Done.
-parsing GTF file: /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.DXIqsdmJjc/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.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00628_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00628_B23MVV7LT4_1.star.sortedByCoord.out.bam
12:00:08 : INFO : Done.
-parsing GTF file: /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[1480000]   -done parsing /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'seq-similar region overlap' => 34,
          'per_id < 96' => 3366,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 34,
          'exons hit < 2' => 3,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 16,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 87,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 54,
          'small anchor length' => 90,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 472,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 16,
          ' ** passed ** ' => 15847,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 12,
          'excessive soft clipping' => 7902,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 203,
          'num genes matched < 2' => 1266,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 30
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[298000]   -fusion SPANNING read extraction for scaff: AC073325.1--ADCY1

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[21000]   -fusion SPANNING read extraction for scaff: AC079610.2--IKZF2

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[9000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[41000]   -fusion SPANNING read extraction for scaff: COX6CP1--COX6C

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[33000]   -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1

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[116000]   -fusion SPANNING read extraction for scaff: GUSB--NAIPP4

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[21000]   -fusion SPANNING read extraction for scaff: IKZF2--LINC01953

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[5000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

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[21000]   -fusion SPANNING read extraction for scaff: LINC01953--IKZF2

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[50000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1

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[46000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2

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[59000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13

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[89000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

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[80000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[76000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[10000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

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[9000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

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[9000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

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[6000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

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[5000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

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[57000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

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[25000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

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[23000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[9000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[5000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[58000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[26000]   -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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[76000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[23000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[25000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

