Done.
-parsing GTF file: /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.YGSl4tcF7M/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.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
10:25:23 : INFO : Done.
-parsing GTF file: /tmp/nxf.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[1170000]   -done parsing /tmp/nxf.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 53,
          'num genes matched < 2' => 12,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 20,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8,
          'small anchor length' => 1,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 21,
          'seq-similar region overlap' => 98,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 15,
          'excessive soft clipping' => 7695,
          'low complexity anchor region' => 2,
          'per_id < 96' => 4603,
          ' ** passed ** ' => 3210
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[6000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[83000]   -fusion SPANNING read extraction for scaff: CPSF7--PIEZO2

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[24000]   -fusion SPANNING read extraction for scaff: CPSF7--AP005139.1

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[168000]   -fusion SPANNING read extraction for scaff: DDX5--SMURF2

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[46000]   -fusion SPANNING read extraction for scaff: DHX38--WWOX

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[59000]   -fusion SPANNING read extraction for scaff: ERC1--RASSF7

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[58000]   -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1

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[61000]   -fusion SPANNING read extraction for scaff: KIAA1958--NTRK2

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[74000]   -fusion SPANNING read extraction for scaff: LMNTD2--ERC1

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[9000]   -fusion SPANNING read extraction for scaff: NAE1--CAPNS2

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[20000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[20000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[23000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[76000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[26000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[29000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

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

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[19000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[30000]   -fusion SPANNING read extraction for scaff: TXNL4B--CTCF

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[58000]   -fusion SPANNING read extraction for scaff: TXNL4B--CARMIL2

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[73000]   -fusion SPANNING read extraction for scaff: WWP2--MPHOSPH6

