Done.
-parsing GTF file: /tmp/nxf.NlXcgTllHe/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.NlXcgTllHe/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.NlXcgTllHe/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.NlXcgTllHe/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.NlXcgTllHe/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.NlXcgTllHe/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
23:39:25 : INFO : Done.
-parsing GTF file: /tmp/nxf.NlXcgTllHe/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.NlXcgTllHe/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

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[2600000]   -done parsing /tmp/nxf.NlXcgTllHe/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 72,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 12,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 55,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 236,
          'num_hits: 10 != num_counted_on_fusion_contigs 6 ' => 12,
          'num genes matched < 2' => 27,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 1112,
          'excessive soft clipping' => 17725,
          'exons hit < 2' => 8,
          'num_hits: 10 != num_counted_on_fusion_contigs 2 ' => 136,
          'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 912,
          'seq-similar region overlap' => 3,
          'small anchor length' => 55,
          ' ** passed ** ' => 10672,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 94,
          'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 24,
          'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 28,
          'per_id < 96' => 13510,
          'low complexity anchor region' => 7,
          'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 174
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.NlXcgTllHe/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[23000]   -fusion SPANNING read extraction for scaff: ABCC4--RNY4P27

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[23000]   -fusion SPANNING read extraction for scaff: ABCC4--MEMO1P5

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[14000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

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[8000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[649000]   -fusion SPANNING read extraction for scaff: CCDC198--NPIPB12

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[72000]   -fusion SPANNING read extraction for scaff: GLI3--AF246928.1

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[71000]   
[72000]   -fusion SPANNING read extraction for scaff: GLI3--AJ009632.2

[1000]   -fusion SPANNING read extraction for scaff: GTF2A1L--STON1-GTF2A1L

[1000]   
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[57000]   
[58000]   -fusion SPANNING read extraction for scaff: GUSBP13--NAIP

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[355000]   
[356000]   -fusion SPANNING read extraction for scaff: KIF5B--RET

[1000]   
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[4000]   
[5000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

[1000]   
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[167000]   
[168000]   -fusion SPANNING read extraction for scaff: NOLC1--GBF1

[1000]   
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[9000]   
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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
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[4000]   
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[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
[2000]   
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[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[1000]   
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[6000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
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[6000]   
[7000]   
[8000]   
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[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
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[4000]   
[5000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[10000]   
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[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
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[6000]   
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[8000]   
[9000]   
[10000]   
[11000]   
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[16000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
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[4000]   
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[6000]   
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[8000]   
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[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
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[39000]   
[40000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[680000]   -fusion SPANNING read extraction for scaff: PTPN2--NPIPB12

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[27000]   
[28000]   -fusion SPANNING read extraction for scaff: RITA1--GLT8D2

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[22000]   
[23000]   -fusion SPANNING read extraction for scaff: RPSAP52--HMGA2

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[86000]   
[87000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[58000]   -fusion SPANNING read extraction for scaff: TAF4--AC114498.1

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[45000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[48000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