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[5000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[29000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 14959,
          'seq similar region alignment' => 19358
        };
EM: Starting log likelihood: -7306.158642
EM: Round [1] log likelihood: -7294.734291
EM: Round [2] log likelihood: -7294.200537
EM: Round [3] log likelihood: -7293.842685
EM: Round [4] log likelihood: -7293.562309
EM: Round [5] log likelihood: -7293.328182
EM: Round [6] log likelihood: -7293.125281
EM: Round [7] log likelihood: -7292.945538
EM: Round [8] log likelihood: -7292.784107
EM: Round [9] log likelihood: -7292.637748
EM: Round [10] log likelihood: -7292.504092
EM: Round [11] log likelihood: -7292.381287
EM: Round [12] log likelihood: -7292.267824
EM: Round [13] log likelihood: -7292.162444
EM: Round [14] log likelihood: -7292.064077
EM: Round [15] log likelihood: -7291.971814
EM: Round [16] log likelihood: -7291.884877
EM: Round [17] log likelihood: -7291.802604
EM: Round [18] log likelihood: -7291.724427
EM: Round [19] log likelihood: -7291.649866
EM: Round [20] log likelihood: -7291.578508
EM: Round [21] log likelihood: -7291.510007
EM: Round [22] log likelihood: -7291.444064
EM: Round [23] log likelihood: -7291.380428
EM: Round [24] log likelihood: -7291.318885
EM: Round [25] log likelihood: -7291.259249
EM: Round [26] log likelihood: -7291.201366
EM: Round [27] log likelihood: -7291.145099
EM: Round [28] log likelihood: -7291.090332
EM: Round [29] log likelihood: -7291.036964
EM: Round [30] log likelihood: -7290.984908
EM: Round [31] log likelihood: -7290.934085
EM: Round [32] log likelihood: -7290.884429
EM: Round [33] log likelihood: -7290.835878
EM: Round [34] log likelihood: -7290.788378
EM: Round [35] log likelihood: -7290.741881
EM: Round [36] log likelihood: -7290.696343
EM: Round [37] log likelihood: -7290.651724
EM: Round [38] log likelihood: -7290.607986
EM: Round [39] log likelihood: -7290.565096
EM: Round [40] log likelihood: -7290.523024
EM: Round [41] log likelihood: -7290.481739
EM: Round [42] log likelihood: -7290.441214
EM: Round [43] log likelihood: -7290.401425
EM: Round [44] log likelihood: -7290.362347
EM: Round [45] log likelihood: -7290.323958
EM: Round [46] log likelihood: -7290.286236
EM: Round [47] log likelihood: -7290.249162
EM: Round [48] log likelihood: -7290.212716
EM: Round [49] log likelihood: -7290.176880
EM: Round [50] log likelihood: -7290.141637
EM: Round [51] log likelihood: -7290.106970
EM: Round [52] log likelihood: -7290.072864
EM: Round [53] log likelihood: -7290.039303
EM: Round [54] log likelihood: -7290.006273
EM: Round [55] log likelihood: -7289.973760
EM: Round [56] log likelihood: -7289.941750
EM: Round [57] log likelihood: -7289.910232
EM: Round [58] log likelihood: -7289.879192
EM: Round [59] log likelihood: -7289.848619
EM: Round [60] log likelihood: -7289.818502
EM: Round [61] log likelihood: -7289.788829
EM: Round [62] log likelihood: -7289.759590
EM: Round [63] log likelihood: -7289.730775
EM: Round [64] log likelihood: -7289.702374
EM: Round [65] log likelihood: -7289.674378
EM: Round [66] log likelihood: -7289.646777
EM: Round [67] log likelihood: -7289.619563
EM: Round [68] log likelihood: -7289.592727
EM: Round [69] log likelihood: -7289.566260
EM: Round [70] log likelihood: -7289.540156
EM: Round [71] log likelihood: -7289.514405
EM: Round [72] log likelihood: -7289.489001
EM: Round [73] log likelihood: -7289.463937
EM: Round [74] log likelihood: -7289.439205
EM: Round [75] log likelihood: -7289.414798
EM: Round [76] log likelihood: -7289.390710
EM: Round [77] log likelihood: -7289.366935
EM: Round [78] log likelihood: -7289.343466
EM: Round [79] log likelihood: -7289.320298
EM: Round [80] log likelihood: -7289.297424
EM: Round [81] log likelihood: -7289.274838
EM: Round [82] log likelihood: -7289.252536
EM: Round [83] log likelihood: -7289.230512
EM: Round [84] log likelihood: -7289.208760
EM: Round [85] log likelihood: -7289.187276
EM: Round [86] log likelihood: -7289.166054
