Done.
-parsing GTF file: /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.bkEML7IVg5/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.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00760_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00760_B23MVV7LT4_1.star.sortedByCoord.out.bam
10:53:20 : INFO : Done.
-parsing GTF file: /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[280000]   -done parsing /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num genes matched < 2' => 1,
          'low complexity anchor region' => 40,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 14,
          'per_id < 96' => 1167,
          'exons hit < 2' => 1,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 61,
          ' ** passed ** ' => 45445,
          'excessive soft clipping' => 1853,
          'seq-similar region overlap' => 56,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 52,
          'small anchor length' => 212
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[7000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2

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[6000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[13000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[43000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[9000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[18000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 429,
          'seq similar region alignment' => 15567
        };
EM: Starting log likelihood: -2001.551866
EM: Round [1] log likelihood: -2001.443877
EM: Round [2] log likelihood: -2001.422332
EM: Round [3] log likelihood: -2001.402281
EM: Round [4] log likelihood: -2001.383474
EM: Round [5] log likelihood: -2001.365809
EM: Round [6] log likelihood: -2001.349195
EM: Round [7] log likelihood: -2001.333551
EM: Round [8] log likelihood: -2001.318805
EM: Round [9] log likelihood: -2001.304892
EM: Round [10] log likelihood: -2001.291750
EM: Round [11] log likelihood: -2001.279326
EM: Round [12] log likelihood: -2001.267570
EM: Round [13] log likelihood: -2001.256437
EM: Round [14] log likelihood: -2001.245885
EM: Round [15] log likelihood: -2001.235876
EM: Round [16] log likelihood: -2001.226376
EM: Round [17] log likelihood: -2001.217351
EM: Round [18] log likelihood: -2001.208772
EM: Round [19] log likelihood: -2001.200612
EM: Round [20] log likelihood: -2001.192845
EM: Round [21] log likelihood: -2001.185446
EM: Round [22] log likelihood: -2001.178395
EM: Round [23] log likelihood: -2001.171671
EM: Round [24] log likelihood: -2001.165254
EM: Round [25] log likelihood: -2001.159127
EM: Round [26] log likelihood: -2001.153274
EM: Round [27] log likelihood: -2001.147678
EM: Round [28] log likelihood: -2001.142326
EM: Round [29] log likelihood: -2001.137204
EM: Round [30] log likelihood: -2001.132299
EM: Round [31] log likelihood: -2001.127599
EM: Round [32] log likelihood: -2001.123093
EM: Round [33] log likelihood: -2001.118770
EM: Round [34] log likelihood: -2001.114622
EM: Round [35] log likelihood: -2001.110638
EM: Round [36] log likelihood: -2001.106810
EM: Round [37] log likelihood: -2001.103129
EM: Round [38] log likelihood: -2001.099588
EM: Round [39] log likelihood: -2001.096180
EM: Round [40] log likelihood: -2001.092897
EM: Round [41] log likelihood: -2001.089734
EM: Round [42] log likelihood: -2001.086684
EM: Round [43] log likelihood: -2001.083741
EM: Round [44] log likelihood: -2001.080900
EM: Round [45] log likelihood: -2001.078156
EM: Round [46] log likelihood: -2001.075504
EM: Round [47] log likelihood: -2001.072939
