Done.
-parsing GTF file: /tmp/nxf.yGW5ZCT6lT/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.yGW5ZCT6lT/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.yGW5ZCT6lT/aih-tih-sc-2798bb-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.yGW5ZCT6lT/aih-tih-sc-2798bb-R1_A23WJ53LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.yGW5ZCT6lT/fi_workdir/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.yGW5ZCT6lT/fi_workdir/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-2798bb-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-2798bb-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
11:15:48 : INFO : Done.
-parsing GTF file: /tmp/nxf.yGW5ZCT6lT/fi_workdir/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.yGW5ZCT6lT/fi_workdir/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam

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[780000]   -done parsing /tmp/nxf.yGW5ZCT6lT/fi_workdir/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 72,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 51,
          'low complexity anchor region' => 2,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 120,
          'num genes matched < 2' => 11,
          'per_id < 96' => 2765,
          'excessive soft clipping' => 5269,
          ' ** passed ** ' => 1599,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2,
          'seq-similar region overlap' => 55
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.yGW5ZCT6lT/fi_workdir/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[192000]   
[193000]   -fusion SPANNING read extraction for scaff: ATRX--AC074035.1

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[161000]   
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[163000]   
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[186000]   
[187000]   
[188000]   
[189000]   
[190000]   
[191000]   
[192000]   
[193000]   -fusion SPANNING read extraction for scaff: ATRX--MTND6P12

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: FAM86B1--ST18

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: FAM86B1--ALKAL1

[1000]   
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[35000]   
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[38000]   
[39000]   
[40000]   
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[42000]   
[43000]   -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1

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

[1000]   
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[3000]   
[4000]   
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[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
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[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
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[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1

[1000]   
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[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13

[1000]   
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[7000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2

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[150000]   
[151000]   -fusion SPANNING read extraction for scaff: RPS5--ZNF71

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[94000]   
[95000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

[1000]   
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[6000]   
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[8000]   
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[10000]   
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[27000]   
[28000]   -fusion SPANNING read extraction for scaff: TLK2--LINC01347