EM: Round [87] log likelihood: -7289.145090
EM: Round [88] log likelihood: -7289.124379
EM: Round [89] log likelihood: -7289.103917
EM: Round [90] log likelihood: -7289.083699
EM: Round [91] log likelihood: -7289.063721
EM: Round [92] log likelihood: -7289.043978
EM: Round [93] log likelihood: -7289.024467
EM: Round [94] log likelihood: -7289.005183
EM: Round [95] log likelihood: -7288.986123
EM: Round [96] log likelihood: -7288.967283
EM: Round [97] log likelihood: -7288.948659
EM: Round [98] log likelihood: -7288.930247
EM: Round [99] log likelihood: -7288.912044
EM: Round [100] log likelihood: -7288.894046
EM: Round [101] log likelihood: -7288.876251
EM: Round [102] log likelihood: -7288.858654
EM: Round [103] log likelihood: -7288.841253
EM: Round [104] log likelihood: -7288.824045
EM: Round [105] log likelihood: -7288.807026
EM: Round [106] log likelihood: -7288.790193
EM: Round [107] log likelihood: -7288.773544
EM: Round [108] log likelihood: -7288.757076
EM: Round [109] log likelihood: -7288.740785
EM: Round [110] log likelihood: -7288.724669
EM: Round [111] log likelihood: -7288.708726
EM: Round [112] log likelihood: -7288.692952
EM: Round [113] log likelihood: -7288.677346
EM: Round [114] log likelihood: -7288.661905
EM: Round [115] log likelihood: -7288.646625
EM: Round [116] log likelihood: -7288.631506
EM: Round [117] log likelihood: -7288.616544
EM: Round [118] log likelihood: -7288.601737
EM: Round [119] log likelihood: -7288.587083
EM: Round [120] log likelihood: -7288.572580
EM: Round [121] log likelihood: -7288.558226
EM: Round [122] log likelihood: -7288.544018
EM: Round [123] log likelihood: -7288.529954
EM: Round [124] log likelihood: -7288.516033
EM: Round [125] log likelihood: -7288.502252
EM: Round [126] log likelihood: -7288.488609
EM: Round [127] log likelihood: -7288.475103
EM: Round [128] log likelihood: -7288.461731
EM: Round [129] log likelihood: -7288.448492
EM: Round [130] log likelihood: -7288.435384
EM: Round [131] log likelihood: -7288.422405
EM: Round [132] log likelihood: -7288.409553
EM: Round [133] log likelihood: -7288.396827
EM: Round [134] log likelihood: -7288.384225
EM: Round [135] log likelihood: -7288.371746
EM: Round [136] log likelihood: -7288.359387
EM: Round [137] log likelihood: -7288.347147
EM: Round [138] log likelihood: -7288.335024
EM: Round [139] log likelihood: -7288.323018
EM: Round [140] log likelihood: -7288.311126
EM: Round [141] log likelihood: -7288.299347
EM: Round [142] log likelihood: -7288.287680
EM: Round [143] log likelihood: -7288.276123
EM: Round [144] log likelihood: -7288.264675
EM: Round [145] log likelihood: -7288.253334
EM: Round [146] log likelihood: -7288.242099
EM: Round [147] log likelihood: -7288.230968
EM: Round [148] log likelihood: -7288.219941
EM: Round [149] log likelihood: -7288.209017
EM: Round [150] log likelihood: -7288.198193
EM: Round [151] log likelihood: -7288.187468
EM: Round [152] log likelihood: -7288.176842
EM: Round [153] log likelihood: -7288.166313
EM: Round [154] log likelihood: -7288.155880
EM: Round [155] log likelihood: -7288.145542
EM: Round [156] log likelihood: -7288.135297
EM: Round [157] log likelihood: -7288.125145
EM: Round [158] log likelihood: -7288.115084
EM: Round [159] log likelihood: -7288.105114
EM: Round [160] log likelihood: -7288.095233
EM: Round [161] log likelihood: -7288.085440
EM: Round [162] log likelihood: -7288.075734
EM: Round [163] log likelihood: -7288.066115
EM: Round [164] log likelihood: -7288.056580
EM: Round [165] log likelihood: -7288.047130
EM: Round [166] log likelihood: -7288.037763
EM: Round [167] log likelihood: -7288.028478
EM: Round [168] log likelihood: -7288.019274
EM: Round [169] log likelihood: -7288.010150
EM: Round [170] log likelihood: -7288.001106
EM: Round [171] log likelihood: -7287.992141
EM: Round [172] log likelihood: -7287.983253
EM: Round [173] log likelihood: -7287.974442
EM: Round [174] log likelihood: -7287.965706
EM: Round [175] log likelihood: -7287.957046
EM: Round [176] log likelihood: -7287.948460