EM: Round [48] log likelihood: -2001.070456
EM: Round [49] log likelihood: -2001.068053
EM: Round [50] log likelihood: -2001.065725
EM: Round [51] log likelihood: -2001.063467
EM: Round [52] log likelihood: -2001.061278
EM: Round [53] log likelihood: -2001.059152
EM: Round [54] log likelihood: -2001.057088
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EM: Round [57] log likelihood: -2001.051234
EM: Round [58] log likelihood: -2001.049387
EM: Round [59] log likelihood: -2001.047587
EM: Round [60] log likelihood: -2001.045833
EM: Round [61] log likelihood: -2001.044122
EM: Round [62] log likelihood: -2001.042452
EM: Round [63] log likelihood: -2001.040821
EM: Round [64] log likelihood: -2001.039228
EM: Round [65] log likelihood: -2001.037671
EM: Round [66] log likelihood: -2001.036147
EM: Round [67] log likelihood: -2001.034656
EM: Round [68] log likelihood: -2001.033196
EM: Round [69] log likelihood: -2001.031766
EM: Round [70] log likelihood: -2001.030363
EM: Round [71] log likelihood: -2001.028987
EM: Round [72] log likelihood: -2001.027637
EM: Round [73] log likelihood: -2001.026311
EM: Round [74] log likelihood: -2001.025008
EM: Round [75] log likelihood: -2001.023727
EM: Round [76] log likelihood: -2001.022468
EM: Round [77] log likelihood: -2001.021229
EM: Round [78] log likelihood: -2001.020009
EM: Round [79] log likelihood: -2001.018807
EM: Round [80] log likelihood: -2001.017623
EM: Round [81] log likelihood: -2001.016456
EM: Round [82] log likelihood: -2001.015305
EM: Round [83] log likelihood: -2001.014170
EM: Round [84] log likelihood: -2001.013049
EM: Round [85] log likelihood: -2001.011942
EM: Round [86] log likelihood: -2001.010849
EM: Round [87] log likelihood: -2001.009768
EM: Round [88] log likelihood: -2001.008700
EM: Round [89] log likelihood: -2001.007643
EM: Round [90] log likelihood: -2001.006598
EM: Round [91] log likelihood: -2001.005564
EM: Round [92] log likelihood: -2001.004539
EM: Round [93] log likelihood: -2001.003525
EM: Round [94] log likelihood: -2001.002520
EM: Round [95] log likelihood: -2001.001525
EM: Round [96] log likelihood: -2001.000538
EM: Round [97] log likelihood: -2000.999559
EM: Round [98] log likelihood: -2000.998589
EM: Round [99] log likelihood: -2000.997626
EM: Round [100] log likelihood: -2000.996670
EM: Round [101] log likelihood: -2000.995722
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EM: Round [103] log likelihood: -2000.993845
EM: Round [104] log likelihood: -2000.992916
EM: Round [105] log likelihood: -2000.991994
EM: Round [106] log likelihood: -2000.991077
EM: Round [107] log likelihood: -2000.990166
EM: Round [108] log likelihood: -2000.989260
EM: Round [109] log likelihood: -2000.988359
EM: Round [110] log likelihood: -2000.987464
EM: Round [111] log likelihood: -2000.986573
EM: Round [112] log likelihood: -2000.985687
EM: Round [113] log likelihood: -2000.984805
EM: Round [114] log likelihood: -2000.983928
EM: Round [115] log likelihood: -2000.983055
EM: Round [116] log likelihood: -2000.982186
EM: Round [117] log likelihood: -2000.981321
EM: Round [118] log likelihood: -2000.980460
EM: Round [119] log likelihood: -2000.979602
EM: Round [120] log likelihood: -2000.978748
EM: Round [121] log likelihood: -2000.977898
EM: Round [122] log likelihood: -2000.977050
EM: Round [123] log likelihood: -2000.976206
EM: Round [124] log likelihood: -2000.975365
EM: Round [125] log likelihood: -2000.974528
EM: Round [126] log likelihood: -2000.973693
EM: Round [127] log likelihood: -2000.972861
EM: Round [128] log likelihood: -2000.972032
EM: Round [129] log likelihood: -2000.971205