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[9000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[27000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 15577,
          'lacks exon overlap' => 24363
        };
EM: Starting log likelihood: -6953.263898
EM: Round [1] log likelihood: -6948.810148
EM: Round [2] log likelihood: -6948.774165
EM: Round [3] log likelihood: -6948.770550
EM: Round [4] log likelihood: -6948.767205
EM: Round [5] log likelihood: -6948.763889
EM: Round [6] log likelihood: -6948.760602
EM: Round [7] log likelihood: -6948.757344
EM: Round [8] log likelihood: -6948.754113
EM: Round [9] log likelihood: -6948.750910
EM: Round [10] log likelihood: -6948.747735
EM: Round [11] log likelihood: -6948.744586
EM: Round [12] log likelihood: -6948.741464
EM: Round [13] log likelihood: -6948.738369
EM: Round [14] log likelihood: -6948.735301
EM: Round [15] log likelihood: -6948.732258
EM: Round [16] log likelihood: -6948.729241
EM: Round [17] log likelihood: -6948.726249
EM: Round [18] log likelihood: -6948.723283
EM: Round [19] log likelihood: -6948.720342
EM: Round [20] log likelihood: -6948.717426
EM: Round [21] log likelihood: -6948.714534
EM: Round [22] log likelihood: -6948.711666
EM: Round [23] log likelihood: -6948.708823
EM: Round [24] log likelihood: -6948.706003
EM: Round [25] log likelihood: -6948.703207
EM: Round [26] log likelihood: -6948.700434
EM: Round [27] log likelihood: -6948.697685
EM: Round [28] log likelihood: -6948.694958
EM: Round [29] log likelihood: -6948.692254
EM: Round [30] log likelihood: -6948.689572
EM: Round [31] log likelihood: -6948.686913
EM: Round [32] log likelihood: -6948.684276
EM: Round [33] log likelihood: -6948.681660
EM: Round [34] log likelihood: -6948.679066
EM: Round [35] log likelihood: -6948.676494
EM: Round [36] log likelihood: -6948.673943
EM: Round [37] log likelihood: -6948.671412
EM: Round [38] log likelihood: -6948.668903
EM: Round [39] log likelihood: -6948.666414
EM: Round [40] log likelihood: -6948.663946
EM: Round [41] log likelihood: -6948.661498
EM: Round [42] log likelihood: -6948.659069
EM: Round [43] log likelihood: -6948.656661
EM: Round [44] log likelihood: -6948.654273
EM: Round [45] log likelihood: -6948.651903
EM: Round [46] log likelihood: -6948.649554
EM: Round [47] log likelihood: -6948.647223
EM: Round [48] log likelihood: -6948.644911
EM: Round [49] log likelihood: -6948.642618
EM: Round [50] log likelihood: -6948.640344
EM: Round [51] log likelihood: -6948.638088
EM: Round [52] log likelihood: -6948.635850
EM: Round [53] log likelihood: -6948.633630
EM: Round [54] log likelihood: -6948.631429
EM: Round [55] log likelihood: -6948.629245
EM: Round [56] log likelihood: -6948.627078
EM: Round [57] log likelihood: -6948.624929
EM: Round [58] log likelihood: -6948.622798
EM: Round [59] log likelihood: -6948.620683
EM: Round [60] log likelihood: -6948.618585
EM: Round [61] log likelihood: -6948.616505
EM: Round [62] log likelihood: -6948.614440
EM: Round [63] log likelihood: -6948.612393
EM: Round [64] log likelihood: -6948.610362
EM: Round [65] log likelihood: -6948.608346
EM: Round [66] log likelihood: -6948.606347
EM: Round [67] log likelihood: -6948.604364
EM: Round [68] log likelihood: -6948.602397
EM: Round [69] log likelihood: -6948.600445
EM: Round [70] log likelihood: -6948.598509
EM: Round [71] log likelihood: -6948.596589
EM: Round [72] log likelihood: -6948.594683
EM: Round [73] log likelihood: -6948.592793
EM: Round [74] log likelihood: -6948.590917
EM: Round [75] log likelihood: -6948.589056
EM: Round [76] log likelihood: -6948.587210
EM: Round [77] log likelihood: -6948.585379
EM: Round [78] log likelihood: -6948.583562
EM: Round [79] log likelihood: -6948.581759
EM: Round [80] log likelihood: -6948.579971
EM: Round [81] log likelihood: -6948.578197
EM: Round [82] log likelihood: -6948.576436
EM: Round [83] log likelihood: -6948.574689