EM: Round [177] log likelihood: -7287.939947
EM: Round [178] log likelihood: -7287.931507
EM: Round [179] log likelihood: -7287.923138
EM: Round [180] log likelihood: -7287.914840
EM: Round [181] log likelihood: -7287.906613
EM: Round [182] log likelihood: -7287.898455
EM: Round [183] log likelihood: -7287.890365
EM: Round [184] log likelihood: -7287.882344
EM: Round [185] log likelihood: -7287.874389
EM: Round [186] log likelihood: -7287.866501
EM: Round [187] log likelihood: -7287.858679
EM: Round [188] log likelihood: -7287.850922
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EM: Round [649] log likelihood: -7286.771904
EM: Round [650] log likelihood: -7286.771358
EM: Round [651] log likelihood: -7286.770814
EM: Round [652] log likelihood: -7286.770272
EM: Round [653] log likelihood: -7286.769732
EM: Round [654] log likelihood: -7286.769194
EM: Round [655] log likelihood: -7286.768659
EM: Round [656] log likelihood: -7286.768125
EM: Round [657] log likelihood: -7286.767593
EM: Round [658] log likelihood: -7286.767064
EM: Round [659] log likelihood: -7286.766536
EM: Round [660] log likelihood: -7286.766011
EM: Round [661] log likelihood: -7286.765487
EM: Round [662] log likelihood: -7286.764966
EM: Round [663] log likelihood: -7286.764446
EM: Round [664] log likelihood: -7286.763929
EM: Round [665] log likelihood: -7286.763413
EM: Round [666] log likelihood: -7286.762900
EM: Round [667] log likelihood: -7286.762388
EM: Round [668] log likelihood: -7286.761878
EM: Round [669] log likelihood: -7286.761370
EM: Round [670] log likelihood: -7286.760864
EM: Round [671] log likelihood: -7286.760360
EM: Round [672] log likelihood: -7286.759858
EM: Round [673] log likelihood: -7286.759358
EM: Round [674] log likelihood: -7286.758860
EM: Round [675] log likelihood: -7286.758363
EM: Round [676] log likelihood: -7286.757869
EM: Round [677] log likelihood: -7286.757376
EM: Round [678] log likelihood: -7286.756885
EM: Round [679] log likelihood: -7286.756396
EM: Round [680] log likelihood: -7286.755908
EM: Round [681] log likelihood: -7286.755423
EM: Round [682] log likelihood: -7286.754939
EM: Round [683] log likelihood: -7286.754457
EM: Round [684] log likelihood: -7286.753977
EM: Round [685] log likelihood: -7286.753498
EM: Round [686] log likelihood: -7286.753022
EM: Round [687] log likelihood: -7286.752547
EM: Round [688] log likelihood: -7286.752074
EM: Round [689] log likelihood: -7286.751602
EM: Round [690] log likelihood: -7286.751132
EM: Round [691] log likelihood: -7286.750664
EM: Round [692] log likelihood: -7286.750198
EM: Round [693] log likelihood: -7286.749733
EM: Round [694] log likelihood: -7286.749270
EM: Round [695] log likelihood: -7286.748809
EM: Round [696] log likelihood: -7286.748349
EM: Round [697] log likelihood: -7286.747891
EM: Round [698] log likelihood: -7286.747435
EM: Round [699] log likelihood: -7286.746980
EM: Round [700] log likelihood: -7286.746527
EM: Round [701] log likelihood: -7286.746076
EM: Round [702] log likelihood: -7286.745626
EM: Round [703] log likelihood: -7286.745178
EM: Round [704] log likelihood: -7286.744731
EM: Round [705] log likelihood: -7286.744286
EM: Round [706] log likelihood: -7286.743843
EM: Round [707] log likelihood: -7286.743401
EM: Round [708] log likelihood: -7286.742960
EM: Round [709] log likelihood: -7286.742521
EM: Round [710] log likelihood: -7286.742084
EM: Round [711] log likelihood: -7286.741648
EM: Round [712] log likelihood: -7286.741214
EM: Round [713] log likelihood: -7286.740782
EM: Round [714] log likelihood: -7286.740350
EM: Round [715] log likelihood: -7286.739921
EM: Round [716] log likelihood: -7286.739493
EM: Round [717] log likelihood: -7286.739066
EM: Round [718] log likelihood: -7286.738641
EM: Round [719] log likelihood: -7286.738217
EM: Round [720] log likelihood: -7286.737795
EM: Round [721] log likelihood: -7286.737374
EM: Round [722] log likelihood: -7286.736955
EM: Round [723] log likelihood: -7286.736537
EM: Round [724] log likelihood: -7286.736121