EM: Round [130] log likelihood: -2000.970381
EM: Round [131] log likelihood: -2000.969560
EM: Round [132] log likelihood: -2000.968741
EM: Round [133] log likelihood: -2000.967925
EM: Round [134] log likelihood: -2000.967111
EM: Round [135] log likelihood: -2000.966300
EM: Round [136] log likelihood: -2000.965490
EM: Round [137] log likelihood: -2000.964683
EM: Round [138] log likelihood: -2000.963879
EM: Round [139] log likelihood: -2000.963076
EM: Round [140] log likelihood: -2000.962275
EM: Round [141] log likelihood: -2000.961477
EM: Round [142] log likelihood: -2000.960680
EM: Round [143] log likelihood: -2000.959886
EM: Round [144] log likelihood: -2000.959093
EM: Round [145] log likelihood: -2000.958302
EM: Round [146] log likelihood: -2000.957513
EM: Round [147] log likelihood: -2000.956726
EM: Round [148] log likelihood: -2000.955941
EM: Round [149] log likelihood: -2000.955157
EM: Round [150] log likelihood: -2000.954375
EM: Round [151] log likelihood: -2000.953595
EM: Round [152] log likelihood: -2000.952817
EM: Round [153] log likelihood: -2000.952040
EM: Round [154] log likelihood: -2000.951265
EM: Round [155] log likelihood: -2000.950492
EM: Round [156] log likelihood: -2000.949720
EM: Round [157] log likelihood: -2000.948949
EM: Round [158] log likelihood: -2000.948180
EM: Round [159] log likelihood: -2000.947413
EM: Round [160] log likelihood: -2000.946647
EM: Round [161] log likelihood: -2000.945883
EM: Round [162] log likelihood: -2000.945120
EM: Round [163] log likelihood: -2000.944359
EM: Round [164] log likelihood: -2000.943599
EM: Round [165] log likelihood: -2000.942841
EM: Round [166] log likelihood: -2000.942084
EM: Round [167] log likelihood: -2000.941328
EM: Round [168] log likelihood: -2000.940574
EM: Round [169] log likelihood: -2000.939821
EM: Round [170] log likelihood: -2000.939069
EM: Round [171] log likelihood: -2000.938319
EM: Round [172] log likelihood: -2000.937570
EM: Round [173] log likelihood: -2000.936823
EM: Round [174] log likelihood: -2000.936076
EM: Round [175] log likelihood: -2000.935332
EM: Round [176] log likelihood: -2000.934588
EM: Round [177] log likelihood: -2000.933846
EM: Round [178] log likelihood: -2000.933105
EM: Round [179] log likelihood: -2000.932365
EM: Round [180] log likelihood: -2000.931627
EM: Round [181] log likelihood: -2000.930889
EM: Round [182] log likelihood: -2000.930153
EM: Round [183] log likelihood: -2000.929419
EM: Round [184] log likelihood: -2000.928685
EM: Round [185] log likelihood: -2000.927953
EM: Round [186] log likelihood: -2000.927222
EM: Round [187] log likelihood: -2000.926492
EM: Round [188] log likelihood: -2000.925764
EM: Round [189] log likelihood: -2000.925036
EM: Round [190] log likelihood: -2000.924310
EM: Round [191] log likelihood: -2000.923585
EM: Round [192] log likelihood: -2000.922861
EM: Round [193] log likelihood: -2000.922138
EM: Round [194] log likelihood: -2000.921417
EM: Round [195] log likelihood: -2000.920697
EM: Round [196] log likelihood: -2000.919978
EM: Round [197] log likelihood: -2000.919260
EM: Round [198] log likelihood: -2000.918543
EM: Round [199] log likelihood: -2000.917827
EM: Round [200] log likelihood: -2000.917113
EM: Round [201] log likelihood: -2000.916399
EM: Round [202] log likelihood: -2000.915687
EM: Round [203] log likelihood: -2000.914976
EM: Round [204] log likelihood: -2000.914266
EM: Round [205] log likelihood: -2000.913557
EM: Round [206] log likelihood: -2000.912850
EM: Round [207] log likelihood: -2000.912143
EM: Round [208] log likelihood: -2000.911438
EM: Round [209] log likelihood: -2000.910734
EM: Round [210] log likelihood: -2000.910030