EM: Round [84] log likelihood: -6948.572956
EM: Round [85] log likelihood: -6948.571237
EM: Round [86] log likelihood: -6948.569531
EM: Round [87] log likelihood: -6948.567839
EM: Round [88] log likelihood: -6948.566159
EM: Round [89] log likelihood: -6948.564493
EM: Round [90] log likelihood: -6948.562840
EM: Round [91] log likelihood: -6948.561200
EM: Round [92] log likelihood: -6948.559572
EM: Round [93] log likelihood: -6948.557957
EM: Round [94] log likelihood: -6948.556355
EM: Round [95] log likelihood: -6948.554765
EM: Round [96] log likelihood: -6948.553188
EM: Round [97] log likelihood: -6948.551622
EM: Round [98] log likelihood: -6948.550069
EM: Round [99] log likelihood: -6948.548528
EM: Round [100] log likelihood: -6948.546999
EM: Round [101] log likelihood: -6948.545482
EM: Round [102] log likelihood: -6948.543976
EM: Round [103] log likelihood: -6948.542482
EM: Round [104] log likelihood: -6948.541000
EM: Round [105] log likelihood: -6948.539529
EM: Round [106] log likelihood: -6948.538069
EM: Round [107] log likelihood: -6948.536621
EM: Round [108] log likelihood: -6948.535183
EM: Round [109] log likelihood: -6948.533757
EM: Round [110] log likelihood: -6948.532342
EM: Round [111] log likelihood: -6948.530938
EM: Round [112] log likelihood: -6948.529544
EM: Round [113] log likelihood: -6948.528161
EM: Round [114] log likelihood: -6948.526789
EM: Round [115] log likelihood: -6948.525427
EM: Round [116] log likelihood: -6948.524076
EM: Round [117] log likelihood: -6948.522735
EM: Round [118] log likelihood: -6948.521404
EM: Round [119] log likelihood: -6948.520084
EM: Round [120] log likelihood: -6948.518773
EM: Round [121] log likelihood: -6948.517473
EM: Round [122] log likelihood: -6948.516182
EM: Round [123] log likelihood: -6948.514901
EM: Round [124] log likelihood: -6948.513630
EM: Round [125] log likelihood: -6948.512369
EM: Round [126] log likelihood: -6948.511117
EM: Round [127] log likelihood: -6948.509875
EM: Round [128] log likelihood: -6948.508642
EM: Round [129] log likelihood: -6948.507419
EM: Round [130] log likelihood: -6948.506205
EM: Round [131] log likelihood: -6948.505000
EM: Round [132] log likelihood: -6948.503804
EM: Round [133] log likelihood: -6948.502617
EM: Round [134] log likelihood: -6948.501440
EM: Round [135] log likelihood: -6948.500271
EM: Round [136] log likelihood: -6948.499111
EM: Round [137] log likelihood: -6948.497960
EM: Round [138] log likelihood: -6948.496817
EM: Round [139] log likelihood: -6948.495683
EM: Round [140] log likelihood: -6948.494558
EM: Round [141] log likelihood: -6948.493441
EM: Round [142] log likelihood: -6948.492333
EM: Round [143] log likelihood: -6948.491233
EM: Round [144] log likelihood: -6948.490141
EM: Round [145] log likelihood: -6948.489057
EM: Round [146] log likelihood: -6948.487982
EM: Round [147] log likelihood: -6948.486914
EM: Round [148] log likelihood: -6948.485855
EM: Round [149] log likelihood: -6948.484804
EM: Round [150] log likelihood: -6948.483760
EM: Round [151] log likelihood: -6948.482725
EM: Round [152] log likelihood: -6948.481697
EM: Round [153] log likelihood: -6948.480677
EM: Round [154] log likelihood: -6948.479664
EM: Round [155] log likelihood: -6948.478659
EM: Round [156] log likelihood: -6948.477662
EM: Round [157] log likelihood: -6948.476672
EM: Round [158] log likelihood: -6948.475689
EM: Round [159] log likelihood: -6948.474714
EM: Round [160] log likelihood: -6948.473746
EM: Round [161] log likelihood: -6948.472785
EM: Round [162] log likelihood: -6948.471831
EM: Round [163] log likelihood: -6948.470885
EM: Round [164] log likelihood: -6948.469946
EM: Round [165] log likelihood: -6948.469013
EM: Round [166] log likelihood: -6948.468088
EM: Round [167] log likelihood: -6948.467169
EM: Round [168] log likelihood: -6948.466257
EM: Round [169] log likelihood: -6948.465352
EM: Round [170] log likelihood: -6948.464454
