Done.
-parsing GTF file: /tmp/nxf.FM8Bn3SE0U/tih_rna_sample_00699_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.FM8Bn3SE0U/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.FM8Bn3SE0U/tih_rna_sample_00699_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.FM8Bn3SE0U/tih_rna_sample_00699_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.FM8Bn3SE0U/fi_workdir/tih_rna_sample_00699_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.FM8Bn3SE0U/fi_workdir/tih_rna_sample_00699_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00699_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00699_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:11:51 : INFO : Done.
-parsing GTF file: /tmp/nxf.FM8Bn3SE0U/fi_workdir/tih_rna_sample_00699_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.FM8Bn3SE0U/fi_workdir/tih_rna_sample_00699_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[5090000]   -done parsing /tmp/nxf.FM8Bn3SE0U/fi_workdir/tih_rna_sample_00699_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'low complexity anchor region' => 19,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 340,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 75,
          'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 12,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1353,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3968,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 700,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 7 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 558,
          'num genes matched < 2' => 437,
          'seq-similar region overlap' => 116,
          'per_id < 96' => 18371,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 31,
          'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 8,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 298,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 570,
          'num_hits: 9 != num_counted_on_fusion_contigs 8 ' => 24,
          'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 8,
          'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 6,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 63,
          'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 20,
          'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 12,
          'exons hit < 2' => 13,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 86,
          'small anchor length' => 91,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 560,
          ' ** passed ** ' => 7983,
          'excessive soft clipping' => 29992
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.FM8Bn3SE0U/fi_workdir/tih_rna_sample_00699_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[57000]   -fusion SPANNING read extraction for scaff: ABR--C20orf96

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[4000]   -fusion SPANNING read extraction for scaff: AC020550.2--APBA1

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[19000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[2000]   -fusion SPANNING read extraction for scaff: AC096582.2--SEPTIN14

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[4000]   -fusion SPANNING read extraction for scaff: AC104041.1--APBA1

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[210000]   -fusion SPANNING read extraction for scaff: AGFG1--COL4A3

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[20000]   -fusion SPANNING read extraction for scaff: ANKRD30A--GAS7

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[11000]   -fusion SPANNING read extraction for scaff: ANKRD30A--RPS27AP1

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[698000]   
[699000]   -fusion SPANNING read extraction for scaff: ATP2A2--ANAPC7

[1000]   
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[8000]   
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[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   -fusion SPANNING read extraction for scaff: ATP6V0A1--AL353803.2

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[59000]   
[60000]   
[61000]   
[62000]   -fusion SPANNING read extraction for scaff: ATP6V0A1--LINC00963

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   -fusion SPANNING read extraction for scaff: BCAS3--KAT2B

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: CCDC134--MEI1

[1000]   
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[5000]   
[6000]   
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[8000]   
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[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   -fusion SPANNING read extraction for scaff: CCNY--PARD3

[1000]   
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[4000]   
[5000]   
[6000]   
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[8000]   
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[95000]   
[96000]   -fusion SPANNING read extraction for scaff: CMIP--BCO1

[1000]   
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[4000]   
[5000]   
[6000]   
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[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: COX6CP1--COX6C

[1000]   
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[6000]   
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[80000]   
[81000]   
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[83000]   
[84000]   
[85000]   
[86000]   -fusion SPANNING read extraction for scaff: CYP2C19--CYP2C18

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[57000]   
[58000]   
[59000]   -fusion SPANNING read extraction for scaff: DHX16--NAPGP2

[1000]   
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[59000]   
[60000]   
[61000]   -fusion SPANNING read extraction for scaff: DHX16--MUC21

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[16000]   -fusion SPANNING read extraction for scaff: DNAJC5--FP236383.3

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[43000]   
[44000]   -fusion SPANNING read extraction for scaff: DONSON--CRYZL1

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[17000]   -fusion SPANNING read extraction for scaff: EFL1--GOLGA6L11P

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[260000]   -fusion SPANNING read extraction for scaff: FAM149B1--RRBP1

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[30000]   
[31000]   -fusion SPANNING read extraction for scaff: GTF2E2--TEX15

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[60000]   
[61000]   -fusion SPANNING read extraction for scaff: HID1--FADS6

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[45000]   
[46000]   -fusion SPANNING read extraction for scaff: IFT81--AC090099.1