EM: Round [211] log likelihood: -2000.909328
EM: Round [212] log likelihood: -2000.908627
EM: Round [213] log likelihood: -2000.907927
EM: Round [214] log likelihood: -2000.907229
EM: Round [215] log likelihood: -2000.906531
EM: Round [216] log likelihood: -2000.905834
EM: Round [217] log likelihood: -2000.905139
EM: Round [218] log likelihood: -2000.904444
EM: Round [219] log likelihood: -2000.903751
EM: Round [220] log likelihood: -2000.903059
EM: Round [221] log likelihood: -2000.902368
EM: Round [222] log likelihood: -2000.901678
EM: Round [223] log likelihood: -2000.900989
EM: Round [224] log likelihood: -2000.900301
EM: Round [225] log likelihood: -2000.899614
EM: Round [226] log likelihood: -2000.898928
EM: Round [227] log likelihood: -2000.898243
EM: Round [228] log likelihood: -2000.897560
EM: Round [229] log likelihood: -2000.896877
EM: Round [230] log likelihood: -2000.896196
EM: Round [231] log likelihood: -2000.895515
EM: Round [232] log likelihood: -2000.894836
EM: Round [233] log likelihood: -2000.894157
EM: Round [234] log likelihood: -2000.893480
EM: Round [235] log likelihood: -2000.892804
EM: Round [236] log likelihood: -2000.892128
EM: Round [237] log likelihood: -2000.891454
EM: Round [238] log likelihood: -2000.890781
EM: Round [239] log likelihood: -2000.890109
EM: Round [240] log likelihood: -2000.889438
EM: Round [241] log likelihood: -2000.888768
EM: Round [242] log likelihood: -2000.888099
EM: Round [243] log likelihood: -2000.887431
EM: Round [244] log likelihood: -2000.886764
EM: Round [245] log likelihood: -2000.886098
EM: Round [246] log likelihood: -2000.885433
EM: Round [247] log likelihood: -2000.884769
EM: Round [248] log likelihood: -2000.884106
EM: Round [249] log likelihood: -2000.883444
EM: Round [250] log likelihood: -2000.882783
EM: Round [251] log likelihood: -2000.882123
EM: Round [252] log likelihood: -2000.881464
EM: Round [253] log likelihood: -2000.880807
EM: Round [254] log likelihood: -2000.880150
EM: Round [255] log likelihood: -2000.879494
EM: Round [256] log likelihood: -2000.878839
EM: Round [257] log likelihood: -2000.878185
EM: Round [258] log likelihood: -2000.877533
EM: Round [259] log likelihood: -2000.876881
EM: Round [260] log likelihood: -2000.876230
EM: Round [261] log likelihood: -2000.875580
EM: Round [262] log likelihood: -2000.874931
EM: Round [263] log likelihood: -2000.874283
EM: Round [264] log likelihood: -2000.873637
EM: Round [265] log likelihood: -2000.872991
EM: Round [266] log likelihood: -2000.872346
EM: Round [267] log likelihood: -2000.871702
EM: Round [268] log likelihood: -2000.871059
EM: Round [269] log likelihood: -2000.870417
EM: Round [270] log likelihood: -2000.869776
EM: Round [271] log likelihood: -2000.869136
EM: Round [272] log likelihood: -2000.868497
EM: Round [273] log likelihood: -2000.867859
EM: Round [274] log likelihood: -2000.867222
EM: Round [275] log likelihood: -2000.866586
EM: Round [276] log likelihood: -2000.865951
EM: Round [277] log likelihood: -2000.865317
EM: Round [278] log likelihood: -2000.864683
EM: Round [279] log likelihood: -2000.864051
EM: Round [280] log likelihood: -2000.863420
EM: Round [281] log likelihood: -2000.862789
EM: Round [282] log likelihood: -2000.862160
EM: Round [283] log likelihood: -2000.861532
EM: Round [284] log likelihood: -2000.860904
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EM: Round [772] log likelihood: -2000.642870
EM: Round [773] log likelihood: -2000.642562
EM: Round [774] log likelihood: -2000.642255
EM: Round [775] log likelihood: -2000.641948
EM: Round [776] log likelihood: -2000.641641
