Done.
-parsing GTF file: /tmp/nxf.sActxdZih0/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.sActxdZih0/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.sActxdZih0/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.sActxdZih0/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.sActxdZih0/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.sActxdZih0/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
10:55:31 : INFO : Done.
-parsing GTF file: /tmp/nxf.sActxdZih0/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.sActxdZih0/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[1400000]   -done parsing /tmp/nxf.sActxdZih0/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'excessive soft clipping' => 11441,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 19,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 48,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 75,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 20,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 21,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 12,
          'small anchor length' => 30,
          'exons hit < 2' => 5,
          ' ** passed ** ' => 8520,
          'seq-similar region overlap' => 3,
          'num genes matched < 2' => 7,
          'per_id < 96' => 7829
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.sActxdZih0/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[15000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[24000]   -fusion SPANNING read extraction for scaff: ACOT11--GLIS1

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[155000]   -fusion SPANNING read extraction for scaff: EPC1--MYO3A

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[53000]   -fusion SPANNING read extraction for scaff: FGGY--ZMYM4

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[204000]   -fusion SPANNING read extraction for scaff: GMDS--GSE1

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[91000]   -fusion SPANNING read extraction for scaff: MAST2--AGBL4

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[45000]   -fusion SPANNING read extraction for scaff: NFIA--DAB1

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[49000]   -fusion SPANNING read extraction for scaff: NFIA--OMA1

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[6000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1

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[6000]   -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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[8000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[8000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[8000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[6000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[6000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[54000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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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--PCDHGA10

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[94000]   
[95000]   -fusion SPANNING read extraction for scaff: SSBP3--PATJ

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[20000]   -fusion SPANNING read extraction for scaff: STIL--LRRC42

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[106000]   
[107000]   -fusion SPANNING read extraction for scaff: TACSTD2--FGGY

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[99000]   
[100000]   -fusion SPANNING read extraction for scaff: TACSTD2--AL603840.1

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[100000]   -fusion SPANNING read extraction for scaff: TACSTD2--AL353681.1

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[29000]   -fusion SPANNING read extraction for scaff: TCEANC2--ROR1

