Done.
-parsing GTF file: /tmp/nxf.TXVRmTkwqu/tih_rna_sample_00434_B23WHTKLT4_2.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.TXVRmTkwqu/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.TXVRmTkwqu/tih_rna_sample_00434_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.TXVRmTkwqu/tih_rna_sample_00434_B23WHTKLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.TXVRmTkwqu/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.TXVRmTkwqu/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00434_B23WHTKLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00434_B23WHTKLT4_2.star.sortedByCoord.out.bam
11:31:27 : INFO : Done.
-parsing GTF file: /tmp/nxf.TXVRmTkwqu/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_2.gtf
-parsing /tmp/nxf.TXVRmTkwqu/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_2.star.cSorted.dupsMarked.bam

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[850000]   -done parsing /tmp/nxf.TXVRmTkwqu/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'per_id < 96' => 3014,
          'small anchor length' => 204,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 21,
          'excessive soft clipping' => 5851,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 56,
          'seq-similar region overlap' => 147,
          'low complexity anchor region' => 7,
          ' ** passed ** ' => 15810,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 4,
          'num genes matched < 2' => 8,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 31
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.TXVRmTkwqu/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[67000]   -fusion SPANNING read extraction for scaff: AC006008.1--DPP6

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[67000]   -fusion SPANNING read extraction for scaff: AC092666.1--DPP6

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[11000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[60000]   -fusion SPANNING read extraction for scaff: NPHP3--ACAD11

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[16000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[16000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[17000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[14000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[14000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[15000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

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[21000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12

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[10000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5

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[10000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7

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[84000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9