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[85000]   
[86000]   -fusion SPANNING read extraction for scaff: IFT81--GLTP

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[457000]   -fusion SPANNING read extraction for scaff: ITGB1--NRP1

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[363000]   -fusion SPANNING read extraction for scaff: MET--KAT2B

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[72000]   
[73000]   -fusion SPANNING read extraction for scaff: NBAS--AC130710.1

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[72000]   
[73000]   -fusion SPANNING read extraction for scaff: NBAS--AC174048.1

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[284000]   
[285000]   -fusion SPANNING read extraction for scaff: P4HB--MYADML2

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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[28000]   
[29000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

[1000]   
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[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[22000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

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[25000]   
[26000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

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[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

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[160000]   
[161000]   -fusion SPANNING read extraction for scaff: PCM1--AC027117.1

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[83000]   
[84000]   -fusion SPANNING read extraction for scaff: PIGU--NCOA6

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[66000]   
[67000]   -fusion SPANNING read extraction for scaff: PRKAG1--PRPF40B

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[50000]   -fusion SPANNING read extraction for scaff: PSMG3--TMEM184A

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[57000]   -fusion SPANNING read extraction for scaff: PYGB--AL080312.1

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[57000]   -fusion SPANNING read extraction for scaff: PYGB--AL035252.2

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[99000]   -fusion SPANNING read extraction for scaff: RABL6--AGPAT2

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[97000]   
[98000]   -fusion SPANNING read extraction for scaff: RABL6--DIPK1B

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[415000]   -fusion SPANNING read extraction for scaff: SIK1--CU639417.3

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[118000]   
[119000]   -fusion SPANNING read extraction for scaff: SPAG9--NME1

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[19000]   -fusion SPANNING read extraction for scaff: STX8--ZBTB46

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[36000]   
[37000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[39000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

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

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[18000]   -fusion SPANNING read extraction for scaff: TMED7--TICAM2

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[23000]   -fusion SPANNING read extraction for scaff: TP53--EDIL3-DT

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[41000]   
[42000]   -fusion SPANNING read extraction for scaff: TP53--EDIL3

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[53000]   -fusion SPANNING read extraction for scaff: TPD52L2--FP236383.3