EM: Round [777] log likelihood: -2000.641335
EM: Round [778] log likelihood: -2000.641030
EM: Round [779] log likelihood: -2000.640725
EM: Round [780] log likelihood: -2000.640420
EM: Round [781] log likelihood: -2000.640116
EM: Round [782] log likelihood: -2000.639812
EM: Round [783] log likelihood: -2000.639508
EM: Round [784] log likelihood: -2000.639205
EM: Round [785] log likelihood: -2000.638903
EM: Round [786] log likelihood: -2000.638601
EM: Round [787] log likelihood: -2000.638299
EM: Round [788] log likelihood: -2000.637998
EM: Round [789] log likelihood: -2000.637697
EM: Round [790] log likelihood: -2000.637396
EM: Round [791] log likelihood: -2000.637096
EM: Round [792] log likelihood: -2000.636797
EM: Round [793] log likelihood: -2000.636498
EM: Round [794] log likelihood: -2000.636199
EM: Round [795] log likelihood: -2000.635901
EM: Round [796] log likelihood: -2000.635603
EM: Round [797] log likelihood: -2000.635305
EM: Round [798] log likelihood: -2000.635008
EM: Round [799] log likelihood: -2000.634712
EM: Round [800] log likelihood: -2000.634415
EM: Round [801] log likelihood: -2000.634119
EM: Round [802] log likelihood: -2000.633824
EM: Round [803] log likelihood: -2000.633529
EM: Round [804] log likelihood: -2000.633235
EM: Round [805] log likelihood: -2000.632940
EM: Round [806] log likelihood: -2000.632647
EM: Round [807] log likelihood: -2000.632353
EM: Round [808] log likelihood: -2000.632060
EM: Round [809] log likelihood: -2000.631768
EM: Round [810] log likelihood: -2000.631476
EM: Round [811] log likelihood: -2000.631184
EM: Round [812] log likelihood: -2000.630893
EM: Round [813] log likelihood: -2000.630602
EM: Round [814] log likelihood: -2000.630311
EM: Round [815] log likelihood: -2000.630021
EM: Round [816] log likelihood: -2000.629732
EM: Round [817] log likelihood: -2000.629443
EM: Round [818] log likelihood: -2000.629154
EM: Round [819] log likelihood: -2000.628865
EM: Round [820] log likelihood: -2000.628577
EM: Round [821] log likelihood: -2000.628290
EM: Round [822] log likelihood: -2000.628002
EM: Round [823] log likelihood: -2000.627716
EM: Round [824] log likelihood: -2000.627429
EM: Round [825] log likelihood: -2000.627143
EM: Round [826] log likelihood: -2000.626858
EM: Round [827] log likelihood: -2000.626572
EM: Round [828] log likelihood: -2000.626288
EM: Round [829] log likelihood: -2000.626003
EM: Round [830] log likelihood: -2000.625719
EM: Round [831] log likelihood: -2000.625436
EM: Round [832] log likelihood: -2000.625152
EM: Round [833] log likelihood: -2000.624869
EM: Round [834] log likelihood: -2000.624587
EM: Round [835] log likelihood: -2000.624305
EM: Round [836] log likelihood: -2000.624023
EM: Round [837] log likelihood: -2000.623742
EM: Round [838] log likelihood: -2000.623461
EM: Round [839] log likelihood: -2000.623181
EM: Round [840] log likelihood: -2000.622901
EM: Round [841] log likelihood: -2000.622621
EM: Round [842] log likelihood: -2000.622342
EM: Round [843] log likelihood: -2000.622063
EM: Round [844] log likelihood: -2000.621785
EM: Round [845] log likelihood: -2000.621506
EM: Round [846] log likelihood: -2000.621229
EM: Round [847] log likelihood: -2000.620951
EM: Round [848] log likelihood: -2000.620674
EM: Round [849] log likelihood: -2000.620398
EM: Round [850] log likelihood: -2000.620122
EM: Round [851] log likelihood: -2000.619846
EM: Round [852] log likelihood: -2000.619571
EM: Round [853] log likelihood: -2000.619296
EM: Round [854] log likelihood: -2000.619021
EM: Round [855] log likelihood: -2000.618747
EM: Round [856] log likelihood: -2000.618473
