round [585] log likelihood: -5735.742049
EM: Round [586] log likelihood: -5735.741850
EM: Round [587] log likelihood: -5735.741653
EM: Round [588] log likelihood: -5735.741457
EM: Round [589] log likelihood: -5735.741262
EM: Round [590] log likelihood: -5735.741068
EM: Round [591] log likelihood: -5735.740876
EM: Round [592] log likelihood: -5735.740684
EM: Round [593] log likelihood: -5735.740494
EM: Round [594] log likelihood: -5735.740304
EM: Round [595] log likelihood: -5735.740116
EM: Round [596] log likelihood: -5735.739928
EM: Round [597] log likelihood: -5735.739742
EM: Round [598] log likelihood: -5735.739557
EM: Round [599] log likelihood: -5735.739373
EM: Round [600] log likelihood: -5735.739190
EM: Round [601] log likelihood: -5735.739008
EM: Round [602] log likelihood: -5735.738827
EM: Round [603] log likelihood: -5735.738647
EM: Round [604] log likelihood: -5735.738468
EM: Round [605] log likelihood: -5735.738290
EM: Round [606] log likelihood: -5735.738113
EM: Round [607] log likelihood: -5735.737937
EM: Round [608] log likelihood: -5735.737762
EM: Round [609] log likelihood: -5735.737588
EM: Round [610] log likelihood: -5735.737415
EM: Round [611] log likelihood: -5735.737243
EM: Round [612] log likelihood: -5735.737072
EM: Round [613] log likelihood: -5735.736902
EM: Round [614] log likelihood: -5735.736733
EM: Round [615] log likelihood: -5735.736565
EM: Round [616] log likelihood: -5735.736398
EM: Round [617] log likelihood: -5735.736232
EM: Round [618] log likelihood: -5735.736067
EM: Round [619] log likelihood: -5735.735902
EM: Round [620] log likelihood: -5735.735739
EM: Round [621] log likelihood: -5735.735576
EM: Round [622] log likelihood: -5735.735415
EM: Round [623] log likelihood: -5735.735254
EM: Round [624] log likelihood: -5735.735094
EM: Round [625] log likelihood: -5735.734936
EM: Round [626] log likelihood: -5735.734778
EM: Round [627] log likelihood: -5735.734621
EM: Round [628] log likelihood: -5735.734465
EM: Round [629] log likelihood: -5735.734309
EM: Round [630] log likelihood: -5735.734155
EM: Round [631] log likelihood: -5735.734001
EM: Round [632] log likelihood: -5735.733849
EM: Round [633] log likelihood: -5735.733697
EM: Round [634] log likelihood: -5735.733546
EM: Round [635] log likelihood: -5735.733396
EM: Round [636] log likelihood: -5735.733247
EM: Round [637] log likelihood: -5735.733098
EM: Round [638] log likelihood: -5735.732951
EM: Round [639] log likelihood: -5735.732804
EM: Round [640] log likelihood: -5735.732658
EM: Round [641] log likelihood: -5735.732513
EM: Round [642] log likelihood: -5735.732369
EM: Round [643] log likelihood: -5735.732226
EM: Round [644] log likelihood: -5735.732083
EM: Round [645] log likelihood: -5735.731941
EM: Round [646] log likelihood: -5735.731800
EM: Round [647] log likelihood: -5735.731660
EM: Round [648] log likelihood: -5735.731521
EM: Round [649] log likelihood: -5735.731382
EM: Round [650] log likelihood: -5735.731244
EM: Round [651] log likelihood: -5735.731107
EM: Round [652] log likelihood: -5735.730971
EM: Round [653] log likelihood: -5735.730835
EM: Round [654] log likelihood: -5735.730700
EM: Round [655] log likelihood: -5735.730566
EM: Round [656] log likelihood: -5735.730433
EM: Round [657] log likelihood: -5735.730301
EM: Round [658] log likelihood: -5735.730169
EM: Round [659] log likelihood: -5735.730038
EM: Round [660] log likelihood: -5735.729908
EM: Round [661] log likelihood: -5735.729778
EM: Round [662] log likelihood: -5735.729649
EM: Round [663] log likelihood: -5735.729521
EM: Round [664] log likelihood: -5735.729394