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[23000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[48000]   -fusion SPANNING read extraction for scaff: UBE2O--ST6GALNAC2
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 32111,
          'seq similar region alignment' => 24737
        };
EM: Starting log likelihood: -13661.289807
EM: Round [1] log likelihood: -13649.091647
EM: Round [2] log likelihood: -13645.308663
EM: Round [3] log likelihood: -13642.663649
EM: Round [4] log likelihood: -13640.732765
EM: Round [5] log likelihood: -13639.281463
EM: Round [6] log likelihood: -13638.164860
EM: Round [7] log likelihood: -13637.288941
EM: Round [8] log likelihood: -13636.590415
EM: Round [9] log likelihood: -13636.025382
EM: Round [10] log likelihood: -13635.562605
EM: Round [11] log likelihood: -13635.179350
EM: Round [12] log likelihood: -13634.858738
EM: Round [13] log likelihood: -13634.588019
EM: Round [14] log likelihood: -13634.357414
EM: Round [15] log likelihood: -13634.159325
EM: Round [16] log likelihood: -13633.987780
EM: Round [17] log likelihood: -13633.838047
EM: Round [18] log likelihood: -13633.706344
EM: Round [19] log likelihood: -13633.589627
EM: Round [20] log likelihood: -13633.485437
EM: Round [21] log likelihood: -13633.391772
EM: Round [22] log likelihood: -13633.307002
EM: Round [23] log likelihood: -13633.229789
EM: Round [24] log likelihood: -13633.159033
EM: Round [25] log likelihood: -13633.093826
EM: Round [26] log likelihood: -13633.033419
EM: Round [27] log likelihood: -13632.977186
EM: Round [28] log likelihood: -13632.924607
EM: Round [29] log likelihood: -13632.875248
EM: Round [30] log likelihood: -13632.828742
EM: Round [31] log likelihood: -13632.784780
EM: Round [32] log likelihood: -13632.743101
EM: Round [33] log likelihood: -13632.703483
EM: Round [34] log likelihood: -13632.665735
EM: Round [35] log likelihood: -13632.629692
EM: Round [36] log likelihood: -13632.595214
EM: Round [37] log likelihood: -13632.562177
EM: Round [38] log likelihood: -13632.530474
EM: Round [39] log likelihood: -13632.500010
EM: Round [40] log likelihood: -13632.470702
EM: Round [41] log likelihood: -13632.442475
EM: Round [42] log likelihood: -13632.415262
EM: Round [43] log likelihood: -13632.389003
EM: Round [44] log likelihood: -13632.363645
EM: Round [45] log likelihood: -13632.339139
EM: Round [46] log likelihood: -13632.315439
EM: Round [47] log likelihood: -13632.292505
EM: Round [48] log likelihood: -13632.270298
EM: Round [49] log likelihood: -13632.248784
EM: Round [50] log likelihood: -13632.227930
EM: Round [51] log likelihood: -13632.207706
EM: Round [52] log likelihood: -13632.188084
EM: Round [53] log likelihood: -13632.169037
EM: Round [54] log likelihood: -13632.150541
EM: Round [55] log likelihood: -13632.132572
EM: Round [56] log likelihood: -13632.115108
EM: Round [57] log likelihood: -13632.098130
EM: Round [58] log likelihood: -13632.081616
EM: Round [59] log likelihood: -13632.065550
EM: Round [60] log likelihood: -13632.049912
EM: Round [61] log likelihood: -13632.034687
EM: Round [62] log likelihood: -13632.019859
EM: Round [63] log likelihood: -13632.005412
EM: Round [64] log likelihood: -13631.991333
EM: Round [65] log likelihood: -13631.977607
EM: Round [66] log likelihood: -13631.964222
EM: Round [67] log likelihood: -13631.951166
EM: Round [68] log likelihood: -13631.938426
EM: Round [69] log likelihood: -13631.925991
EM: Round [70] log likelihood: -13631.913851
EM: Round [71] log likelihood: -13631.901995
EM: Round [72] log likelihood: -13631.890414
EM: Round [73] log likelihood: -13631.879097
EM: Round [74] log likelihood: -13631.868036
EM: Round [75] log likelihood: -13631.857223
EM: Round [76] log likelihood: -13631.846648
EM: Round [77] log likelihood: -13631.836305
EM: Round [78] log likelihood: -13631.826186
EM: Round [79] log likelihood: -13631.816282
EM: Round [80] log likelihood: -13631.806588
EM: Round [81] log likelihood: -13631.797097
EM: Round [82] log likelihood: -13631.787802
EM: Round [83] log likelihood: -13631.778697
EM: Round [84] log likelihood: -13631.769776
EM: Round [85] log likelihood: -13631.761033
EM: Round [86] log likelihood: -13631.752464
EM: Round [87] log likelihood: -13631.744063