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[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
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[15000]   
[16000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 5653,
          'lacks exon overlap' => 16798
        };
EM: Starting log likelihood: -1665.681170
EM: Round [1] log likelihood: -1665.409400
EM: Round [2] log likelihood: -1665.332634
EM: Round [3] log likelihood: -1665.262463
EM: Round [4] log likelihood: -1665.198135
EM: Round [5] log likelihood: -1665.139055
EM: Round [6] log likelihood: -1665.084705
EM: Round [7] log likelihood: -1665.034630
EM: Round [8] log likelihood: -1664.988433
EM: Round [9] log likelihood: -1664.945759
EM: Round [10] log likelihood: -1664.906297
EM: Round [11] log likelihood: -1664.869766
EM: Round [12] log likelihood: -1664.835918
EM: Round [13] log likelihood: -1664.804529
EM: Round [14] log likelihood: -1664.775396
EM: Round [15] log likelihood: -1664.748340
EM: Round [16] log likelihood: -1664.723193
EM: Round [17] log likelihood: -1664.699809
EM: Round [18] log likelihood: -1664.678050
EM: Round [19] log likelihood: -1664.657794
EM: Round [20] log likelihood: -1664.638927
EM: Round [21] log likelihood: -1664.621346
EM: Round [22] log likelihood: -1664.604957
EM: Round [23] log likelihood: -1664.589673
EM: Round [24] log likelihood: -1664.575415
EM: Round [25] log likelihood: -1664.562110
EM: Round [26] log likelihood: -1664.549689
EM: Round [27] log likelihood: -1664.538091
EM: Round [28] log likelihood: -1664.527259
EM: Round [29] log likelihood: -1664.517139
EM: Round [30] log likelihood: -1664.507682
EM: Round [31] log likelihood: -1664.498843
EM: Round [32] log likelihood: -1664.490581
EM: Round [33] log likelihood: -1664.482855
EM: Round [34] log likelihood: -1664.475631
EM: Round [35] log likelihood: -1664.468873
EM: Round [36] log likelihood: -1664.462552
EM: Round [37] log likelihood: -1664.456638
EM: Round [38] log likelihood: -1664.451104
EM: Round [39] log likelihood: -1664.445925
EM: Round [40] log likelihood: -1664.441078
EM: Round [41] log likelihood: -1664.436541
EM: Round [42] log likelihood: -1664.432294
EM: Round [43] log likelihood: -1664.428318
EM: Round [44] log likelihood: -1664.424595
EM: Round [45] log likelihood: -1664.421109
EM: Round [46] log likelihood: -1664.417844
EM: Round [47] log likelihood: -1664.414787
EM: Round [48] log likelihood: -1664.411923
EM: Round [49] log likelihood: -1664.409241
EM: Round [50] log likelihood: -1664.406729
EM: Round [51] log likelihood: -1664.404376
EM: Round [52] log likelihood: -1664.402172
EM: Round [53] log likelihood: -1664.400106
EM: Round [54] log likelihood: -1664.398171
EM: Round [55] log likelihood: -1664.396359
EM: Round [56] log likelihood: -1664.394660
EM: Round [57] log likelihood: -1664.393069
EM: Round [58] log likelihood: -1664.391577
EM: Round [59] log likelihood: -1664.390180
EM: Round [60] log likelihood: -1664.388871
EM: Round [61] log likelihood: -1664.387644
EM: Round [62] log likelihood: -1664.386494
EM: Round [63] log likelihood: -1664.385416
EM: Round [64] log likelihood: -1664.384406
EM: Round [65] log likelihood: -1664.383460
EM: Round [66] log likelihood: -1664.382572
EM: Round [67] log likelihood: -1664.381741
EM: Round [68] log likelihood: -1664.380962
EM: Round [69] log likelihood: -1664.380231
EM: Round [70] log likelihood: -1664.379547
EM: Round [71] log likelihood: -1664.378905
EM: Round [72] log likelihood: -1664.378304
EM: Round [73] log likelihood: -1664.377740
EM: Round [74] log likelihood: -1664.377212
EM: Round [75] log likelihood: -1664.376717
EM: Round [76] log likelihood: -1664.376252
EM: Round [77] log likelihood: -1664.375817
EM: Round [78] log likelihood: -1664.375409
EM: Round [79] log likelihood: -1664.375027
EM: Round [80] log likelihood: -1664.374668
EM: Round [81] log likelihood: -1664.374332
EM: Round [82] log likelihood: -1664.374018
EM: Round [83] log likelihood: -1664.373722
EM: Round [84] log likelihood: -1664.373446
EM: Round [85] log likelihood: -1664.373186
EM: Round [86] log likelihood: -1664.372943
EM: Round [87] log likelihood: -1664.372715
EM: Round [88] log likelihood: -1664.372501
EM: Round [89] log likelihood: -1664.372301
EM: Round [90] log likelihood: -1664.372113
EM: Round [91] log likelihood: -1664.371937
EM: Round [92] log likelihood: -1664.371772
EM: Round [93] log likelihood: -1664.371617
EM: Round [94] log likelihood: -1664.371472
EM: Round [95] log likelihood: -1664.371336
EM: Round [96] log likelihood: -1664.371209
EM: Round [97] log likelihood: -1664.371089
EM: Round [98] log likelihood: -1664.370977
EM: Round [99] log likelihood: -1664.370872
EM: Round [100] log likelihood: -1664.370774
EM: Stopping iterations at round 100 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.yGW5ZCT6lT/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.yGW5ZCT6lT/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.yGW5ZCT6lT/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.yGW5ZCT6lT/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.yGW5ZCT6lT/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.yGW5ZCT6lT/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.yGW5ZCT6lT/aih-tih-sc-2798bb-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.yGW5ZCT6lT/fi_workdir/aih-tih-sc-2798bb-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.yGW5ZCT6lT/fi_workdir/aih-tih-sc-2798bb-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.yGW5ZCT6lT/fi_workdir/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.yGW5ZCT6lT/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.yGW5ZCT6lT/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1305.990832
EM: Round [1] log likelihood: -1305.986341
EM: Round [2] log likelihood: -1305.986336
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.yGW5ZCT6lT/aih-tih-sc-2798bb-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 296427168
Warning - not locating file: /tmp/nxf.yGW5ZCT6lT/aih-tih-sc-2798bb-R1_A23WJ53LT4_1.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 [ENSG00000214837.8]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
ls: cannot access 'IGV_inputs': No such file or directory