EM: Round [725] log likelihood: -7286.735706
EM: Round [726] log likelihood: -7286.735292
EM: Round [727] log likelihood: -7286.734880
EM: Round [728] log likelihood: -7286.734469
EM: Round [729] log likelihood: -7286.734060
EM: Round [730] log likelihood: -7286.733652
EM: Round [731] log likelihood: -7286.733245
EM: Round [732] log likelihood: -7286.732840
EM: Round [733] log likelihood: -7286.732436
EM: Round [734] log likelihood: -7286.732034
EM: Round [735] log likelihood: -7286.731633
EM: Round [736] log likelihood: -7286.731233
EM: Round [737] log likelihood: -7286.730835
EM: Round [738] log likelihood: -7286.730438
EM: Round [739] log likelihood: -7286.730042
EM: Round [740] log likelihood: -7286.729647
EM: Round [741] log likelihood: -7286.729254
EM: Round [742] log likelihood: -7286.728863
EM: Round [743] log likelihood: -7286.728472
EM: Round [744] log likelihood: -7286.728083
EM: Round [745] log likelihood: -7286.727695
EM: Round [746] log likelihood: -7286.727309
EM: Round [747] log likelihood: -7286.726923
EM: Round [748] log likelihood: -7286.726539
EM: Round [749] log likelihood: -7286.726157
EM: Round [750] log likelihood: -7286.725775
EM: Round [751] log likelihood: -7286.725395
EM: Round [752] log likelihood: -7286.725016
EM: Round [753] log likelihood: -7286.724638
EM: Round [754] log likelihood: -7286.724262
EM: Round [755] log likelihood: -7286.723886
EM: Round [756] log likelihood: -7286.723512
EM: Round [757] log likelihood: -7286.723139
EM: Round [758] log likelihood: -7286.722768
EM: Round [759] log likelihood: -7286.722397
EM: Round [760] log likelihood: -7286.722028
EM: Round [761] log likelihood: -7286.721660
EM: Round [762] log likelihood: -7286.721293
EM: Round [763] log likelihood: -7286.720928
EM: Round [764] log likelihood: -7286.720563
EM: Round [765] log likelihood: -7286.720200
EM: Round [766] log likelihood: -7286.719838
EM: Round [767] log likelihood: -7286.719477
EM: Round [768] log likelihood: -7286.719117
EM: Round [769] log likelihood: -7286.718758
EM: Round [770] log likelihood: -7286.718401
EM: Round [771] log likelihood: -7286.718044
EM: Round [772] log likelihood: -7286.717689
EM: Round [773] log likelihood: -7286.717335
EM: Round [774] log likelihood: -7286.716982
EM: Round [775] log likelihood: -7286.716630
EM: Round [776] log likelihood: -7286.716279
EM: Round [777] log likelihood: -7286.715929
EM: Round [778] log likelihood: -7286.715581
EM: Round [779] log likelihood: -7286.715233
EM: Round [780] log likelihood: -7286.714887
EM: Round [781] log likelihood: -7286.714542
EM: Round [782] log likelihood: -7286.714197
EM: Round [783] log likelihood: -7286.713854
EM: Round [784] log likelihood: -7286.713512
EM: Round [785] log likelihood: -7286.713171
EM: Round [786] log likelihood: -7286.712831
EM: Round [787] log likelihood: -7286.712492
EM: Round [788] log likelihood: -7286.712154
EM: Round [789] log likelihood: -7286.711817
EM: Round [790] log likelihood: -7286.711482
EM: Round [791] log likelihood: -7286.711147
EM: Round [792] log likelihood: -7286.710813
EM: Round [793] log likelihood: -7286.710480
EM: Round [794] log likelihood: -7286.710149
EM: Round [795] log likelihood: -7286.709818
EM: Round [796] log likelihood: -7286.709488
EM: Round [797] log likelihood: -7286.709160
EM: Round [798] log likelihood: -7286.708832
EM: Round [799] log likelihood: -7286.708505
EM: Round [800] log likelihood: -7286.708180
EM: Round [801] log likelihood: -7286.707855
EM: Round [802] log likelihood: -7286.707531
EM: Round [803] log likelihood: -7286.707208
EM: Round [804] log likelihood: -7286.706887
EM: Round [805] log likelihood: -7286.706566
EM: Round [806] log likelihood: -7286.706246
EM: Round [807] log likelihood: -7286.705927
EM: Round [808] log likelihood: -7286.705609
EM: Round [809] log likelihood: -7286.705292
EM: Round [810] log likelihood: -7286.704976
EM: Round [811] log likelihood: -7286.704661
EM: Round [812] log likelihood: -7286.704347
EM: Round [813] log likelihood: -7286.704034
EM: Round [814] log likelihood: -7286.703721