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[28000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[6000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[21000]   
[22000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[42000]   
[43000]   -fusion SPANNING read extraction for scaff: ZNF362--STIL
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 12879,
          'seq similar region alignment' => 16202
        };
EM: Starting log likelihood: -7594.991991
EM: Round [1] log likelihood: -7593.665968
EM: Round [2] log likelihood: -7593.345308
EM: Round [3] log likelihood: -7593.060504
EM: Round [4] log likelihood: -7592.804612
EM: Round [5] log likelihood: -7592.572665
EM: Round [6] log likelihood: -7592.360876
EM: Round [7] log likelihood: -7592.166285
EM: Round [8] log likelihood: -7591.986541
EM: Round [9] log likelihood: -7591.819739
EM: Round [10] log likelihood: -7591.664321
EM: Round [11] log likelihood: -7591.518991
EM: Round [12] log likelihood: -7591.382661
EM: Round [13] log likelihood: -7591.254409
EM: Round [14] log likelihood: -7591.133447
EM: Round [15] log likelihood: -7591.019097
EM: Round [16] log likelihood: -7590.910770
EM: Round [17] log likelihood: -7590.807950
EM: Round [18] log likelihood: -7590.710187
EM: Round [19] log likelihood: -7590.617080
EM: Round [20] log likelihood: -7590.528276
EM: Round [21] log likelihood: -7590.443458
EM: Round [22] log likelihood: -7590.362345
EM: Round [23] log likelihood: -7590.284680
EM: Round [24] log likelihood: -7590.210236
EM: Round [25] log likelihood: -7590.138805
EM: Round [26] log likelihood: -7590.070197
EM: Round [27] log likelihood: -7590.004242
EM: Round [28] log likelihood: -7589.940781
EM: Round [29] log likelihood: -7589.879672
EM: Round [30] log likelihood: -7589.820783
EM: Round [31] log likelihood: -7589.763991
EM: Round [32] log likelihood: -7589.709186
EM: Round [33] log likelihood: -7589.656263
EM: Round [34] log likelihood: -7589.605126
EM: Round [35] log likelihood: -7589.555687
EM: Round [36] log likelihood: -7589.507863
EM: Round [37] log likelihood: -7589.461577
EM: Round [38] log likelihood: -7589.416756
EM: Round [39] log likelihood: -7589.373334
EM: Round [40] log likelihood: -7589.331248
EM: Round [41] log likelihood: -7589.290439
EM: Round [42] log likelihood: -7589.250852
EM: Round [43] log likelihood: -7589.212435
EM: Round [44] log likelihood: -7589.175139
EM: Round [45] log likelihood: -7589.138918
EM: Round [46] log likelihood: -7589.103728
EM: Round [47] log likelihood: -7589.069530
EM: Round [48] log likelihood: -7589.036283
EM: Round [49] log likelihood: -7589.003953
EM: Round [50] log likelihood: -7588.972503
EM: Round [51] log likelihood: -7588.941902
EM: Round [52] log likelihood: -7588.912117
EM: Round [53] log likelihood: -7588.883120
EM: Round [54] log likelihood: -7588.854882
EM: Round [55] log likelihood: -7588.827377
EM: Round [56] log likelihood: -7588.800580
EM: Round [57] log likelihood: -7588.774465
EM: Round [58] log likelihood: -7588.749010
EM: Round [59] log likelihood: -7588.724192
EM: Round [60] log likelihood: -7588.699992
EM: Round [61] log likelihood: -7588.676388
EM: Round [62] log likelihood: -7588.653362
EM: Round [63] log likelihood: -7588.630895
EM: Round [64] log likelihood: -7588.608969
EM: Round [65] log likelihood: -7588.587568
EM: Round [66] log likelihood: -7588.566676
EM: Round [67] log likelihood: -7588.546276
EM: Round [68] log likelihood: -7588.526354
EM: Round [69] log likelihood: -7588.506897
EM: Round [70] log likelihood: -7588.487889
EM: Round [71] log likelihood: -7588.469319
EM: Round [72] log likelihood: -7588.451173
EM: Round [73] log likelihood: -7588.433439
EM: Round [74] log likelihood: -7588.416106
EM: Round [75] log likelihood: -7588.399162
EM: Round [76] log likelihood: -7588.382596
EM: Round [77] log likelihood: -7588.366398
EM: Round [78] log likelihood: -7588.350558
EM: Round [79] log likelihood: -7588.335066
EM: Round [80] log likelihood: -7588.319913
EM: Round [81] log likelihood: -7588.305089
EM: Round [82] log likelihood: -7588.290586
EM: Round [83] log likelihood: -7588.276396
EM: Round [84] log likelihood: -7588.262510
EM: Round [85] log likelihood: -7588.248920
EM: Round [86] log likelihood: -7588.235620
EM: Round [87] log likelihood: -7588.222600
EM: Round [88] log likelihood: -7588.209855
EM: Round [89] log likelihood: -7588.197377
EM: Round [90] log likelihood: -7588.185160
EM: Round [91] log likelihood: -7588.173197
EM: Round [92] log likelihood: -7588.161482