EM: Round [171] log likelihood: -6948.463563
EM: Round [172] log likelihood: -6948.462678
EM: Round [173] log likelihood: -6948.461799
EM: Round [174] log likelihood: -6948.460928
EM: Round [175] log likelihood: -6948.460062
EM: Round [176] log likelihood: -6948.459203
EM: Round [177] log likelihood: -6948.458351
EM: Round [178] log likelihood: -6948.457504
EM: Round [179] log likelihood: -6948.456664
EM: Round [180] log likelihood: -6948.455831
EM: Round [181] log likelihood: -6948.455003
EM: Round [182] log likelihood: -6948.454181
EM: Round [183] log likelihood: -6948.453366
EM: Round [184] log likelihood: -6948.452557
EM: Round [185] log likelihood: -6948.451753
EM: Round [186] log likelihood: -6948.450956
EM: Round [187] log likelihood: -6948.450164
EM: Round [188] log likelihood: -6948.449378
EM: Round [189] log likelihood: -6948.448598
EM: Round [190] log likelihood: -6948.447824
EM: Round [191] log likelihood: -6948.447056
EM: Round [192] log likelihood: -6948.446293
EM: Round [193] log likelihood: -6948.445536
EM: Round [194] log likelihood: -6948.444784
EM: Round [195] log likelihood: -6948.444038
EM: Round [196] log likelihood: -6948.443297
EM: Round [197] log likelihood: -6948.442562
EM: Round [198] log likelihood: -6948.441832
EM: Round [199] log likelihood: -6948.441108
EM: Round [200] log likelihood: -6948.440389
EM: Round [201] log likelihood: -6948.439675
EM: Round [202] log likelihood: -6948.438966
EM: Round [203] log likelihood: -6948.438263
EM: Round [204] log likelihood: -6948.437565
EM: Round [205] log likelihood: -6948.436872
EM: Round [206] log likelihood: -6948.436184
EM: Round [207] log likelihood: -6948.435501
EM: Round [208] log likelihood: -6948.434823
EM: Round [209] log likelihood: -6948.434150
EM: Round [210] log likelihood: -6948.433481
EM: Round [211] log likelihood: -6948.432818
EM: Round [212] log likelihood: -6948.432160
EM: Round [213] log likelihood: -6948.431506
EM: Round [214] log likelihood: -6948.430858
EM: Round [215] log likelihood: -6948.430214
EM: Round [216] log likelihood: -6948.429574
EM: Round [217] log likelihood: -6948.428940
EM: Round [218] log likelihood: -6948.428310
EM: Round [219] log likelihood: -6948.427684
EM: Round [220] log likelihood: -6948.427064
EM: Round [221] log likelihood: -6948.426447
EM: Round [222] log likelihood: -6948.425835
EM: Round [223] log likelihood: -6948.425228
EM: Round [224] log likelihood: -6948.424625
EM: Round [225] log likelihood: -6948.424027
EM: Round [226] log likelihood: -6948.423432
EM: Round [227] log likelihood: -6948.422843
EM: Round [228] log likelihood: -6948.422257
EM: Round [229] log likelihood: -6948.421676
EM: Round [230] log likelihood: -6948.421099
EM: Round [231] log likelihood: -6948.420526
EM: Round [232] log likelihood: -6948.419957
EM: Round [233] log likelihood: -6948.419393
EM: Round [234] log likelihood: -6948.418832
EM: Round [235] log likelihood: -6948.418276
EM: Round [236] log likelihood: -6948.417724
EM: Round [237] log likelihood: -6948.417175
EM: Round [238] log likelihood: -6948.416631
EM: Round [239] log likelihood: -6948.416090
EM: Round [240] log likelihood: -6948.415554
EM: Round [241] log likelihood: -6948.415021
EM: Round [242] log likelihood: -6948.414493
EM: Round [243] log likelihood: -6948.413968
EM: Round [244] log likelihood: -6948.413447
EM: Round [245] log likelihood: -6948.412929
EM: Round [246] log likelihood: -6948.412416
EM: Round [247] log likelihood: -6948.411906
EM: Round [248] log likelihood: -6948.411400
EM: Round [249] log likelihood: -6948.410897
EM: Round [250] log likelihood: -6948.410399
EM: Round [251] log likelihood: -6948.409903
EM: Round [252] log likelihood: -6948.409412
EM: Round [253] log likelihood: -6948.408924
EM: Round [254] log likelihood: -6948.408439
EM: Round [255] log likelihood: -6948.407958
EM: Round [256] log likelihood: -6948.407480
EM: Round [257] log likelihood: -6948.407006