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[22000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[85000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[31000]   -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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[38000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 2949,
          'seq similar region alignment' => 48227
        };
EM: Starting log likelihood: -3791.755692
EM: Round [1] log likelihood: -3791.591531
EM: Round [2] log likelihood: -3791.482673
EM: Round [3] log likelihood: -3791.380188
EM: Round [4] log likelihood: -3791.283586
EM: Round [5] log likelihood: -3791.192475
EM: Round [6] log likelihood: -3791.106497
EM: Round [7] log likelihood: -3791.025322
EM: Round [8] log likelihood: -3790.948644
EM: Round [9] log likelihood: -3790.876178
EM: Round [10] log likelihood: -3790.807662
EM: Round [11] log likelihood: -3790.742853
EM: Round [12] log likelihood: -3790.681523
EM: Round [13] log likelihood: -3790.623462
EM: Round [14] log likelihood: -3790.568475
EM: Round [15] log likelihood: -3790.516377
EM: Round [16] log likelihood: -3790.466999
EM: Round [17] log likelihood: -3790.420182
EM: Round [18] log likelihood: -3790.375778
EM: Round [19] log likelihood: -3790.333646
EM: Round [20] log likelihood: -3790.293658
EM: Round [21] log likelihood: -3790.255692
EM: Round [22] log likelihood: -3790.219634
EM: Round [23] log likelihood: -3790.185378
EM: Round [24] log likelihood: -3790.152822
EM: Round [25] log likelihood: -3790.121875
EM: Round [26] log likelihood: -3790.092446
EM: Round [27] log likelihood: -3790.064454
EM: Round [28] log likelihood: -3790.037821
EM: Round [29] log likelihood: -3790.012474
EM: Round [30] log likelihood: -3789.988344
EM: Round [31] log likelihood: -3789.965366
EM: Round [32] log likelihood: -3789.943479
EM: Round [33] log likelihood: -3789.922627
EM: Round [34] log likelihood: -3789.902754
EM: Round [35] log likelihood: -3789.883811
EM: Round [36] log likelihood: -3789.865749
EM: Round [37] log likelihood: -3789.848522
EM: Round [38] log likelihood: -3789.832089
EM: Round [39] log likelihood: -3789.816408
EM: Round [40] log likelihood: -3789.801442
EM: Round [41] log likelihood: -3789.787155
EM: Round [42] log likelihood: -3789.773513
EM: Round [43] log likelihood: -3789.760484
EM: Round [44] log likelihood: -3789.748036
EM: Round [45] log likelihood: -3789.736143
EM: Round [46] log likelihood: -3789.724776
EM: Round [47] log likelihood: -3789.713910
EM: Round [48] log likelihood: -3789.703520
EM: Round [49] log likelihood: -3789.693584
EM: Round [50] log likelihood: -3789.684080
EM: Round [51] log likelihood: -3789.674987
EM: Round [52] log likelihood: -3789.666285
EM: Round [53] log likelihood: -3789.657956
EM: Round [54] log likelihood: -3789.649983
EM: Round [55] log likelihood: -3789.642349
EM: Round [56] log likelihood: -3789.635037
EM: Round [57] log likelihood: -3789.628034
EM: Round [58] log likelihood: -3789.621324
EM: Round [59] log likelihood: -3789.614894
EM: Round [60] log likelihood: -3789.608732
EM: Round [61] log likelihood: -3789.602825
EM: Round [62] log likelihood: -3789.597162
EM: Round [63] log likelihood: -3789.591731
EM: Round [64] log likelihood: -3789.586522
EM: Round [65] log likelihood: -3789.581526
EM: Round [66] log likelihood: -3789.576733
EM: Round [67] log likelihood: -3789.572133
EM: Round [68] log likelihood: -3789.567719
EM: Round [69] log likelihood: -3789.563482
EM: Round [70] log likelihood: -3789.559414
EM: Round [71] log likelihood: -3789.555508
EM: Round [72] log likelihood: -3789.551757
EM: Round [73] log likelihood: -3789.548155
EM: Round [74] log likelihood: -3789.544694
EM: Round [75] log likelihood: -3789.541370
EM: Round [76] log likelihood: -3789.538175
EM: Round [77] log likelihood: -3789.535105
EM: Round [78] log likelihood: -3789.532155
EM: Round [79] log likelihood: -3789.529318
EM: Round [80] log likelihood: -3789.526592
EM: Round [81] log likelihood: -3789.523970
EM: Round [82] log likelihood: -3789.521449
EM: Round [83] log likelihood: -3789.519024
EM: Round [84] log likelihood: -3789.516692
EM: Round [85] log likelihood: -3789.514448
EM: Round [86] log likelihood: -3789.512290
EM: Round [87] log likelihood: -3789.510213
EM: Round [88] log likelihood: -3789.508214
EM: Round [89] log likelihood: -3789.506291
EM: Round [90] log likelihood: -3789.504439
EM: Round [91] log likelihood: -3789.502657
EM: Round [92] log likelihood: -3789.500941
EM: Round [93] log likelihood: -3789.499289
EM: Round [94] log likelihood: -3789.497699
EM: Round [95] log likelihood: -3789.496167
EM: Round [96] log likelihood: -3789.494692
EM: Round [97] log likelihood: -3789.493271
EM: Round [98] log likelihood: -3789.491902
EM: Round [99] log likelihood: -3789.490584
EM: Round [100] log likelihood: -3789.489313
EM: Round [101] log likelihood: -3789.488089