EM: Round [88] log likelihood: -13631.735825
EM: Round [89] log likelihood: -13631.727744
EM: Round [90] log likelihood: -13631.719817
EM: Round [91] log likelihood: -13631.712040
EM: Round [92] log likelihood: -13631.704406
EM: Round [93] log likelihood: -13631.696914
EM: Round [94] log likelihood: -13631.689558
EM: Round [95] log likelihood: -13631.682334
EM: Round [96] log likelihood: -13631.675240
EM: Round [97] log likelihood: -13631.668272
EM: Round [98] log likelihood: -13631.661425
EM: Round [99] log likelihood: -13631.654698
EM: Round [100] log likelihood: -13631.648086
EM: Round [101] log likelihood: -13631.641587
EM: Round [102] log likelihood: -13631.635198
EM: Round [103] log likelihood: -13631.628916
EM: Round [104] log likelihood: -13631.622737
EM: Round [105] log likelihood: -13631.616661
EM: Round [106] log likelihood: -13631.610683
EM: Round [107] log likelihood: -13631.604802
EM: Round [108] log likelihood: -13631.599016
EM: Round [109] log likelihood: -13631.593321
EM: Round [110] log likelihood: -13631.587716
EM: Round [111] log likelihood: -13631.582198
EM: Round [112] log likelihood: -13631.576766
EM: Round [113] log likelihood: -13631.571418
EM: Round [114] log likelihood: -13631.566151
EM: Round [115] log likelihood: -13631.560964
EM: Round [116] log likelihood: -13631.555855
EM: Round [117] log likelihood: -13631.550822
EM: Round [118] log likelihood: -13631.545864
EM: Round [119] log likelihood: -13631.540978
EM: Round [120] log likelihood: -13631.536164
EM: Round [121] log likelihood: -13631.531420
EM: Round [122] log likelihood: -13631.526744
EM: Round [123] log likelihood: -13631.522134
EM: Round [124] log likelihood: -13631.517591
EM: Round [125] log likelihood: -13631.513111
EM: Round [126] log likelihood: -13631.508694
EM: Round [127] log likelihood: -13631.504339
EM: Round [128] log likelihood: -13631.500044
EM: Round [129] log likelihood: -13631.495808
EM: Round [130] log likelihood: -13631.491630
EM: Round [131] log likelihood: -13631.487509
EM: Round [132] log likelihood: -13631.483444
EM: Round [133] log likelihood: -13631.479433
EM: Round [134] log likelihood: -13631.475476
EM: Round [135] log likelihood: -13631.471572
EM: Round [136] log likelihood: -13631.467719
EM: Round [137] log likelihood: -13631.463917
EM: Round [138] log likelihood: -13631.460165
EM: Round [139] log likelihood: -13631.456462
EM: Round [140] log likelihood: -13631.452807
EM: Round [141] log likelihood: -13631.449198
EM: Round [142] log likelihood: -13631.445637
EM: Round [143] log likelihood: -13631.442120
EM: Round [144] log likelihood: -13631.438649
EM: Round [145] log likelihood: -13631.435221
EM: Round [146] log likelihood: -13631.431837
EM: Round [147] log likelihood: -13631.428495
EM: Round [148] log likelihood: -13631.425195
EM: Round [149] log likelihood: -13631.421936
EM: Round [150] log likelihood: -13631.418718
EM: Round [151] log likelihood: -13631.415539
EM: Round [152] log likelihood: -13631.412399
EM: Round [153] log likelihood: -13631.409298
EM: Round [154] log likelihood: -13631.406235
EM: Round [155] log likelihood: -13631.403209
EM: Round [156] log likelihood: -13631.400220
EM: Round [157] log likelihood: -13631.397267
EM: Round [158] log likelihood: -13631.394349
EM: Round [159] log likelihood: -13631.391467
EM: Round [160] log likelihood: -13631.388619
EM: Round [161] log likelihood: -13631.385805
EM: Round [162] log likelihood: -13631.383024
EM: Round [163] log likelihood: -13631.380277
EM: Round [164] log likelihood: -13631.377561
EM: Round [165] log likelihood: -13631.374878
EM: Round [166] log likelihood: -13631.372227
EM: Round [167] log likelihood: -13631.369606
EM: Round [168] log likelihood: -13631.367016
EM: Round [169] log likelihood: -13631.364456
EM: Round [170] log likelihood: -13631.361926
EM: Round [171] log likelihood: -13631.359425
EM: Round [172] log likelihood: -13631.356953
EM: Round [173] log likelihood: -13631.354510
EM: Round [174] log likelihood: -13631.352095
EM: Round [175] log likelihood: -13631.349707
EM: Round [176] log likelihood: -13631.347347
EM: Round [177] log likelihood: -13631.345013
EM: Round [178] log likelihood: -13631.342707
EM: Round [179] log likelihood: -13631.340426
