Done.
-parsing GTF file: /tmp/nxf.9Wp59bDXvy/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.9Wp59bDXvy/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.9Wp59bDXvy/aih-tih-sc-3270ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.9Wp59bDXvy/aih-tih-sc-3270ab-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.9Wp59bDXvy/fi_workdir/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.9Wp59bDXvy/fi_workdir/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-3270ab-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-3270ab-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
22:25:05 : INFO : Done.
-parsing GTF file: /tmp/nxf.9Wp59bDXvy/fi_workdir/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.9Wp59bDXvy/fi_workdir/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[1920000]   -done parsing /tmp/nxf.9Wp59bDXvy/fi_workdir/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 8 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 7,
          'low complexity anchor region' => 1,
          'excessive soft clipping' => 12740,
          'per_id < 96' => 10715,
          'seq-similar region overlap' => 27,
          'exons hit < 2' => 4,
          ' ** passed ** ' => 3610,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 242,
          'num genes matched < 2' => 20,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 3,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 33,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 52,
          'small anchor length' => 86,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 6
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.9Wp59bDXvy/fi_workdir/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[65000]   -fusion SPANNING read extraction for scaff: ABLIM1--WAPL

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[38000]   -fusion SPANNING read extraction for scaff: GSR--AC068672.1

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[38000]   -fusion SPANNING read extraction for scaff: GSR--AC090816.1

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[57000]   -fusion SPANNING read extraction for scaff: GSR--NRG1

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[38000]   -fusion SPANNING read extraction for scaff: GSR--NRG1-IT3

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

[1000]   
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[21000]   -fusion SPANNING read extraction for scaff: LRP12--ZFPM2

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[21000]   -fusion SPANNING read extraction for scaff: MACROD2--NRG1

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[64000]   -fusion SPANNING read extraction for scaff: MLKL--CHSY1

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[32000]   -fusion SPANNING read extraction for scaff: MLKL--SELENOS

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[4000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[6000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[5000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[4000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

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[6000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

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[4000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

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[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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

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[27000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[23000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[55000]   -fusion SPANNING read extraction for scaff: PRSS27--TPSB2

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[40000]   -fusion SPANNING read extraction for scaff: SEC24B--CDKL2

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[54000]   -fusion SPANNING read extraction for scaff: SRSF3--UHRF1BP1

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[85000]   
[86000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[449000]   
[450000]   -fusion SPANNING read extraction for scaff: TAF15--AP2B1

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[28000]   
[29000]   -fusion SPANNING read extraction for scaff: TLK2--AL669831.1

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[13000]   
[14000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

[1000]   
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[33000]   
[34000]   -fusion SPANNING read extraction for scaff: UHRF1BP1--EYS

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[529000]   
[530000]   -fusion SPANNING read extraction for scaff: ZNF318--DST