EM: Round [102] log likelihood: -3789.486910
EM: Round [103] log likelihood: -3789.485773
EM: Round [104] log likelihood: -3789.484678
EM: Round [105] log likelihood: -3789.483622
EM: Round [106] log likelihood: -3789.482605
EM: Round [107] log likelihood: -3789.481624
EM: Round [108] log likelihood: -3789.480678
EM: Round [109] log likelihood: -3789.479766
EM: Round [110] log likelihood: -3789.478887
EM: Round [111] log likelihood: -3789.478040
EM: Round [112] log likelihood: -3789.477223
EM: Round [113] log likelihood: -3789.476434
EM: Round [114] log likelihood: -3789.475674
EM: Round [115] log likelihood: -3789.474941
EM: Round [116] log likelihood: -3789.474234
EM: Round [117] log likelihood: -3789.473552
EM: Round [118] log likelihood: -3789.472894
EM: Round [119] log likelihood: -3789.472259
EM: Round [120] log likelihood: -3789.471647
EM: Round [121] log likelihood: -3789.471056
EM: Round [122] log likelihood: -3789.470486
EM: Round [123] log likelihood: -3789.469936
EM: Round [124] log likelihood: -3789.469405
EM: Round [125] log likelihood: -3789.468893
EM: Round [126] log likelihood: -3789.468399
EM: Round [127] log likelihood: -3789.467922
EM: Round [128] log likelihood: -3789.467461
EM: Round [129] log likelihood: -3789.467017
EM: Round [130] log likelihood: -3789.466588
EM: Round [131] log likelihood: -3789.466174
EM: Round [132] log likelihood: -3789.465775
EM: Round [133] log likelihood: -3789.465389
EM: Round [134] log likelihood: -3789.465017
EM: Round [135] log likelihood: -3789.464657
EM: Round [136] log likelihood: -3789.464310
EM: Round [137] log likelihood: -3789.463975
EM: Round [138] log likelihood: -3789.463652
EM: Round [139] log likelihood: -3789.463339
EM: Round [140] log likelihood: -3789.463038
EM: Round [141] log likelihood: -3789.462747
EM: Round [142] log likelihood: -3789.462465
EM: Round [143] log likelihood: -3789.462194
EM: Round [144] log likelihood: -3789.461932
EM: Round [145] log likelihood: -3789.461679
EM: Round [146] log likelihood: -3789.461434
EM: Round [147] log likelihood: -3789.461198
EM: Round [148] log likelihood: -3789.460970
EM: Round [149] log likelihood: -3789.460750
EM: Round [150] log likelihood: -3789.460537
EM: Round [151] log likelihood: -3789.460331
EM: Round [152] log likelihood: -3789.460133
EM: Round [153] log likelihood: -3789.459941
EM: Round [154] log likelihood: -3789.459756
EM: Round [155] log likelihood: -3789.459577
EM: Round [156] log likelihood: -3789.459405
EM: Round [157] log likelihood: -3789.459238
EM: Round [158] log likelihood: -3789.459077
EM: Round [159] log likelihood: -3789.458921
EM: Round [160] log likelihood: -3789.458770
EM: Round [161] log likelihood: -3789.458625
EM: Round [162] log likelihood: -3789.458485
EM: Round [163] log likelihood: -3789.458349
EM: Round [164] log likelihood: -3789.458218
EM: Round [165] log likelihood: -3789.458092
EM: Round [166] log likelihood: -3789.457969
EM: Round [167] log likelihood: -3789.457851
EM: Round [168] log likelihood: -3789.457737
EM: Round [169] log likelihood: -3789.457627
EM: Round [170] log likelihood: -3789.457520
EM: Round [171] log likelihood: -3789.457417
EM: Round [172] log likelihood: -3789.457318
EM: Stopping iterations at round 172 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.TXVRmTkwqu/tih_rna_sample_00434_B23WHTKLT4_2.consolidated.bam into /tmp/nxf.TXVRmTkwqu/tih_rna_sample_00434_B23WHTKLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.TXVRmTkwqu/tih_rna_sample_00434_B23WHTKLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.TXVRmTkwqu/tih_rna_sample_00434_B23WHTKLT4_2.consolidated.bam.read_coords > /tmp/nxf.TXVRmTkwqu/tih_rna_sample_00434_B23WHTKLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.TXVRmTkwqu/tih_rna_sample_00434_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.TXVRmTkwqu/tih_rna_sample_00434_B23WHTKLT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.TXVRmTkwqu/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_2.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.TXVRmTkwqu/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_2.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.TXVRmTkwqu/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.TXVRmTkwqu/tih_rna_sample_00434_B23WHTKLT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.TXVRmTkwqu/tih_rna_sample_00434_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3107.677971
EM: Round [1] log likelihood: -3107.629357
EM: Round [2] log likelihood: -3107.629285
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.TXVRmTkwqu/tih_rna_sample_00434_B23WHTKLT4_2_1.fastp.fastq.gz: 295891828
Warning - not locating file: /tmp/nxf.TXVRmTkwqu/tih_rna_sample_00434_B23WHTKLT4_2.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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]
ls: cannot access 'IGV_inputs': No such file or directory