EM: Round [258] log likelihood: -6948.406536
EM: Round [259] log likelihood: -6948.406068
EM: Round [260] log likelihood: -6948.405604
EM: Round [261] log likelihood: -6948.405144
EM: Round [262] log likelihood: -6948.404686
EM: Round [263] log likelihood: -6948.404232
EM: Round [264] log likelihood: -6948.403782
EM: Round [265] log likelihood: -6948.403334
EM: Round [266] log likelihood: -6948.402890
EM: Round [267] log likelihood: -6948.402449
EM: Round [268] log likelihood: -6948.402011
EM: Round [269] log likelihood: -6948.401577
EM: Round [270] log likelihood: -6948.401145
EM: Round [271] log likelihood: -6948.400717
EM: Round [272] log likelihood: -6948.400291
EM: Round [273] log likelihood: -6948.399869
EM: Round [274] log likelihood: -6948.399450
EM: Round [275] log likelihood: -6948.399034
EM: Round [276] log likelihood: -6948.398620
EM: Round [277] log likelihood: -6948.398210
EM: Round [278] log likelihood: -6948.397803
EM: Round [279] log likelihood: -6948.397398
EM: Round [280] log likelihood: -6948.396997
EM: Round [281] log likelihood: -6948.396598
EM: Round [282] log likelihood: -6948.396203
EM: Round [283] log likelihood: -6948.395810
EM: Round [284] log likelihood: -6948.395420
EM: Round [285] log likelihood: -6948.395032
EM: Round [286] log likelihood: -6948.394648
EM: Round [287] log likelihood: -6948.394266
EM: Round [288] log likelihood: -6948.393887
EM: Round [289] log likelihood: -6948.393511
EM: Round [290] log likelihood: -6948.393137
EM: Round [291] log likelihood: -6948.392767
EM: Round [292] log likelihood: -6948.392398
EM: Round [293] log likelihood: -6948.392033
EM: Round [294] log likelihood: -6948.391670
EM: Round [295] log likelihood: -6948.391310
EM: Round [296] log likelihood: -6948.390952
EM: Round [297] log likelihood: -6948.390597
EM: Round [298] log likelihood: -6948.390244
EM: Round [299] log likelihood: -6948.389894
EM: Round [300] log likelihood: -6948.389546
EM: Round [301] log likelihood: -6948.389201
EM: Round [302] log likelihood: -6948.388858
EM: Round [303] log likelihood: -6948.388518
EM: Round [304] log likelihood: -6948.388180
EM: Round [305] log likelihood: -6948.387845
EM: Round [306] log likelihood: -6948.387512
EM: Round [307] log likelihood: -6948.387182
EM: Round [308] log likelihood: -6948.386853
EM: Round [309] log likelihood: -6948.386528
EM: Round [310] log likelihood: -6948.386204
EM: Round [311] log likelihood: -6948.385883
EM: Round [312] log likelihood: -6948.385564
EM: Round [313] log likelihood: -6948.385247
EM: Round [314] log likelihood: -6948.384933
EM: Round [315] log likelihood: -6948.384621
EM: Round [316] log likelihood: -6948.384311
EM: Round [317] log likelihood: -6948.384003
EM: Round [318] log likelihood: -6948.383698
EM: Round [319] log likelihood: -6948.383394
EM: Round [320] log likelihood: -6948.383093
EM: Round [321] log likelihood: -6948.382794
EM: Round [322] log likelihood: -6948.382497
EM: Round [323] log likelihood: -6948.382203
EM: Round [324] log likelihood: -6948.381910
EM: Round [325] log likelihood: -6948.381620
EM: Round [326] log likelihood: -6948.381331
EM: Round [327] log likelihood: -6948.381045
EM: Round [328] log likelihood: -6948.380760
EM: Round [329] log likelihood: -6948.380478
EM: Round [330] log likelihood: -6948.380198
EM: Round [331] log likelihood: -6948.379919
EM: Round [332] log likelihood: -6948.379643
EM: Round [333] log likelihood: -6948.379369
EM: Round [334] log likelihood: -6948.379096
EM: Round [335] log likelihood: -6948.378826
EM: Round [336] log likelihood: -6948.378557
EM: Round [337] log likelihood: -6948.378290
EM: Round [338] log likelihood: -6948.378026
EM: Round [339] log likelihood: -6948.377763
EM: Round [340] log likelihood: -6948.377502
EM: Round [341] log likelihood: -6948.377243
EM: Round [342] log likelihood: -6948.376986
EM: Round [343] log likelihood: -6948.376730
EM: Round [344] log likelihood: -6948.376476