EM: Round [180] log likelihood: -13631.338171
EM: Round [181] log likelihood: -13631.335942
EM: Round [182] log likelihood: -13631.333738
EM: Round [183] log likelihood: -13631.331559
EM: Round [184] log likelihood: -13631.329404
EM: Round [185] log likelihood: -13631.327274
EM: Round [186] log likelihood: -13631.325167
EM: Round [187] log likelihood: -13631.323084
EM: Round [188] log likelihood: -13631.321024
EM: Round [189] log likelihood: -13631.318987
EM: Round [190] log likelihood: -13631.316973
EM: Round [191] log likelihood: -13631.314981
EM: Round [192] log likelihood: -13631.313011
EM: Round [193] log likelihood: -13631.311063
EM: Round [194] log likelihood: -13631.309137
EM: Round [195] log likelihood: -13631.307231
EM: Round [196] log likelihood: -13631.305347
EM: Round [197] log likelihood: -13631.303483
EM: Round [198] log likelihood: -13631.301640
EM: Round [199] log likelihood: -13631.299817
EM: Round [200] log likelihood: -13631.298014
EM: Round [201] log likelihood: -13631.296230
EM: Round [202] log likelihood: -13631.294466
EM: Round [203] log likelihood: -13631.292721
EM: Round [204] log likelihood: -13631.290995
EM: Round [205] log likelihood: -13631.289288
EM: Round [206] log likelihood: -13631.287599
EM: Round [207] log likelihood: -13631.285929
EM: Round [208] log likelihood: -13631.284276
EM: Round [209] log likelihood: -13631.282642
EM: Round [210] log likelihood: -13631.281025
EM: Round [211] log likelihood: -13631.279425
EM: Round [212] log likelihood: -13631.277843
EM: Round [213] log likelihood: -13631.276277
EM: Round [214] log likelihood: -13631.274729
EM: Round [215] log likelihood: -13631.273197
EM: Round [216] log likelihood: -13631.271681
EM: Round [217] log likelihood: -13631.270181
EM: Round [218] log likelihood: -13631.268698
EM: Round [219] log likelihood: -13631.267230
EM: Round [220] log likelihood: -13631.265778
EM: Round [221] log likelihood: -13631.264341
EM: Round [222] log likelihood: -13631.262920
EM: Round [223] log likelihood: -13631.261514
EM: Round [224] log likelihood: -13631.260122
EM: Round [225] log likelihood: -13631.258746
EM: Round [226] log likelihood: -13631.257383
EM: Round [227] log likelihood: -13631.256036
EM: Round [228] log likelihood: -13631.254702
EM: Round [229] log likelihood: -13631.253382
EM: Round [230] log likelihood: -13631.252077
EM: Round [231] log likelihood: -13631.250785
EM: Round [232] log likelihood: -13631.249507
EM: Round [233] log likelihood: -13631.248242
EM: Round [234] log likelihood: -13631.246990
EM: Round [235] log likelihood: -13631.245751
EM: Round [236] log likelihood: -13631.244526
EM: Round [237] log likelihood: -13631.243313
EM: Round [238] log likelihood: -13631.242113
EM: Round [239] log likelihood: -13631.240925
EM: Round [240] log likelihood: -13631.239750
EM: Round [241] log likelihood: -13631.238587
EM: Round [242] log likelihood: -13631.237436
EM: Round [243] log likelihood: -13631.236297
EM: Round [244] log likelihood: -13631.235170
EM: Round [245] log likelihood: -13631.234054
EM: Round [246] log likelihood: -13631.232951
EM: Round [247] log likelihood: -13631.231858
EM: Round [248] log likelihood: -13631.230777
EM: Round [249] log likelihood: -13631.229707
EM: Round [250] log likelihood: -13631.228648
EM: Round [251] log likelihood: -13631.227600
EM: Round [252] log likelihood: -13631.226563
EM: Round [253] log likelihood: -13631.225536
EM: Round [254] log likelihood: -13631.224520
EM: Round [255] log likelihood: -13631.223515
EM: Round [256] log likelihood: -13631.222520
EM: Round [257] log likelihood: -13631.221535
EM: Round [258] log likelihood: -13631.220560
EM: Round [259] log likelihood: -13631.219595
EM: Round [260] log likelihood: -13631.218640
EM: Round [261] log likelihood: -13631.217695
EM: Round [262] log likelihood: -13631.216760
EM: Round [263] log likelihood: -13631.215834
EM: Round [264] log likelihood: -13631.214917
EM: Round [265] log likelihood: -13631.214010
EM: Round [266] log likelihood: -13631.213112
EM: Round [267] log likelihood: -13631.212223
EM: Round [268] log likelihood: -13631.211344
EM: Round [269] log likelihood: -13631.210473
EM: Round [270] log likelihood: -13631.209611
EM: Round [271] log likelihood: -13631.208758