EM: Round [93] log likelihood: -7588.150009
EM: Round [94] log likelihood: -7588.138772
EM: Round [95] log likelihood: -7588.127765
EM: Round [96] log likelihood: -7588.116983
EM: Round [97] log likelihood: -7588.106420
EM: Round [98] log likelihood: -7588.096072
EM: Round [99] log likelihood: -7588.085932
EM: Round [100] log likelihood: -7588.075997
EM: Round [101] log likelihood: -7588.066261
EM: Round [102] log likelihood: -7588.056720
EM: Round [103] log likelihood: -7588.047369
EM: Round [104] log likelihood: -7588.038204
EM: Round [105] log likelihood: -7588.029221
EM: Round [106] log likelihood: -7588.020416
EM: Round [107] log likelihood: -7588.011784
EM: Round [108] log likelihood: -7588.003321
EM: Round [109] log likelihood: -7587.995024
EM: Round [110] log likelihood: -7587.986890
EM: Round [111] log likelihood: -7587.978914
EM: Round [112] log likelihood: -7587.971093
EM: Round [113] log likelihood: -7587.963424
EM: Round [114] log likelihood: -7587.955903
EM: Round [115] log likelihood: -7587.948527
EM: Round [116] log likelihood: -7587.941293
EM: Round [117] log likelihood: -7587.934198
EM: Round [118] log likelihood: -7587.927239
EM: Round [119] log likelihood: -7587.920413
EM: Round [120] log likelihood: -7587.913717
EM: Round [121] log likelihood: -7587.907148
EM: Round [122] log likelihood: -7587.900704
EM: Round [123] log likelihood: -7587.894382
EM: Round [124] log likelihood: -7587.888180
EM: Round [125] log likelihood: -7587.882095
EM: Round [126] log likelihood: -7587.876124
EM: Round [127] log likelihood: -7587.870266
EM: Round [128] log likelihood: -7587.864517
EM: Round [129] log likelihood: -7587.858876
EM: Round [130] log likelihood: -7587.853340
EM: Round [131] log likelihood: -7587.847908
EM: Round [132] log likelihood: -7587.842576
EM: Round [133] log likelihood: -7587.837344
EM: Round [134] log likelihood: -7587.832209
EM: Round [135] log likelihood: -7587.827169
EM: Round [136] log likelihood: -7587.822222
EM: Round [137] log likelihood: -7587.817366
EM: Round [138] log likelihood: -7587.812600
EM: Round [139] log likelihood: -7587.807922
EM: Round [140] log likelihood: -7587.803330
EM: Round [141] log likelihood: -7587.798821
EM: Round [142] log likelihood: -7587.794396
EM: Round [143] log likelihood: -7587.790051
EM: Round [144] log likelihood: -7587.785786
EM: Round [145] log likelihood: -7587.781598
EM: Round [146] log likelihood: -7587.777487
EM: Round [147] log likelihood: -7587.773450
EM: Round [148] log likelihood: -7587.769487
EM: Round [149] log likelihood: -7587.765596
EM: Round [150] log likelihood: -7587.761775
EM: Round [151] log likelihood: -7587.758024
EM: Round [152] log likelihood: -7587.754340
EM: Round [153] log likelihood: -7587.750722
EM: Round [154] log likelihood: -7587.747170
EM: Round [155] log likelihood: -7587.743682
EM: Round [156] log likelihood: -7587.740257
EM: Round [157] log likelihood: -7587.736893
EM: Round [158] log likelihood: -7587.733589
EM: Round [159] log likelihood: -7587.730345
EM: Round [160] log likelihood: -7587.727159
EM: Round [161] log likelihood: -7587.724029
EM: Round [162] log likelihood: -7587.720956
EM: Round [163] log likelihood: -7587.717938
EM: Round [164] log likelihood: -7587.714973
EM: Round [165] log likelihood: -7587.712061
EM: Round [166] log likelihood: -7587.709201
EM: Round [167] log likelihood: -7587.706392
EM: Round [168] log likelihood: -7587.703633
EM: Round [169] log likelihood: -7587.700923
EM: Round [170] log likelihood: -7587.698261
EM: Round [171] log likelihood: -7587.695646
EM: Round [172] log likelihood: -7587.693077
EM: Round [173] log likelihood: -7587.690554
EM: Round [174] log likelihood: -7587.688075
EM: Round [175] log likelihood: -7587.685640
EM: Round [176] log likelihood: -7587.683248
EM: Round [177] log likelihood: -7587.680898
EM: Round [178] log likelihood: -7587.678590
EM: Round [179] log likelihood: -7587.676322
EM: Round [180] log likelihood: -7587.674094
EM: Round [181] log likelihood: -7587.671906
EM: Round [182] log likelihood: -7587.669755
EM: Round [183] log likelihood: -7587.667643
EM: Round [184] log likelihood: -7587.665568
EM: Round [185] log likelihood: -7587.663528
EM: Round [186] log likelihood: -7587.661525
EM: Round [187] log likelihood: -7587.659557
EM: Round [188] log likelihood: -7587.657623
EM: Round [189] log likelihood: -7587.655723
EM: Round [190] log likelihood: -7587.653856
EM: Round [191] log likelihood: -7587.652022
EM: Round [192] log likelihood: -7587.650220