EM: Round [815] log likelihood: -7286.703410
EM: Round [816] log likelihood: -7286.703100
EM: Round [817] log likelihood: -7286.702790
EM: Round [818] log likelihood: -7286.702481
EM: Round [819] log likelihood: -7286.702174
EM: Round [820] log likelihood: -7286.701867
EM: Round [821] log likelihood: -7286.701561
EM: Round [822] log likelihood: -7286.701256
EM: Round [823] log likelihood: -7286.700952
EM: Round [824] log likelihood: -7286.700649
EM: Round [825] log likelihood: -7286.700346
EM: Round [826] log likelihood: -7286.700045
EM: Round [827] log likelihood: -7286.699744
EM: Round [828] log likelihood: -7286.699444
EM: Round [829] log likelihood: -7286.699145
EM: Round [830] log likelihood: -7286.698847
EM: Round [831] log likelihood: -7286.698550
EM: Round [832] log likelihood: -7286.698254
EM: Round [833] log likelihood: -7286.697958
EM: Round [834] log likelihood: -7286.697664
EM: Round [835] log likelihood: -7286.697370
EM: Round [836] log likelihood: -7286.697077
EM: Round [837] log likelihood: -7286.696785
EM: Round [838] log likelihood: -7286.696494
EM: Round [839] log likelihood: -7286.696203
EM: Round [840] log likelihood: -7286.695914
EM: Round [841] log likelihood: -7286.695625
EM: Round [842] log likelihood: -7286.695337
EM: Round [843] log likelihood: -7286.695050
EM: Round [844] log likelihood: -7286.694763
EM: Round [845] log likelihood: -7286.694478
EM: Round [846] log likelihood: -7286.694193
EM: Round [847] log likelihood: -7286.693909
EM: Round [848] log likelihood: -7286.693626
EM: Round [849] log likelihood: -7286.693344
EM: Round [850] log likelihood: -7286.693062
EM: Round [851] log likelihood: -7286.692781
EM: Round [852] log likelihood: -7286.692501
EM: Round [853] log likelihood: -7286.692222
EM: Round [854] log likelihood: -7286.691944
EM: Round [855] log likelihood: -7286.691666
EM: Round [856] log likelihood: -7286.691389
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EM: Round [868] log likelihood: -7286.688125
EM: Round [869] log likelihood: -7286.687857
EM: Round [870] log likelihood: -7286.687591
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EM: Round [873] log likelihood: -7286.686796
EM: Round [874] log likelihood: -7286.686532
EM: Round [875] log likelihood: -7286.686269
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EM: Round [877] log likelihood: -7286.685745
EM: Round [878] log likelihood: -7286.685484
EM: Round [879] log likelihood: -7286.685224
EM: Round [880] log likelihood: -7286.684965
EM: Round [881] log likelihood: -7286.684706
EM: Round [882] log likelihood: -7286.684448
EM: Round [883] log likelihood: -7286.684190
EM: Round [884] log likelihood: -7286.683934
EM: Round [885] log likelihood: -7286.683677
EM: Round [886] log likelihood: -7286.683422
EM: Round [887] log likelihood: -7286.683167
EM: Round [888] log likelihood: -7286.682913
EM: Round [889] log likelihood: -7286.682660
EM: Round [890] log likelihood: -7286.682407
EM: Round [891] log likelihood: -7286.682155
EM: Round [892] log likelihood: -7286.681904
EM: Round [893] log likelihood: -7286.681653
EM: Round [894] log likelihood: -7286.681403
EM: Round [895] log likelihood: -7286.681154
EM: Round [896] log likelihood: -7286.680905
EM: Round [897] log likelihood: -7286.680657
EM: Round [898] log likelihood: -7286.680409
EM: Round [899] log likelihood: -7286.680162
EM: Round [900] log likelihood: -7286.679916
EM: Round [901] log likelihood: -7286.679670
EM: Round [902] log likelihood: -7286.679425
EM: Round [903] log likelihood: -7286.679181
EM: Round [904] log likelihood: -7286.678937
EM: Round [905] log likelihood: -7286.678694
EM: Round [906] log likelihood: -7286.678452
EM: Round [907] log likelihood: -7286.678210
EM: Round [908] log likelihood: -7286.677969
EM: Round [909] log likelihood: -7286.677728
EM: Round [910] log likelihood: -7286.677488
EM: Round [911] log likelihood: -7286.677249
EM: Round [912] log likelihood: -7286.677010
EM: Round [913] log likelihood: -7286.676771
EM: Round [914] log likelihood: -7286.676534