EM: Round [665] log likelihood: -5735.729267
EM: Round [666] log likelihood: -5735.729141
EM: Round [667] log likelihood: -5735.729016
EM: Round [668] log likelihood: -5735.728891
EM: Round [669] log likelihood: -5735.728768
EM: Round [670] log likelihood: -5735.728644
EM: Round [671] log likelihood: -5735.728522
EM: Round [672] log likelihood: -5735.728400
EM: Round [673] log likelihood: -5735.728279
EM: Round [674] log likelihood: -5735.728159
EM: Round [675] log likelihood: -5735.728039
EM: Round [676] log likelihood: -5735.727920
EM: Round [677] log likelihood: -5735.727802
EM: Round [678] log likelihood: -5735.727684
EM: Round [679] log likelihood: -5735.727567
EM: Round [680] log likelihood: -5735.727450
EM: Round [681] log likelihood: -5735.727335
EM: Round [682] log likelihood: -5735.727220
EM: Round [683] log likelihood: -5735.727105
EM: Round [684] log likelihood: -5735.726991
EM: Round [685] log likelihood: -5735.726878
EM: Round [686] log likelihood: -5735.726766
EM: Round [687] log likelihood: -5735.726654
EM: Round [688] log likelihood: -5735.726542
EM: Round [689] log likelihood: -5735.726432
EM: Round [690] log likelihood: -5735.726322
EM: Round [691] log likelihood: -5735.726212
EM: Round [692] log likelihood: -5735.726104
EM: Round [693] log likelihood: -5735.725995
EM: Round [694] log likelihood: -5735.725888
EM: Round [695] log likelihood: -5735.725781
EM: Round [696] log likelihood: -5735.725674
EM: Round [697] log likelihood: -5735.725569
EM: Round [698] log likelihood: -5735.725463
EM: Round [699] log likelihood: -5735.725359
EM: Round [700] log likelihood: -5735.725255
EM: Round [701] log likelihood: -5735.725151
EM: Round [702] log likelihood: -5735.725048
EM: Round [703] log likelihood: -5735.724946
EM: Round [704] log likelihood: -5735.724844
EM: Round [705] log likelihood: -5735.724743
EM: Round [706] log likelihood: -5735.724643
EM: Round [707] log likelihood: -5735.724543
EM: Round [708] log likelihood: -5735.724443
EM: Stopping iterations at round 708 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.u5Dl6gKIDx/aih-tih-sc-488877-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.u5Dl6gKIDx/aih-tih-sc-488877-R1_A23WJ53LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.u5Dl6gKIDx/aih-tih-sc-488877-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.u5Dl6gKIDx/aih-tih-sc-488877-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.u5Dl6gKIDx/aih-tih-sc-488877-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.u5Dl6gKIDx/aih-tih-sc-488877-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.u5Dl6gKIDx/aih-tih-sc-488877-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.u5Dl6gKIDx/fi_workdir/aih-tih-sc-488877-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.u5Dl6gKIDx/fi_workdir/aih-tih-sc-488877-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.u5Dl6gKIDx/fi_workdir/aih-tih-sc-488877-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.u5Dl6gKIDx/aih-tih-sc-488877-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.u5Dl6gKIDx/aih-tih-sc-488877-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3915.802291
EM: Round [1] log likelihood: -3915.625364
EM: Round [2] log likelihood: -3915.625088
EM: Round [3] log likelihood: -3915.625088
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.u5Dl6gKIDx/aih-tih-sc-488877-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 295846524
Warning - not locating file: /tmp/nxf.u5Dl6gKIDx/aih-tih-sc-488877-R1_A23WJ53LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
ls: cannot access 'IGV_inputs': No such file or directory