EM: Round [857] log likelihood: -2000.618199
EM: Round [858] log likelihood: -2000.617926
EM: Round [859] log likelihood: -2000.617654
EM: Round [860] log likelihood: -2000.617381
EM: Round [861] log likelihood: -2000.617109
EM: Round [862] log likelihood: -2000.616838
EM: Round [863] log likelihood: -2000.616567
EM: Round [864] log likelihood: -2000.616296
EM: Round [865] log likelihood: -2000.616025
EM: Round [866] log likelihood: -2000.615755
EM: Round [867] log likelihood: -2000.615486
EM: Round [868] log likelihood: -2000.615216
EM: Round [869] log likelihood: -2000.614947
EM: Round [870] log likelihood: -2000.614679
EM: Round [871] log likelihood: -2000.614411
EM: Round [872] log likelihood: -2000.614143
EM: Round [873] log likelihood: -2000.613876
EM: Round [874] log likelihood: -2000.613609
EM: Round [875] log likelihood: -2000.613342
EM: Round [876] log likelihood: -2000.613076
EM: Round [877] log likelihood: -2000.612810
EM: Round [878] log likelihood: -2000.612544
EM: Round [879] log likelihood: -2000.612279
EM: Round [880] log likelihood: -2000.612014
EM: Round [881] log likelihood: -2000.611750
EM: Round [882] log likelihood: -2000.611486
EM: Round [883] log likelihood: -2000.611222
EM: Round [884] log likelihood: -2000.610958
EM: Round [885] log likelihood: -2000.610696
EM: Round [886] log likelihood: -2000.610433
EM: Round [887] log likelihood: -2000.610171
EM: Round [888] log likelihood: -2000.609909
EM: Round [889] log likelihood: -2000.609647
EM: Round [890] log likelihood: -2000.609386
EM: Round [891] log likelihood: -2000.609125
EM: Round [892] log likelihood: -2000.608865
EM: Round [893] log likelihood: -2000.608605
EM: Round [894] log likelihood: -2000.608345
EM: Round [895] log likelihood: -2000.608086
EM: Round [896] log likelihood: -2000.607827
EM: Round [897] log likelihood: -2000.607568
EM: Round [898] log likelihood: -2000.607310
EM: Round [899] log likelihood: -2000.607052
EM: Round [900] log likelihood: -2000.606795
EM: Round [901] log likelihood: -2000.606537
EM: Round [902] log likelihood: -2000.606281
EM: Round [903] log likelihood: -2000.606024
EM: Round [904] log likelihood: -2000.605768
EM: Round [905] log likelihood: -2000.605512
EM: Round [906] log likelihood: -2000.605257
EM: Round [907] log likelihood: -2000.605002
EM: Round [908] log likelihood: -2000.604747
EM: Round [909] log likelihood: -2000.604493
EM: Round [910] log likelihood: -2000.604239
EM: Round [911] log likelihood: -2000.603985
EM: Round [912] log likelihood: -2000.603732
EM: Round [913] log likelihood: -2000.603479
EM: Round [914] log likelihood: -2000.603227
EM: Round [915] log likelihood: -2000.602974
EM: Round [916] log likelihood: -2000.602723
EM: Round [917] log likelihood: -2000.602471
EM: Round [918] log likelihood: -2000.602220
EM: Round [919] log likelihood: -2000.601969
EM: Round [920] log likelihood: -2000.601719
EM: Round [921] log likelihood: -2000.601469
EM: Round [922] log likelihood: -2000.601219
EM: Round [923] log likelihood: -2000.600969
EM: Round [924] log likelihood: -2000.600720
EM: Round [925] log likelihood: -2000.600472
EM: Round [926] log likelihood: -2000.600223
EM: Round [927] log likelihood: -2000.599975
EM: Round [928] log likelihood: -2000.599728
EM: Round [929] log likelihood: -2000.599480
EM: Round [930] log likelihood: -2000.599233
EM: Round [931] log likelihood: -2000.598987
EM: Round [932] log likelihood: -2000.598740
EM: Round [933] log likelihood: -2000.598494
EM: Round [934] log likelihood: -2000.598249
EM: Round [935] log likelihood: -2000.598003
EM: Round [936] log likelihood: -2000.597758