EM: Round [272] log likelihood: -13631.207913
EM: Round [273] log likelihood: -13631.207077
EM: Round [274] log likelihood: -13631.206250
EM: Round [275] log likelihood: -13631.205431
EM: Round [276] log likelihood: -13631.204620
EM: Round [277] log likelihood: -13631.203818
EM: Round [278] log likelihood: -13631.203023
EM: Round [279] log likelihood: -13631.202237
EM: Round [280] log likelihood: -13631.201458
EM: Round [281] log likelihood: -13631.200687
EM: Round [282] log likelihood: -13631.199925
EM: Round [283] log likelihood: -13631.199169
EM: Round [284] log likelihood: -13631.198422
EM: Round [285] log likelihood: -13631.197682
EM: Round [286] log likelihood: -13631.196949
EM: Round [287] log likelihood: -13631.196224
EM: Round [288] log likelihood: -13631.195506
EM: Round [289] log likelihood: -13631.194795
EM: Round [290] log likelihood: -13631.194091
EM: Round [291] log likelihood: -13631.193395
EM: Round [292] log likelihood: -13631.192705
EM: Round [293] log likelihood: -13631.192022
EM: Round [294] log likelihood: -13631.191346
EM: Round [295] log likelihood: -13631.190677
EM: Round [296] log likelihood: -13631.190014
EM: Round [297] log likelihood: -13631.189359
EM: Round [298] log likelihood: -13631.188709
EM: Round [299] log likelihood: -13631.188066
EM: Round [300] log likelihood: -13631.187430
EM: Round [301] log likelihood: -13631.186800
EM: Round [302] log likelihood: -13631.186176
EM: Round [303] log likelihood: -13631.185558
EM: Round [304] log likelihood: -13631.184946
EM: Round [305] log likelihood: -13631.184341
EM: Round [306] log likelihood: -13631.183741
EM: Round [307] log likelihood: -13631.183148
EM: Round [308] log likelihood: -13631.182560
EM: Round [309] log likelihood: -13631.181978
EM: Round [310] log likelihood: -13631.181402
EM: Round [311] log likelihood: -13631.180832
EM: Round [312] log likelihood: -13631.180267
EM: Round [313] log likelihood: -13631.179708
EM: Round [314] log likelihood: -13631.179154
EM: Round [315] log likelihood: -13631.178606
EM: Round [316] log likelihood: -13631.178063
EM: Round [317] log likelihood: -13631.177525
EM: Round [318] log likelihood: -13631.176993
EM: Round [319] log likelihood: -13631.176466
EM: Round [320] log likelihood: -13631.175945
EM: Round [321] log likelihood: -13631.175428
EM: Round [322] log likelihood: -13631.174916
EM: Round [323] log likelihood: -13631.174410
EM: Round [324] log likelihood: -13631.173908
EM: Round [325] log likelihood: -13631.173411
EM: Round [326] log likelihood: -13631.172920
EM: Round [327] log likelihood: -13631.172433
EM: Round [328] log likelihood: -13631.171950
EM: Round [329] log likelihood: -13631.171473
EM: Round [330] log likelihood: -13631.171000
EM: Round [331] log likelihood: -13631.170532
EM: Round [332] log likelihood: -13631.170068
EM: Round [333] log likelihood: -13631.169609
EM: Round [334] log likelihood: -13631.169154
EM: Round [335] log likelihood: -13631.168704
EM: Round [336] log likelihood: -13631.168258
EM: Round [337] log likelihood: -13631.167817
EM: Round [338] log likelihood: -13631.167379
EM: Round [339] log likelihood: -13631.166946
EM: Round [340] log likelihood: -13631.166518
EM: Round [341] log likelihood: -13631.166093
EM: Round [342] log likelihood: -13631.165673
EM: Round [343] log likelihood: -13631.165256
EM: Round [344] log likelihood: -13631.164844
EM: Round [345] log likelihood: -13631.164435
EM: Round [346] log likelihood: -13631.164031
EM: Round [347] log likelihood: -13631.163630
EM: Round [348] log likelihood: -13631.163234
EM: Round [349] log likelihood: -13631.162841
EM: Round [350] log likelihood: -13631.162452
EM: Round [351] log likelihood: -13631.162067
EM: Round [352] log likelihood: -13631.161685
EM: Round [353] log likelihood: -13631.161307
EM: Round [354] log likelihood: -13631.160933
EM: Round [355] log likelihood: -13631.160562
EM: Round [356] log likelihood: -13631.160195
EM: Round [357] log likelihood: -13631.159832
EM: Round [358] log likelihood: -13631.159472
EM: Round [359] log likelihood: -13631.159115
EM: Round [360] log likelihood: -13631.158762
EM: Round [361] log likelihood: -13631.158412
EM: Round [362] log likelihood: -13631.158066
EM: Round [363] log likelihood: -13631.157723