EM: Round [193] log likelihood: -7587.648449
EM: Round [194] log likelihood: -7587.646709
EM: Round [195] log likelihood: -7587.644999
EM: Round [196] log likelihood: -7587.643319
EM: Round [197] log likelihood: -7587.641669
EM: Round [198] log likelihood: -7587.640047
EM: Round [199] log likelihood: -7587.638453
EM: Round [200] log likelihood: -7587.636887
EM: Round [201] log likelihood: -7587.635348
EM: Round [202] log likelihood: -7587.633836
EM: Round [203] log likelihood: -7587.632350
EM: Round [204] log likelihood: -7587.630890
EM: Round [205] log likelihood: -7587.629455
EM: Round [206] log likelihood: -7587.628045
EM: Round [207] log likelihood: -7587.626659
EM: Round [208] log likelihood: -7587.625297
EM: Round [209] log likelihood: -7587.623959
EM: Round [210] log likelihood: -7587.622644
EM: Round [211] log likelihood: -7587.621352
EM: Round [212] log likelihood: -7587.620082
EM: Round [213] log likelihood: -7587.618834
EM: Round [214] log likelihood: -7587.617608
EM: Round [215] log likelihood: -7587.616403
EM: Round [216] log likelihood: -7587.615218
EM: Round [217] log likelihood: -7587.614054
EM: Round [218] log likelihood: -7587.612910
EM: Round [219] log likelihood: -7587.611786
EM: Round [220] log likelihood: -7587.610681
EM: Round [221] log likelihood: -7587.609595
EM: Round [222] log likelihood: -7587.608527
EM: Round [223] log likelihood: -7587.607479
EM: Round [224] log likelihood: -7587.606448
EM: Round [225] log likelihood: -7587.605435
EM: Round [226] log likelihood: -7587.604439
EM: Round [227] log likelihood: -7587.603460
EM: Round [228] log likelihood: -7587.602498
EM: Round [229] log likelihood: -7587.601553
EM: Round [230] log likelihood: -7587.600624
EM: Round [231] log likelihood: -7587.599711
EM: Round [232] log likelihood: -7587.598813
EM: Round [233] log likelihood: -7587.597931
EM: Round [234] log likelihood: -7587.597064
EM: Round [235] log likelihood: -7587.596212
EM: Round [236] log likelihood: -7587.595375
EM: Round [237] log likelihood: -7587.594551
EM: Round [238] log likelihood: -7587.593742
EM: Round [239] log likelihood: -7587.592947
EM: Round [240] log likelihood: -7587.592165
EM: Round [241] log likelihood: -7587.591397
EM: Round [242] log likelihood: -7587.590642
EM: Round [243] log likelihood: -7587.589900
EM: Round [244] log likelihood: -7587.589170
EM: Round [245] log likelihood: -7587.588453
EM: Round [246] log likelihood: -7587.587748
EM: Round [247] log likelihood: -7587.587056
EM: Round [248] log likelihood: -7587.586375
EM: Round [249] log likelihood: -7587.585705
EM: Round [250] log likelihood: -7587.585048
EM: Round [251] log likelihood: -7587.584401
EM: Round [252] log likelihood: -7587.583765
EM: Round [253] log likelihood: -7587.583141
EM: Round [254] log likelihood: -7587.582526
EM: Round [255] log likelihood: -7587.581923
EM: Round [256] log likelihood: -7587.581329
EM: Round [257] log likelihood: -7587.580746
EM: Round [258] log likelihood: -7587.580173
EM: Round [259] log likelihood: -7587.579609
EM: Round [260] log likelihood: -7587.579056
EM: Round [261] log likelihood: -7587.578511
EM: Round [262] log likelihood: -7587.577976
EM: Round [263] log likelihood: -7587.577450
EM: Round [264] log likelihood: -7587.576933
EM: Round [265] log likelihood: -7587.576424
EM: Round [266] log likelihood: -7587.575925
EM: Round [267] log likelihood: -7587.575433
EM: Round [268] log likelihood: -7587.574951
EM: Round [269] log likelihood: -7587.574476
EM: Round [270] log likelihood: -7587.574009
EM: Round [271] log likelihood: -7587.573551
EM: Round [272] log likelihood: -7587.573100
EM: Round [273] log likelihood: -7587.572657
EM: Round [274] log likelihood: -7587.572221
EM: Round [275] log likelihood: -7587.571793
EM: Round [276] log likelihood: -7587.571372
EM: Round [277] log likelihood: -7587.570958
EM: Round [278] log likelihood: -7587.570551
EM: Round [279] log likelihood: -7587.570152
EM: Round [280] log likelihood: -7587.569759
EM: Round [281] log likelihood: -7587.569372
EM: Round [282] log likelihood: -7587.568992
EM: Round [283] log likelihood: -7587.568619
EM: Round [284] log likelihood: -7587.568252
EM: Round [285] log likelihood: -7587.567891
EM: Round [286] log likelihood: -7587.567536
EM: Round [287] log likelihood: -7587.567188
EM: Round [288] log likelihood: -7587.566845
EM: Round [289] log likelihood: -7587.566508
EM: Round [290] log likelihood: -7587.566177
EM: Round [291] log likelihood: -7587.565851
EM: Round [292] log likelihood: -7587.565531