EM: Round [937] log likelihood: -2000.597514
EM: Round [938] log likelihood: -2000.597270
EM: Round [939] log likelihood: -2000.597026
EM: Round [940] log likelihood: -2000.596782
EM: Round [941] log likelihood: -2000.596539
EM: Round [942] log likelihood: -2000.596296
EM: Round [943] log likelihood: -2000.596053
EM: Round [944] log likelihood: -2000.595811
EM: Round [945] log likelihood: -2000.595569
EM: Round [946] log likelihood: -2000.595328
EM: Round [947] log likelihood: -2000.595086
EM: Round [948] log likelihood: -2000.594845
EM: Round [949] log likelihood: -2000.594605
EM: Round [950] log likelihood: -2000.594365
EM: Round [951] log likelihood: -2000.594125
EM: Round [952] log likelihood: -2000.593885
EM: Round [953] log likelihood: -2000.593646
EM: Round [954] log likelihood: -2000.593407
EM: Round [955] log likelihood: -2000.593169
EM: Round [956] log likelihood: -2000.592930
EM: Round [957] log likelihood: -2000.592692
EM: Round [958] log likelihood: -2000.592455
EM: Round [959] log likelihood: -2000.592218
EM: Round [960] log likelihood: -2000.591981
EM: Round [961] log likelihood: -2000.591744
EM: Round [962] log likelihood: -2000.591508
EM: Round [963] log likelihood: -2000.591272
EM: Round [964] log likelihood: -2000.591036
EM: Round [965] log likelihood: -2000.590801
EM: Round [966] log likelihood: -2000.590566
EM: Round [967] log likelihood: -2000.590331
EM: Round [968] log likelihood: -2000.590097
EM: Round [969] log likelihood: -2000.589863
EM: Round [970] log likelihood: -2000.589630
EM: Round [971] log likelihood: -2000.589396
EM: Round [972] log likelihood: -2000.589163
EM: Round [973] log likelihood: -2000.588930
EM: Round [974] log likelihood: -2000.588698
EM: Round [975] log likelihood: -2000.588466
EM: Round [976] log likelihood: -2000.588234
EM: Round [977] log likelihood: -2000.588003
EM: Round [978] log likelihood: -2000.587772
EM: Round [979] log likelihood: -2000.587541
EM: Round [980] log likelihood: -2000.587311
EM: Round [981] log likelihood: -2000.587081
EM: Round [982] log likelihood: -2000.586851
EM: Round [983] log likelihood: -2000.586621
EM: Round [984] log likelihood: -2000.586392
EM: Round [985] log likelihood: -2000.586163
EM: Round [986] log likelihood: -2000.585935
EM: Round [987] log likelihood: -2000.585707
EM: Round [988] log likelihood: -2000.585479
EM: Round [989] log likelihood: -2000.585251
EM: Round [990] log likelihood: -2000.585024
EM: Round [991] log likelihood: -2000.584797
EM: Round [992] log likelihood: -2000.584570
EM: Round [993] log likelihood: -2000.584344
EM: Round [994] log likelihood: -2000.584118
EM: Round [995] log likelihood: -2000.583892
EM: Round [996] log likelihood: -2000.583667
EM: Round [997] log likelihood: -2000.583442
EM: Round [998] log likelihood: -2000.583217
EM: Round [999] log likelihood: -2000.582992
EM: Round [1000] log likelihood: -2000.582768
EM: Round [1001] log likelihood: -2000.582544
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_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.bkEML7IVg5/fi_workdir/tih_rna_sample_00760_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1471.053203
EM: Round [1] log likelihood: -1471.040550
EM: Round [2] log likelihood: -1471.040412
EM: Round [3] log likelihood: -1471.040410
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1_1.fastp.fastq.gz: 239789527
Warning - not locating file: /tmp/nxf.bkEML7IVg5/tih_rna_sample_00760_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
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 [ENSG00000280136.2]
ls: cannot access 'IGV_inputs': No such file or directory