Done.
-parsing GTF file: /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.vKgislKKwM/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.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-19e09e-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-19e09e-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
10:52:54 : INFO : Done.
-parsing GTF file: /tmp/nxf.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam

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[630000]   -done parsing /tmp/nxf.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'seq-similar region overlap' => 699,
          'per_id < 96' => 2777,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 90,
          'exons hit < 2' => 2,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 166,
          'low complexity anchor region' => 40,
          ' ** passed ** ' => 41525,
          'small anchor length' => 252,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
          'excessive soft clipping' => 3548,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 8
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[159000]   -fusion SPANNING read extraction for scaff: CX3CL1--RBPMS

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[29000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA8

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[21000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA9

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA10

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB7

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11

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[21000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA12

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[72000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC3

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC4

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC5

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[69000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[27000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[18000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 49863,
          'lacks exon overlap' => 1056
        };
EM: Starting log likelihood: -5374.922613
EM: Round [1] log likelihood: -5370.144139
EM: Round [2] log likelihood: -5366.183558
EM: Round [3] log likelihood: -5362.886135
EM: Round [4] log likelihood: -5360.129327
EM: Round [5] log likelihood: -5357.815275
EM: Round [6] log likelihood: -5355.865289
EM: Round [7] log likelihood: -5354.215730
EM: Round [8] log likelihood: -5352.814878
EM: Round [9] log likelihood: -5351.620531
EM: Round [10] log likelihood: -5350.598128
EM: Round [11] log likelihood: -5349.719285
EM: Round [12] log likelihood: -5348.960623
EM: Round [13] log likelihood: -5348.302844
EM: Round [14] log likelihood: -5347.729981
EM: Round [15] log likelihood: -5347.228798
EM: Round [16] log likelihood: -5346.788302
EM: Round [17] log likelihood: -5346.399343
EM: Round [18] log likelihood: -5346.054296
EM: Round [19] log likelihood: -5345.746790
EM: Round [20] log likelihood: -5345.471495
EM: Round [21] log likelihood: -5345.223940
EM: Round [22] log likelihood: -5345.000371
EM: Round [23] log likelihood: -5344.797624
EM: Round [24] log likelihood: -5344.613030
EM: Round [25] log likelihood: -5344.444329
EM: Round [26] log likelihood: -5344.289605
EM: Round [27] log likelihood: -5344.147225
EM: Round [28] log likelihood: -5344.015798
EM: Round [29] log likelihood: -5343.894130
EM: Round [30] log likelihood: -5343.781198
EM: Round [31] log likelihood: -5343.676116
EM: Round [32] log likelihood: -5343.578119
EM: Round [33] log likelihood: -5343.486542
EM: Round [34] log likelihood: -5343.400805
EM: Round [35] log likelihood: -5343.320397
EM: Round [36] log likelihood: -5343.244872
EM: Round [37] log likelihood: -5343.173833
EM: Round [38] log likelihood: -5343.106928
EM: Round [39] log likelihood: -5343.043844
EM: Round [40] log likelihood: -5342.984299
EM: Round [41] log likelihood: -5342.928041
EM: Round [42] log likelihood: -5342.874842
EM: Round [43] log likelihood: -5342.824495
EM: Round [44] log likelihood: -5342.776811
EM: Round [45] log likelihood: -5342.731619
EM: Round [46] log likelihood: -5342.688762
EM: Round [47] log likelihood: -5342.648095
EM: Round [48] log likelihood: -5342.609485
EM: Round [49] log likelihood: -5342.572808
EM: Round [50] log likelihood: -5342.537950
EM: Round [51] log likelihood: -5342.504806
EM: Round [52] log likelihood: -5342.473277
EM: Round [53] log likelihood: -5342.443270
EM: Round [54] log likelihood: -5342.414701
EM: Round [55] log likelihood: -5342.387489
EM: Round [56] log likelihood: -5342.361558
EM: Round [57] log likelihood: -5342.336839
EM: Round [58] log likelihood: -5342.313265
EM: Round [59] log likelihood: -5342.290774
EM: Round [60] log likelihood: -5342.269308
EM: Round [61] log likelihood: -5342.248811
EM: Round [62] log likelihood: -5342.229231
EM: Round [63] log likelihood: -5342.210521
EM: Round [64] log likelihood: -5342.192632
EM: Round [65] log likelihood: -5342.175523
EM: Round [66] log likelihood: -5342.159152
EM: Round [67] log likelihood: -5342.143480
EM: Round [68] log likelihood: -5342.128470
EM: Round [69] log likelihood: -5342.114089
EM: Round [70] log likelihood: -5342.100302
EM: Round [71] log likelihood: -5342.087079
EM: Round [72] log likelihood: -5342.074391
EM: Round [73] log likelihood: -5342.062210
EM: Round [74] log likelihood: -5342.050510
EM: Round [75] log likelihood: -5342.039266
EM: Round [76] log likelihood: -5342.028454
EM: Round [77] log likelihood: -5342.018052
EM: Round [78] log likelihood: -5342.008039
EM: Round [79] log likelihood: -5341.998395
EM: Round [80] log likelihood: -5341.989101
EM: Round [81] log likelihood: -5341.980140
EM: Round [82] log likelihood: -5341.971494
EM: Round [83] log likelihood: -5341.963147
EM: Round [84] log likelihood: -5341.955084
EM: Round [85] log likelihood: -5341.947290
EM: Round [86] log likelihood: -5341.939752
EM: Round [87] log likelihood: -5341.932458
EM: Round [88] log likelihood: -5341.925394
EM: Round [89] log likelihood: -5341.918549
EM: Round [90] log likelihood: -5341.911912
EM: Round [91] log likelihood: -5341.905473
EM: Round [92] log likelihood: -5341.899221
EM: Round [93] log likelihood: -5341.893148
EM: Round [94] log likelihood: -5341.887244
EM: Round [95] log likelihood: -5341.881502
EM: Round [96] log likelihood: -5341.875912
EM: Round [97] log likelihood: -5341.870468
EM: Round [98] log likelihood: -5341.865162
EM: Round [99] log likelihood: -5341.859988
EM: Round [100] log likelihood: -5341.854939
EM: Round [101] log likelihood: -5341.850009
EM: Round [102] log likelihood: -5341.845192
EM: Round [103] log likelihood: -5341.840483
EM: Round [104] log likelihood: -5341.835877
EM: Round [105] log likelihood: -5341.831368
EM: Round [106] log likelihood: -5341.826952
EM: Round [107] log likelihood: -5341.822625
EM: Round [108] log likelihood: -5341.818382
EM: Round [109] log likelihood: -5341.814219
EM: Round [110] log likelihood: -5341.810133
EM: Round [111] log likelihood: -5341.806120
EM: Round [112] log likelihood: -5341.802177
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[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_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.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_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.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3872.296876
EM: Round [1] log likelihood: -3872.296876
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 226554601
Warning - not locating file: /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.gmap_trinity_GG.fusions.gff3.bed
ls: cannot access 'IGV_inputs': No such file or directory