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[87000]   
[88000]   -fusion SPANNING read extraction for scaff: ZSWIM6--CFTR
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 9390,
          'seq similar region alignment' => 19197
        };
EM: Starting log likelihood: -2852.469988
EM: Round [1] log likelihood: -2852.388782
EM: Round [2] log likelihood: -2852.374235
EM: Round [3] log likelihood: -2852.360368
EM: Round [4] log likelihood: -2852.347129
EM: Round [5] log likelihood: -2852.334481
EM: Round [6] log likelihood: -2852.322392
EM: Round [7] log likelihood: -2852.310831
EM: Round [8] log likelihood: -2852.299768
EM: Round [9] log likelihood: -2852.289178
EM: Round [10] log likelihood: -2852.279034
EM: Round [11] log likelihood: -2852.269315
EM: Round [12] log likelihood: -2852.259999
EM: Round [13] log likelihood: -2852.251065
EM: Round [14] log likelihood: -2852.242494
EM: Round [15] log likelihood: -2852.234270
EM: Round [16] log likelihood: -2852.226374
EM: Round [17] log likelihood: -2852.218792
EM: Round [18] log likelihood: -2852.211509
EM: Round [19] log likelihood: -2852.204511
EM: Round [20] log likelihood: -2852.197786
EM: Round [21] log likelihood: -2852.191319
EM: Round [22] log likelihood: -2852.185102
EM: Round [23] log likelihood: -2852.179121
EM: Round [24] log likelihood: -2852.173367
EM: Round [25] log likelihood: -2852.167830
EM: Round [26] log likelihood: -2852.162500
EM: Round [27] log likelihood: -2852.157370
EM: Round [28] log likelihood: -2852.152430
EM: Round [29] log likelihood: -2852.147672
EM: Round [30] log likelihood: -2852.143089
EM: Round [31] log likelihood: -2852.138674
EM: Round [32] log likelihood: -2852.134420
EM: Round [33] log likelihood: -2852.130321
EM: Round [34] log likelihood: -2852.126369
EM: Round [35] log likelihood: -2852.122560
EM: Round [36] log likelihood: -2852.118887
EM: Round [37] log likelihood: -2852.115346
EM: Round [38] log likelihood: -2852.111931
EM: Round [39] log likelihood: -2852.108637
EM: Round [40] log likelihood: -2852.105459
EM: Round [41] log likelihood: -2852.102394
EM: Round [42] log likelihood: -2852.099437
EM: Round [43] log likelihood: -2852.096583
EM: Round [44] log likelihood: -2852.093829
EM: Round [45] log likelihood: -2852.091171
EM: Round [46] log likelihood: -2852.088605
EM: Round [47] log likelihood: -2852.086129
EM: Round [48] log likelihood: -2852.083738
EM: Round [49] log likelihood: -2852.081430
EM: Round [50] log likelihood: -2852.079201
EM: Round [51] log likelihood: -2852.077049
EM: Round [52] log likelihood: -2852.074971
EM: Round [53] log likelihood: -2852.072963
EM: Round [54] log likelihood: -2852.071025
EM: Round [55] log likelihood: -2852.069152
EM: Round [56] log likelihood: -2852.067344
EM: Round [57] log likelihood: -2852.065596
EM: Round [58] log likelihood: -2852.063908
EM: Round [59] log likelihood: -2852.062278
EM: Round [60] log likelihood: -2852.060702
EM: Round [61] log likelihood: -2852.059179
EM: Round [62] log likelihood: -2852.057708
EM: Round [63] log likelihood: -2852.056286
EM: Round [64] log likelihood: -2852.054913
EM: Round [65] log likelihood: -2852.053585
EM: Round [66] log likelihood: -2852.052301
EM: Round [67] log likelihood: -2852.051061
EM: Round [68] log likelihood: -2852.049862
EM: Round [69] log likelihood: -2852.048703
EM: Round [70] log likelihood: -2852.047583
EM: Round [71] log likelihood: -2852.046501
EM: Round [72] log likelihood: -2852.045454
EM: Round [73] log likelihood: -2852.044442
EM: Round [74] log likelihood: -2852.043463
EM: Round [75] log likelihood: -2852.042518
EM: Round [76] log likelihood: -2852.041603
EM: Round [77] log likelihood: -2852.040719
EM: Round [78] log likelihood: -2852.039864
EM: Round [79] log likelihood: -2852.039037
EM: Round [80] log likelihood: -2852.038238
EM: Round [81] log likelihood: -2852.037465
EM: Round [82] log likelihood: -2852.036717
EM: Round [83] log likelihood: -2852.035995
EM: Round [84] log likelihood: -2852.035296
EM: Round [85] log likelihood: -2852.034620
EM: Round [86] log likelihood: -2852.033966
EM: Round [87] log likelihood: -2852.033334
EM: Round [88] log likelihood: -2852.032722
EM: Round [89] log likelihood: -2852.032131
EM: Round [90] log likelihood: -2852.031559
EM: Round [91] log likelihood: -2852.031005
EM: Round [92] log likelihood: -2852.030470
EM: Round [93] log likelihood: -2852.029953
EM: Round [94] log likelihood: -2852.029452
EM: Round [95] log likelihood: -2852.028968
EM: Round [96] log likelihood: -2852.028500
EM: Round [97] log likelihood: -2852.028047
EM: Round [98] log likelihood: -2852.027608
EM: Round [99] log likelihood: -2852.027184
EM: Round [100] log likelihood: -2852.026774
EM: Round [101] log likelihood: -2852.026378
EM: Round [102] log likelihood: -2852.025994
EM: Round [103] log likelihood: -2852.025623
EM: Round [104] log likelihood: -2852.025263
EM: Round [105] log likelihood: -2852.024916
EM: Round [106] log likelihood: -2852.024580
EM: Round [107] log likelihood: -2852.024255
EM: Round [108] log likelihood: -2852.023940
EM: Round [109] log likelihood: -2852.023636
EM: Round [110] log likelihood: -2852.023342
EM: Round [111] log likelihood: -2852.023057
EM: Round [112] log likelihood: -2852.022781
EM: Round [113] log likelihood: -2852.022515
EM: Round [114] log likelihood: -2852.022257
EM: Round [115] log likelihood: -2852.022007
EM: Round [116] log likelihood: -2852.021766
EM: Round [117] log likelihood: -2852.021532
EM: Round [118] log likelihood: -2852.021306
EM: Round [119] log likelihood: -2852.021087
EM: Round [120] log likelihood: -2852.020876
EM: Round [121] log likelihood: -2852.020671
EM: Round [122] log likelihood: -2852.020473
EM: Round [123] log likelihood: -2852.020281
EM: Round [124] log likelihood: -2852.020096
EM: Round [125] log likelihood: -2852.019917
EM: Round [126] log likelihood: -2852.019743
EM: Round [127] log likelihood: -2852.019575
EM: Round [128] log likelihood: -2852.019412
EM: Round [129] log likelihood: -2852.019255
EM: Round [130] log likelihood: -2852.019103
EM: Round [131] log likelihood: -2852.018956
EM: Round [132] log likelihood: -2852.018813
EM: Round [133] log likelihood: -2852.018676
EM: Round [134] log likelihood: -2852.018542
EM: Round [135] log likelihood: -2852.018413
EM: Round [136] log likelihood: -2852.018288
EM: Round [137] log likelihood: -2852.018167
EM: Round [138] log likelihood: -2852.018051
EM: Round [139] log likelihood: -2852.017937
EM: Round [140] log likelihood: -2852.017828
EM: Round [141] log likelihood: -2852.017722
EM: Round [142] log likelihood: -2852.017620
EM: Round [143] log likelihood: -2852.017520
EM: Stopping iterations at round 143 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.9Wp59bDXvy/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.9Wp59bDXvy/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.9Wp59bDXvy/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.9Wp59bDXvy/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.9Wp59bDXvy/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.9Wp59bDXvy/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.9Wp59bDXvy/aih-tih-sc-3270ab-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.9Wp59bDXvy/fi_workdir/aih-tih-sc-3270ab-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.9Wp59bDXvy/fi_workdir/aih-tih-sc-3270ab-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.9Wp59bDXvy/fi_workdir/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.9Wp59bDXvy/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.9Wp59bDXvy/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2491.263214
EM: Round [1] log likelihood: -2491.197252
EM: Round [2] log likelihood: -2491.197240
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.9Wp59bDXvy/aih-tih-sc-3270ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296063924
Warning - not locating file: /tmp/nxf.9Wp59bDXvy/aih-tih-sc-3270ab-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000228327.3]
ls: cannot access 'IGV_inputs': No such file or directory