EM: Round [293] log likelihood: -7587.565217
EM: Round [294] log likelihood: -7587.564907
EM: Round [295] log likelihood: -7587.564603
EM: Round [296] log likelihood: -7587.564304
EM: Round [297] log likelihood: -7587.564010
EM: Round [298] log likelihood: -7587.563722
EM: Round [299] log likelihood: -7587.563438
EM: Round [300] log likelihood: -7587.563158
EM: Round [301] log likelihood: -7587.562884
EM: Round [302] log likelihood: -7587.562614
EM: Round [303] log likelihood: -7587.562349
EM: Round [304] log likelihood: -7587.562088
EM: Round [305] log likelihood: -7587.561832
EM: Round [306] log likelihood: -7587.561580
EM: Round [307] log likelihood: -7587.561332
EM: Round [308] log likelihood: -7587.561089
EM: Round [309] log likelihood: -7587.560850
EM: Round [310] log likelihood: -7587.560614
EM: Round [311] log likelihood: -7587.560383
EM: Round [312] log likelihood: -7587.560155
EM: Round [313] log likelihood: -7587.559932
EM: Round [314] log likelihood: -7587.559712
EM: Round [315] log likelihood: -7587.559496
EM: Round [316] log likelihood: -7587.559284
EM: Round [317] log likelihood: -7587.559075
EM: Round [318] log likelihood: -7587.558870
EM: Round [319] log likelihood: -7587.558668
EM: Round [320] log likelihood: -7587.558469
EM: Round [321] log likelihood: -7587.558274
EM: Round [322] log likelihood: -7587.558083
EM: Round [323] log likelihood: -7587.557894
EM: Round [324] log likelihood: -7587.557709
EM: Round [325] log likelihood: -7587.557527
EM: Round [326] log likelihood: -7587.557348
EM: Round [327] log likelihood: -7587.557171
EM: Round [328] log likelihood: -7587.556998
EM: Round [329] log likelihood: -7587.556828
EM: Round [330] log likelihood: -7587.556661
EM: Round [331] log likelihood: -7587.556496
EM: Round [332] log likelihood: -7587.556335
EM: Round [333] log likelihood: -7587.556176
EM: Round [334] log likelihood: -7587.556020
EM: Round [335] log likelihood: -7587.555866
EM: Round [336] log likelihood: -7587.555715
EM: Round [337] log likelihood: -7587.555567
EM: Round [338] log likelihood: -7587.555421
EM: Round [339] log likelihood: -7587.555277
EM: Round [340] log likelihood: -7587.555136
EM: Round [341] log likelihood: -7587.554997
EM: Round [342] log likelihood: -7587.554861
EM: Round [343] log likelihood: -7587.554727
EM: Round [344] log likelihood: -7587.554595
EM: Round [345] log likelihood: -7587.554466
EM: Round [346] log likelihood: -7587.554338
EM: Round [347] log likelihood: -7587.554213
EM: Round [348] log likelihood: -7587.554090
EM: Round [349] log likelihood: -7587.553969
EM: Round [350] log likelihood: -7587.553850
EM: Round [351] log likelihood: -7587.553733
EM: Round [352] log likelihood: -7587.553618
EM: Round [353] log likelihood: -7587.553505
EM: Round [354] log likelihood: -7587.553394
EM: Round [355] log likelihood: -7587.553285
EM: Round [356] log likelihood: -7587.553177
EM: Round [357] log likelihood: -7587.553072
EM: Round [358] log likelihood: -7587.552968
EM: Round [359] log likelihood: -7587.552866
EM: Round [360] log likelihood: -7587.552766
EM: Round [361] log likelihood: -7587.552667
EM: Stopping iterations at round 361 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.sActxdZih0/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.sActxdZih0/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.sActxdZih0/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.sActxdZih0/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.sActxdZih0/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.sActxdZih0/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.sActxdZih0/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.sActxdZih0/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_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.sActxdZih0/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_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.sActxdZih0/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.sActxdZih0/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.sActxdZih0/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -7226.827783
EM: Round [1] log likelihood: -7226.323402
EM: Round [2] log likelihood: -7226.323175
EM: Round [3] log likelihood: -7226.323174
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.sActxdZih0/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296887005
Warning - not locating file: /tmp/nxf.sActxdZih0/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
ls: cannot access 'IGV_inputs': No such file or directory