EM: Round [364] log likelihood: -13631.157383
EM: Round [365] log likelihood: -13631.157046
EM: Round [366] log likelihood: -13631.156713
EM: Round [367] log likelihood: -13631.156383
EM: Round [368] log likelihood: -13631.156056
EM: Round [369] log likelihood: -13631.155732
EM: Round [370] log likelihood: -13631.155411
EM: Round [371] log likelihood: -13631.155093
EM: Round [372] log likelihood: -13631.154779
EM: Round [373] log likelihood: -13631.154467
EM: Round [374] log likelihood: -13631.154158
EM: Round [375] log likelihood: -13631.153852
EM: Round [376] log likelihood: -13631.153549
EM: Round [377] log likelihood: -13631.153249
EM: Round [378] log likelihood: -13631.152952
EM: Round [379] log likelihood: -13631.152658
EM: Round [380] log likelihood: -13631.152366
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EM: Round [382] log likelihood: -13631.151792
EM: Round [383] log likelihood: -13631.151508
EM: Round [384] log likelihood: -13631.151228
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EM: Round [386] log likelihood: -13631.150674
EM: Round [387] log likelihood: -13631.150402
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EM: Round [389] log likelihood: -13631.149864
EM: Round [390] log likelihood: -13631.149599
EM: Round [391] log likelihood: -13631.149336
EM: Round [392] log likelihood: -13631.149076
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EM: Round [395] log likelihood: -13631.148310
EM: Round [396] log likelihood: -13631.148060
EM: Round [397] log likelihood: -13631.147812
EM: Round [398] log likelihood: -13631.147566
EM: Round [399] log likelihood: -13631.147322
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EM: Round [403] log likelihood: -13631.146371
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EM: Round [409] log likelihood: -13631.145010
EM: Round [410] log likelihood: -13631.144790
EM: Round [411] log likelihood: -13631.144573
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EM: Round [413] log likelihood: -13631.144144
EM: Round [414] log likelihood: -13631.143932
EM: Round [415] log likelihood: -13631.143723
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EM: Round [417] log likelihood: -13631.143310
EM: Round [418] log likelihood: -13631.143106
EM: Round [419] log likelihood: -13631.142904
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EM: Round [423] log likelihood: -13631.142116
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EM: Round [427] log likelihood: -13631.141356
EM: Round [428] log likelihood: -13631.141170
EM: Round [429] log likelihood: -13631.140986
EM: Round [430] log likelihood: -13631.140804
EM: Round [431] log likelihood: -13631.140624
EM: Round [432] log likelihood: -13631.140445
EM: Round [433] log likelihood: -13631.140268
EM: Round [434] log likelihood: -13631.140092
EM: Round [435] log likelihood: -13631.139918
EM: Round [436] log likelihood: -13631.139746
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EM: Round [438] log likelihood: -13631.139406
EM: Round [439] log likelihood: -13631.139239
EM: Round [440] log likelihood: -13631.139072
EM: Round [441] log likelihood: -13631.138908
EM: Round [442] log likelihood: -13631.138745
EM: Round [443] log likelihood: -13631.138583
EM: Round [444] log likelihood: -13631.138423
EM: Round [445] log likelihood: -13631.138265
EM: Round [446] log likelihood: -13631.138108
EM: Round [447] log likelihood: -13631.137952
EM: Round [448] log likelihood: -13631.137798
EM: Round [449] log likelihood: -13631.137645
EM: Round [450] log likelihood: -13631.137493
EM: Round [451] log likelihood: -13631.137343
EM: Round [452] log likelihood: -13631.137195
EM: Round [453] log likelihood: -13631.137047
EM: Round [454] log likelihood: -13631.136901
EM: Round [455] log likelihood: -13631.136757
EM: Round [456] log likelihood: -13631.136613
EM: Round [457] log likelihood: -13631.136471
EM: Round [458] log likelihood: -13631.136330
EM: Round [459] log likelihood: -13631.136191
EM: Round [460] log likelihood: -13631.136053
EM: Round [461] log likelihood: -13631.135916
EM: Round [462] log likelihood: -13631.135780
EM: Round [463] log likelihood: -13631.135646
EM: Round [464] log likelihood: -13631.135512