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[203000]   -fusion SPANNING read extraction for scaff: ZFHX3--CNTNAP4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 47046,
          'seq similar region alignment' => 19027
        };
EM: Starting log likelihood: -3012.042627
EM: Round [1] log likelihood: -3011.682253
EM: Round [2] log likelihood: -3011.396539
EM: Round [3] log likelihood: -3011.133574
EM: Round [4] log likelihood: -3010.890806
EM: Round [5] log likelihood: -3010.666324
EM: Round [6] log likelihood: -3010.458448
EM: Round [7] log likelihood: -3010.265695
EM: Round [8] log likelihood: -3010.086749
EM: Round [9] log likelihood: -3009.920437
EM: Round [10] log likelihood: -3009.765713
EM: Round [11] log likelihood: -3009.621635
EM: Round [12] log likelihood: -3009.487357
EM: Round [13] log likelihood: -3009.362113
EM: Round [14] log likelihood: -3009.245211
EM: Round [15] log likelihood: -3009.136023
EM: Round [16] log likelihood: -3009.033976
EM: Round [17] log likelihood: -3008.938549
EM: Round [18] log likelihood: -3008.849264
EM: Round [19] log likelihood: -3008.765686
EM: Round [20] log likelihood: -3008.687413
EM: Round [21] log likelihood: -3008.614078
EM: Round [22] log likelihood: -3008.545341
EM: Round [23] log likelihood: -3008.480891
EM: Round [24] log likelihood: -3008.420439
EM: Round [25] log likelihood: -3008.363719
EM: Round [26] log likelihood: -3008.310485
EM: Round [27] log likelihood: -3008.260508
EM: Round [28] log likelihood: -3008.213576
EM: Round [29] log likelihood: -3008.169494
EM: Round [30] log likelihood: -3008.128079
EM: Round [31] log likelihood: -3008.089161
EM: Round [32] log likelihood: -3008.052582
EM: Round [33] log likelihood: -3008.018195
EM: Round [34] log likelihood: -3007.985863
EM: Round [35] log likelihood: -3007.955458
EM: Round [36] log likelihood: -3007.926861
EM: Round [37] log likelihood: -3007.899960
EM: Round [38] log likelihood: -3007.874652
EM: Round [39] log likelihood: -3007.850838
EM: Round [40] log likelihood: -3007.828429
EM: Round [41] log likelihood: -3007.807338
EM: Round [42] log likelihood: -3007.787487
EM: Round [43] log likelihood: -3007.768800
EM: Round [44] log likelihood: -3007.751207
EM: Round [45] log likelihood: -3007.734643
EM: Round [46] log likelihood: -3007.719047
EM: Round [47] log likelihood: -3007.704360
EM: Round [48] log likelihood: -3007.690529
EM: Round [49] log likelihood: -3007.677503
EM: Round [50] log likelihood: -3007.665234
EM: Round [51] log likelihood: -3007.653678
EM: Round [52] log likelihood: -3007.642792
EM: Round [53] log likelihood: -3007.632538
EM: Round [54] log likelihood: -3007.622877
EM: Round [55] log likelihood: -3007.613776
EM: Round [56] log likelihood: -3007.605201
EM: Round [57] log likelihood: -3007.597121
EM: Round [58] log likelihood: -3007.589509
EM: Round [59] log likelihood: -3007.582335
EM: Round [60] log likelihood: -3007.575576
EM: Round [61] log likelihood: -3007.569206
EM: Round [62] log likelihood: -3007.563203
EM: Round [63] log likelihood: -3007.557546
EM: Round [64] log likelihood: -3007.552215
EM: Round [65] log likelihood: -3007.547191
EM: Round [66] log likelihood: -3007.542455
EM: Round [67] log likelihood: -3007.537992
EM: Round [68] log likelihood: -3007.533786
EM: Round [69] log likelihood: -3007.529821
EM: Round [70] log likelihood: -3007.526084
EM: Round [71] log likelihood: -3007.522562
EM: Round [72] log likelihood: -3007.519241
EM: Round [73] log likelihood: -3007.516112
EM: Round [74] log likelihood: -3007.513162
EM: Round [75] log likelihood: -3007.510381
EM: Round [76] log likelihood: -3007.507760
EM: Round [77] log likelihood: -3007.505289
EM: Round [78] log likelihood: -3007.502959
EM: Round [79] log likelihood: -3007.500763
EM: Round [80] log likelihood: -3007.498693
EM: Round [81] log likelihood: -3007.496742
EM: Round [82] log likelihood: -3007.494902
EM: Round [83] log likelihood: -3007.493168
EM: Round [84] log likelihood: -3007.491533
EM: Round [85] log likelihood: -3007.489992
EM: Round [86] log likelihood: -3007.488539
EM: Round [87] log likelihood: -3007.487169
EM: Round [88] log likelihood: -3007.485878
EM: Round [89] log likelihood: -3007.484661
EM: Round [90] log likelihood: -3007.483513
EM: Round [91] log likelihood: -3007.482431
EM: Round [92] log likelihood: -3007.481410
EM: Round [93] log likelihood: -3007.480449
EM: Round [94] log likelihood: -3007.479542
EM: Round [95] log likelihood: -3007.478687
EM: Round [96] log likelihood: -3007.477881
EM: Round [97] log likelihood: -3007.477121
EM: Round [98] log likelihood: -3007.476405
EM: Round [99] log likelihood: -3007.475729
EM: Round [100] log likelihood: -3007.475093
EM: Round [101] log likelihood: -3007.474492
EM: Round [102] log likelihood: -3007.473926
EM: Round [103] log likelihood: -3007.473392
EM: Round [104] log likelihood: -3007.472889
EM: Round [105] log likelihood: -3007.472415
EM: Round [106] log likelihood: -3007.471968
EM: Round [107] log likelihood: -3007.471546
EM: Round [108] log likelihood: -3007.471148
EM: Round [109] log likelihood: -3007.470774
EM: Round [110] log likelihood: -3007.470420
EM: Round [111] log likelihood: -3007.470087
EM: Round [112] log likelihood: -3007.469773
EM: Round [113] log likelihood: -3007.469477
EM: Round [114] log likelihood: -3007.469197
EM: Round [115] log likelihood: -3007.468934
EM: Round [116] log likelihood: -3007.468686
EM: Round [117] log likelihood: -3007.468452
EM: Round [118] log likelihood: -3007.468231
EM: Round [119] log likelihood: -3007.468023
EM: Round [120] log likelihood: -3007.467827
EM: Round [121] log likelihood: -3007.467642
EM: Round [122] log likelihood: -3007.467467
EM: Round [123] log likelihood: -3007.467303
EM: Round [124] log likelihood: -3007.467148
EM: Round [125] log likelihood: -3007.467002
EM: Round [126] log likelihood: -3007.466864
EM: Round [127] log likelihood: -3007.466734
EM: Round [128] log likelihood: -3007.466611
EM: Round [129] log likelihood: -3007.466496
EM: Round [130] log likelihood: -3007.466387
EM: Round [131] log likelihood: -3007.466284
EM: Round [132] log likelihood: -3007.466188
EM: Stopping iterations at round 132 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-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.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-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.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-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.YGSl4tcF7M/fi_workdir/aih-tih-sc-45523c-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2836.006779
EM: Round [1] log likelihood: -2836.006748
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 241112810
Warning - not locating file: /tmp/nxf.YGSl4tcF7M/aih-tih-sc-45523c-R1_A23YTGFLT4_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 [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 [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