EM: Round [915] log likelihood: -7286.676297
EM: Round [916] log likelihood: -7286.676060
EM: Round [917] log likelihood: -7286.675825
EM: Round [918] log likelihood: -7286.675589
EM: Round [919] log likelihood: -7286.675355
EM: Round [920] log likelihood: -7286.675121
EM: Round [921] log likelihood: -7286.674887
EM: Round [922] log likelihood: -7286.674654
EM: Round [923] log likelihood: -7286.674422
EM: Round [924] log likelihood: -7286.674190
EM: Round [925] log likelihood: -7286.673959
EM: Round [926] log likelihood: -7286.673728
EM: Round [927] log likelihood: -7286.673498
EM: Round [928] log likelihood: -7286.673269
EM: Round [929] log likelihood: -7286.673040
EM: Round [930] log likelihood: -7286.672812
EM: Round [931] log likelihood: -7286.672584
EM: Round [932] log likelihood: -7286.672357
EM: Round [933] log likelihood: -7286.672130
EM: Round [934] log likelihood: -7286.671904
EM: Round [935] log likelihood: -7286.671678
EM: Round [936] log likelihood: -7286.671453
EM: Round [937] log likelihood: -7286.671229
EM: Round [938] log likelihood: -7286.671005
EM: Round [939] log likelihood: -7286.670781
EM: Round [940] log likelihood: -7286.670559
EM: Round [941] log likelihood: -7286.670336
EM: Round [942] log likelihood: -7286.670115
EM: Round [943] log likelihood: -7286.669893
EM: Round [944] log likelihood: -7286.669673
EM: Round [945] log likelihood: -7286.669452
EM: Round [946] log likelihood: -7286.669233
EM: Round [947] log likelihood: -7286.669014
EM: Round [948] log likelihood: -7286.668795
EM: Round [949] log likelihood: -7286.668577
EM: Round [950] log likelihood: -7286.668359
EM: Round [951] log likelihood: -7286.668142
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EM: Round [954] log likelihood: -7286.667494
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EM: Round [957] log likelihood: -7286.666851
EM: Round [958] log likelihood: -7286.666637
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EM: Round [964] log likelihood: -7286.665367
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EM: Round [966] log likelihood: -7286.664947
EM: Round [967] log likelihood: -7286.664738
EM: Round [968] log likelihood: -7286.664530
EM: Round [969] log likelihood: -7286.664322
EM: Round [970] log likelihood: -7286.664114
EM: Round [971] log likelihood: -7286.663907
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EM: Round [973] log likelihood: -7286.663494
EM: Round [974] log likelihood: -7286.663289
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EM: Round [977] log likelihood: -7286.662674
EM: Round [978] log likelihood: -7286.662471
EM: Round [979] log likelihood: -7286.662267
EM: Round [980] log likelihood: -7286.662064
EM: Round [981] log likelihood: -7286.661862
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EM: Round [986] log likelihood: -7286.660857
EM: Round [987] log likelihood: -7286.660657
EM: Round [988] log likelihood: -7286.660458
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EM: Round [990] log likelihood: -7286.660061
EM: Round [991] log likelihood: -7286.659863
EM: Round [992] log likelihood: -7286.659665
EM: Round [993] log likelihood: -7286.659468
EM: Round [994] log likelihood: -7286.659272
EM: Round [995] log likelihood: -7286.659075
EM: Round [996] log likelihood: -7286.658880
EM: Round [997] log likelihood: -7286.658685
EM: Round [998] log likelihood: -7286.658490
EM: Round [999] log likelihood: -7286.658295
EM: Round [1000] log likelihood: -7286.658101
EM: Round [1001] log likelihood: -7286.657908
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_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.DXIqsdmJjc/fi_workdir/tih_rna_sample_00628_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -4842.850267
EM: Round [1] log likelihood: -4842.413175
EM: Round [2] log likelihood: -4842.410535
EM: Round [3] log likelihood: -4842.409504
EM: Round [4] log likelihood: -4842.408480
EM: Round [5] log likelihood: -4842.407458
EM: Round [6] log likelihood: -4842.406438
EM: Round [7] log likelihood: -4842.405420