EM: Round [465] log likelihood: -13631.135380
EM: Round [466] log likelihood: -13631.135249
EM: Round [467] log likelihood: -13631.135120
EM: Round [468] log likelihood: -13631.134991
EM: Round [469] log likelihood: -13631.134864
EM: Round [470] log likelihood: -13631.134738
EM: Round [471] log likelihood: -13631.134613
EM: Round [472] log likelihood: -13631.134489
EM: Round [473] log likelihood: -13631.134366
EM: Round [474] log likelihood: -13631.134244
EM: Round [475] log likelihood: -13631.134124
EM: Round [476] log likelihood: -13631.134004
EM: Round [477] log likelihood: -13631.133886
EM: Round [478] log likelihood: -13631.133769
EM: Round [479] log likelihood: -13631.133652
EM: Round [480] log likelihood: -13631.133537
EM: Round [481] log likelihood: -13631.133423
EM: Round [482] log likelihood: -13631.133310
EM: Round [483] log likelihood: -13631.133198
EM: Round [484] log likelihood: -13631.133086
EM: Round [485] log likelihood: -13631.132976
EM: Round [486] log likelihood: -13631.132867
EM: Round [487] log likelihood: -13631.132759
EM: Round [488] log likelihood: -13631.132652
EM: Round [489] log likelihood: -13631.132545
EM: Round [490] log likelihood: -13631.132440
EM: Round [491] log likelihood: -13631.132336
EM: Round [492] log likelihood: -13631.132232
EM: Round [493] log likelihood: -13631.132130
EM: Round [494] log likelihood: -13631.132028
EM: Round [495] log likelihood: -13631.131928
EM: Round [496] log likelihood: -13631.131828
EM: Stopping iterations at round 496 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.FM8Bn3SE0U/tih_rna_sample_00699_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.FM8Bn3SE0U/tih_rna_sample_00699_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.FM8Bn3SE0U/tih_rna_sample_00699_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.FM8Bn3SE0U/tih_rna_sample_00699_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.FM8Bn3SE0U/tih_rna_sample_00699_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.FM8Bn3SE0U/tih_rna_sample_00699_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.FM8Bn3SE0U/tih_rna_sample_00699_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.FM8Bn3SE0U/fi_workdir/tih_rna_sample_00699_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.FM8Bn3SE0U/fi_workdir/tih_rna_sample_00699_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.FM8Bn3SE0U/fi_workdir/tih_rna_sample_00699_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.FM8Bn3SE0U/tih_rna_sample_00699_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.FM8Bn3SE0U/tih_rna_sample_00699_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -10184.639238
EM: Round [1] log likelihood: -10180.182513
EM: Round [2] log likelihood: -10180.172856
EM: Round [3] log likelihood: -10180.172736
EM: Round [4] log likelihood: -10180.172733
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.FM8Bn3SE0U/tih_rna_sample_00699_B23MVV7LT4_1_1.fastp.fastq.gz: 296530329
Warning - not locating file: /tmp/nxf.FM8Bn3SE0U/tih_rna_sample_00699_B23MVV7LT4_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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000255470.1]
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 [ENSG00000223698.3]
WARNING, no entry stored in dbm for [ENSG00000223698.3]
WARNING, no entry stored in dbm for [ENSG00000251378.1]
WARNING, no entry stored in dbm for [ENSG00000251378.1]
WARNING, no entry stored in dbm for [ENSG00000259692.6]
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 [ENSG00000253671.3]
WARNING, no entry stored in dbm for [ENSG00000253671.3]
WARNING, no entry stored in dbm for [ENSG00000253671.3]
WARNING, no entry stored in dbm for [ENSG00000253671.3]
WARNING, no entry stored in dbm for [ENSG00000253671.3]
WARNING, no entry stored in dbm for [ENSG00000253671.3]
WARNING, no entry stored in dbm for [ENSG00000253671.3]
WARNING, no entry stored in dbm for [ENSG00000280441.3]
WARNING, no entry stored in dbm for [ENSG00000280441.3]
WARNING, no entry stored in dbm for [ENSG00000280013.1]
WARNING, no entry stored in dbm for [ENSG00000280441.3]
WARNING, no entry stored in dbm for [ENSG00000280441.3]
WARNING, no entry stored in dbm for [ENSG00000250320.6]
ls: cannot access 'IGV_inputs': No such file or directory