EM: Round [345] log likelihood: -6948.376225
EM: Round [346] log likelihood: -6948.375975
EM: Round [347] log likelihood: -6948.375726
EM: Round [348] log likelihood: -6948.375480
EM: Round [349] log likelihood: -6948.375235
EM: Round [350] log likelihood: -6948.374992
EM: Round [351] log likelihood: -6948.374751
EM: Round [352] log likelihood: -6948.374511
EM: Round [353] log likelihood: -6948.374273
EM: Round [354] log likelihood: -6948.374037
EM: Round [355] log likelihood: -6948.373803
EM: Round [356] log likelihood: -6948.373570
EM: Round [357] log likelihood: -6948.373339
EM: Round [358] log likelihood: -6948.373109
EM: Round [359] log likelihood: -6948.372882
EM: Round [360] log likelihood: -6948.372655
EM: Round [361] log likelihood: -6948.372431
EM: Round [362] log likelihood: -6948.372208
EM: Round [363] log likelihood: -6948.371986
EM: Round [364] log likelihood: -6948.371766
EM: Round [365] log likelihood: -6948.371548
EM: Round [366] log likelihood: -6948.371331
EM: Round [367] log likelihood: -6948.371116
EM: Round [368] log likelihood: -6948.370902
EM: Round [369] log likelihood: -6948.370690
EM: Round [370] log likelihood: -6948.370479
EM: Round [371] log likelihood: -6948.370270
EM: Round [372] log likelihood: -6948.370062
EM: Round [373] log likelihood: -6948.369856
EM: Round [374] log likelihood: -6948.369651
EM: Round [375] log likelihood: -6948.369448
EM: Round [376] log likelihood: -6948.369246
EM: Round [377] log likelihood: -6948.369046
EM: Round [378] log likelihood: -6948.368846
EM: Round [379] log likelihood: -6948.368649
EM: Round [380] log likelihood: -6948.368453
EM: Round [381] log likelihood: -6948.368258
EM: Round [382] log likelihood: -6948.368064
EM: Round [383] log likelihood: -6948.367872
EM: Round [384] log likelihood: -6948.367682
EM: Round [385] log likelihood: -6948.367492
EM: Round [386] log likelihood: -6948.367304
EM: Round [387] log likelihood: -6948.367117
EM: Round [388] log likelihood: -6948.366932
EM: Round [389] log likelihood: -6948.366748
EM: Round [390] log likelihood: -6948.366565
EM: Round [391] log likelihood: -6948.366384
EM: Round [392] log likelihood: -6948.366204
EM: Round [393] log likelihood: -6948.366025
EM: Round [394] log likelihood: -6948.365847
EM: Round [395] log likelihood: -6948.365671
EM: Round [396] log likelihood: -6948.365496
EM: Round [397] log likelihood: -6948.365322
EM: Round [398] log likelihood: -6948.365149
EM: Round [399] log likelihood: -6948.364978
EM: Round [400] log likelihood: -6948.364807
EM: Round [401] log likelihood: -6948.364638
EM: Round [402] log likelihood: -6948.364471
EM: Round [403] log likelihood: -6948.364304
EM: Round [404] log likelihood: -6948.364138
EM: Round [405] log likelihood: -6948.363974
EM: Round [406] log likelihood: -6948.363811
EM: Round [407] log likelihood: -6948.363649
EM: Round [408] log likelihood: -6948.363488
EM: Round [409] log likelihood: -6948.363329
EM: Round [410] log likelihood: -6948.363170
EM: Round [411] log likelihood: -6948.363013
EM: Round [412] log likelihood: -6948.362856
EM: Round [413] log likelihood: -6948.362701
EM: Round [414] log likelihood: -6948.362547
EM: Round [415] log likelihood: -6948.362394
EM: Round [416] log likelihood: -6948.362242
EM: Round [417] log likelihood: -6948.362091
EM: Round [418] log likelihood: -6948.361941
EM: Round [419] log likelihood: -6948.361792
EM: Round [420] log likelihood: -6948.361645
EM: Round [421] log likelihood: -6948.361498
EM: Round [422] log likelihood: -6948.361352
EM: Round [423] log likelihood: -6948.361208
EM: Round [424] log likelihood: -6948.361064
EM: Round [425] log likelihood: -6948.360922
EM: Round [426] log likelihood: -6948.360780
EM: Round [427] log likelihood: -6948.360640
EM: Round [428] log likelihood: -6948.360500
EM: Round [429] log likelihood: -6948.360362
EM: Round [430] log likelihood: -6948.360224
EM: Round [431] log likelihood: -6948.360087