EM: Round [8] log likelihood: -4842.404405
EM: Round [9] log likelihood: -4842.403391
EM: Round [10] log likelihood: -4842.402380
EM: Round [11] log likelihood: -4842.401370
EM: Round [12] log likelihood: -4842.400363
EM: Round [13] log likelihood: -4842.399357
EM: Round [14] log likelihood: -4842.398354
EM: Round [15] log likelihood: -4842.397353
EM: Round [16] log likelihood: -4842.396354
EM: Round [17] log likelihood: -4842.395356
EM: Round [18] log likelihood: -4842.394361
EM: Round [19] log likelihood: -4842.393368
EM: Round [20] log likelihood: -4842.392377
EM: Round [21] log likelihood: -4842.391388
EM: Round [22] log likelihood: -4842.390401
EM: Round [23] log likelihood: -4842.389416
EM: Round [24] log likelihood: -4842.388432
EM: Round [25] log likelihood: -4842.387451
EM: Round [26] log likelihood: -4842.386472
EM: Round [27] log likelihood: -4842.385495
EM: Round [28] log likelihood: -4842.384519
EM: Round [29] log likelihood: -4842.383546
EM: Round [30] log likelihood: -4842.382575
EM: Round [31] log likelihood: -4842.381605
EM: Round [32] log likelihood: -4842.380638
EM: Round [33] log likelihood: -4842.379672
EM: Round [34] log likelihood: -4842.378709
EM: Round [35] log likelihood: -4842.377747
EM: Round [36] log likelihood: -4842.376787
EM: Round [37] log likelihood: -4842.375829
EM: Round [38] log likelihood: -4842.374873
EM: Round [39] log likelihood: -4842.373919
EM: Round [40] log likelihood: -4842.372967
EM: Round [41] log likelihood: -4842.372017
EM: Round [42] log likelihood: -4842.371068
EM: Round [43] log likelihood: -4842.370122
EM: Round [44] log likelihood: -4842.369177
EM: Round [45] log likelihood: -4842.368234
EM: Round [46] log likelihood: -4842.367293
EM: Round [47] log likelihood: -4842.366354
EM: Round [48] log likelihood: -4842.365417
EM: Round [49] log likelihood: -4842.364482
EM: Round [50] log likelihood: -4842.363548
EM: Round [51] log likelihood: -4842.362616
EM: Round [52] log likelihood: -4842.361687
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EM: Round [970] log likelihood: -4841.922927
EM: Round [971] log likelihood: -4841.922696
EM: Round [972] log likelihood: -4841.922464
EM: Round [973] log likelihood: -4841.922233
EM: Round [974] log likelihood: -4841.922002
EM: Round [975] log likelihood: -4841.921771
EM: Round [976] log likelihood: -4841.921541
EM: Round [977] log likelihood: -4841.921311
EM: Round [978] log likelihood: -4841.921081
EM: Round [979] log likelihood: -4841.920852
EM: Round [980] log likelihood: -4841.920623
EM: Round [981] log likelihood: -4841.920394
EM: Round [982] log likelihood: -4841.920165
EM: Round [983] log likelihood: -4841.919937
EM: Round [984] log likelihood: -4841.919709
EM: Round [985] log likelihood: -4841.919481
EM: Round [986] log likelihood: -4841.919254
EM: Round [987] log likelihood: -4841.919027
EM: Round [988] log likelihood: -4841.918800
EM: Round [989] log likelihood: -4841.918573
EM: Round [990] log likelihood: -4841.918347
EM: Round [991] log likelihood: -4841.918121
EM: Round [992] log likelihood: -4841.917895
EM: Round [993] log likelihood: -4841.917670
EM: Round [994] log likelihood: -4841.917444
EM: Round [995] log likelihood: -4841.917220
EM: Round [996] log likelihood: -4841.916995
EM: Round [997] log likelihood: -4841.916771
EM: Round [998] log likelihood: -4841.916547
EM: Round [999] log likelihood: -4841.916323
EM: Round [1000] log likelihood: -4841.916099
EM: Round [1001] log likelihood: -4841.915876
-total frags in /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1_1.fastp.fastq.gz: 295699773
Warning - not locating file: /tmp/nxf.DXIqsdmJjc/tih_rna_sample_00628_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000260318.1]
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 [ENSG00000251634.2]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000225537.1]
WARNING, no entry stored in dbm for [ENSG00000225537.1]
WARNING, no entry stored in dbm for [ENSG00000225537.1]
ls: cannot access 'IGV_inputs': No such file or directory