EM: Round [432] log likelihood: -6948.359952
EM: Round [433] log likelihood: -6948.359817
EM: Round [434] log likelihood: -6948.359683
EM: Round [435] log likelihood: -6948.359550
EM: Round [436] log likelihood: -6948.359419
EM: Round [437] log likelihood: -6948.359288
EM: Round [438] log likelihood: -6948.359158
EM: Round [439] log likelihood: -6948.359028
EM: Round [440] log likelihood: -6948.358900
EM: Round [441] log likelihood: -6948.358773
EM: Round [442] log likelihood: -6948.358647
EM: Round [443] log likelihood: -6948.358521
EM: Round [444] log likelihood: -6948.358397
EM: Round [445] log likelihood: -6948.358273
EM: Round [446] log likelihood: -6948.358150
EM: Round [447] log likelihood: -6948.358028
EM: Round [448] log likelihood: -6948.357907
EM: Round [449] log likelihood: -6948.357787
EM: Round [450] log likelihood: -6948.357667
EM: Round [451] log likelihood: -6948.357549
EM: Round [452] log likelihood: -6948.357431
EM: Round [453] log likelihood: -6948.357314
EM: Round [454] log likelihood: -6948.357198
EM: Round [455] log likelihood: -6948.357082
EM: Round [456] log likelihood: -6948.356968
EM: Round [457] log likelihood: -6948.356854
EM: Round [458] log likelihood: -6948.356742
EM: Round [459] log likelihood: -6948.356629
EM: Round [460] log likelihood: -6948.356518
EM: Round [461] log likelihood: -6948.356408
EM: Round [462] log likelihood: -6948.356298
EM: Round [463] log likelihood: -6948.356189
EM: Round [464] log likelihood: -6948.356081
EM: Round [465] log likelihood: -6948.355973
EM: Round [466] log likelihood: -6948.355867
EM: Round [467] log likelihood: -6948.355761
EM: Round [468] log likelihood: -6948.355656
EM: Round [469] log likelihood: -6948.355551
EM: Round [470] log likelihood: -6948.355448
EM: Round [471] log likelihood: -6948.355345
EM: Round [472] log likelihood: -6948.355243
EM: Round [473] log likelihood: -6948.355141
EM: Round [474] log likelihood: -6948.355040
EM: Round [475] log likelihood: -6948.354940
EM: Round [476] log likelihood: -6948.354841
EM: Stopping iterations at round 476 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.NlXcgTllHe/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.NlXcgTllHe/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.NlXcgTllHe/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.NlXcgTllHe/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.NlXcgTllHe/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.NlXcgTllHe/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.NlXcgTllHe/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.NlXcgTllHe/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_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.NlXcgTllHe/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_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.NlXcgTllHe/fi_workdir/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.NlXcgTllHe/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.NlXcgTllHe/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -6659.769458
EM: Round [1] log likelihood: -6657.900350
EM: Round [2] log likelihood: -6657.882090
EM: Round [3] log likelihood: -6657.881951
EM: Round [4] log likelihood: -6657.881950
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.NlXcgTllHe/659_bjQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295586759
Warning - not locating file: /tmp/nxf.NlXcgTllHe/659_bjQ-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000198237.8]
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]
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 [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 [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000235146.2]
WARNING, no entry stored in dbm for [ENSG00000241749.4]
WARNING, no entry stored in dbm for [ENSG00000241749.4]
WARNING, no entry stored in dbm for [ENSG00000068781.21]
ls: cannot access 'IGV_inputs': No such file or directory