Done.
-parsing GTF file: /tmp/nxf.yOtAvc2Emi/aih-tih-sc-13d441-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.yOtAvc2Emi/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.yOtAvc2Emi/aih-tih-sc-13d441-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.yOtAvc2Emi/aih-tih-sc-13d441-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.yOtAvc2Emi/fi_workdir/aih-tih-sc-13d441-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.yOtAvc2Emi/fi_workdir/aih-tih-sc-13d441-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-13d441-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-13d441-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
21:56:00 : INFO : Done.
-parsing GTF file: /tmp/nxf.yOtAvc2Emi/fi_workdir/aih-tih-sc-13d441-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.yOtAvc2Emi/fi_workdir/aih-tih-sc-13d441-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[720000]   -done parsing /tmp/nxf.yOtAvc2Emi/fi_workdir/aih-tih-sc-13d441-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 17,
          'seq-similar region overlap' => 143,
          'num genes matched < 2' => 21,
          'excessive soft clipping' => 3093,
          ' ** passed ** ' => 10362,
          'per_id < 96' => 2363,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2,
          'small anchor length' => 63,
          'low complexity anchor region' => 6,
          'exons hit < 2' => 5,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 36
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.yOtAvc2Emi/fi_workdir/aih-tih-sc-13d441-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[16000]   -fusion SPANNING read extraction for scaff: AC015712.1--FAM13C

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[22000]   -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B

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[3000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

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[13000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[13000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[13000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

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[9000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

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[27000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

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[65000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[9000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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

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[27000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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

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[65000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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

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[74000]   -fusion SPANNING read extraction for scaff: RBBP4--FAM13C

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[79000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[31000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[35000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 37033,
          'lacks exon overlap' => 4928
        };
EM: Starting log likelihood: -3058.769487
EM: Round [1] log likelihood: -3057.312958
EM: Round [2] log likelihood: -3056.851556
EM: Round [3] log likelihood: -3056.442342
EM: Round [4] log likelihood: -3056.077253
EM: Round [5] log likelihood: -3055.750910
EM: Round [6] log likelihood: -3055.458692
EM: Round [7] log likelihood: -3055.196609
EM: Round [8] log likelihood: -3054.961204
EM: Round [9] log likelihood: -3054.749467
EM: Round [10] log likelihood: -3054.558770
EM: Round [11] log likelihood: -3054.386812
EM: Round [12] log likelihood: -3054.231571
EM: Round [13] log likelihood: -3054.091267
EM: Round [14] log likelihood: -3053.964331
EM: Round [15] log likelihood: -3053.849375
EM: Round [16] log likelihood: -3053.745167
EM: Round [17] log likelihood: -3053.650617
EM: Round [18] log likelihood: -3053.564754
EM: Round [19] log likelihood: -3053.486712
EM: Round [20] log likelihood: -3053.415723
EM: Round [21] log likelihood: -3053.351097
EM: Round [22] log likelihood: -3053.292219
EM: Round [23] log likelihood: -3053.238538
EM: Round [24] log likelihood: -3053.189561
EM: Round [25] log likelihood: -3053.144844
EM: Round [26] log likelihood: -3053.103990
EM: Round [27] log likelihood: -3053.066641
EM: Round [28] log likelihood: -3053.032475
EM: Round [29] log likelihood: -3053.001201
EM: Round [30] log likelihood: -3052.972558
EM: Round [31] log likelihood: -3052.946310
EM: Round [32] log likelihood: -3052.922242
EM: Round [33] log likelihood: -3052.900163
EM: Round [34] log likelihood: -3052.879898
EM: Round [35] log likelihood: -3052.861287
EM: Round [36] log likelihood: -3052.844189
EM: Round [37] log likelihood: -3052.828472
EM: Round [38] log likelihood: -3052.814019
EM: Round [39] log likelihood: -3052.800722
EM: Round [40] log likelihood: -3052.788484
EM: Round [41] log likelihood: -3052.777215
EM: Round [42] log likelihood: -3052.766836
EM: Round [43] log likelihood: -3052.757271
EM: Round [44] log likelihood: -3052.748455
EM: Round [45] log likelihood: -3052.740326
EM: Round [46] log likelihood: -3052.732827
EM: Round [47] log likelihood: -3052.725907
EM: Round [48] log likelihood: -3052.719521
EM: Round [49] log likelihood: -3052.713625
EM: Round [50] log likelihood: -3052.708179
EM: Round [51] log likelihood: -3052.703149
EM: Round [52] log likelihood: -3052.698500
EM: Round [53] log likelihood: -3052.694204
EM: Round [54] log likelihood: -3052.690232
EM: Round [55] log likelihood: -3052.686560
EM: Round [56] log likelihood: -3052.683163
EM: Round [57] log likelihood: -3052.680020
EM: Round [58] log likelihood: -3052.677113
EM: Round [59] log likelihood: -3052.674422
EM: Round [60] log likelihood: -3052.671931
EM: Round [61] log likelihood: -3052.669625
EM: Round [62] log likelihood: -3052.667490
EM: Round [63] log likelihood: -3052.665513
EM: Round [64] log likelihood: -3052.663681
EM: Round [65] log likelihood: -3052.661984
EM: Round [66] log likelihood: -3052.660412
EM: Round [67] log likelihood: -3052.658956
EM: Round [68] log likelihood: -3052.657606
EM: Round [69] log likelihood: -3052.656354
EM: Round [70] log likelihood: -3052.655194
EM: Round [71] log likelihood: -3052.654119
EM: Round [72] log likelihood: -3052.653122
EM: Round [73] log likelihood: -3052.652197
EM: Round [74] log likelihood: -3052.651340
EM: Round [75] log likelihood: -3052.650545
EM: Round [76] log likelihood: -3052.649807
EM: Round [77] log likelihood: -3052.649123
EM: Round [78] log likelihood: -3052.648488
EM: Round [79] log likelihood: -3052.647899
EM: Round [80] log likelihood: -3052.647353
EM: Round [81] log likelihood: -3052.646846
EM: Round [82] log likelihood: -3052.646375
EM: Round [83] log likelihood: -3052.645939
EM: Round [84] log likelihood: -3052.645533
EM: Round [85] log likelihood: -3052.645157
EM: Round [86] log likelihood: -3052.644808
EM: Round [87] log likelihood: -3052.644484
EM: Round [88] log likelihood: -3052.644183
EM: Round [89] log likelihood: -3052.643904
EM: Round [90] log likelihood: -3052.643645
EM: Round [91] log likelihood: -3052.643404
EM: Round [92] log likelihood: -3052.643181
EM: Round [93] log likelihood: -3052.642973
EM: Round [94] log likelihood: -3052.642781
EM: Round [95] log likelihood: -3052.642602
EM: Round [96] log likelihood: -3052.642436
EM: Round [97] log likelihood: -3052.642281
EM: Round [98] log likelihood: -3052.642138
EM: Round [99] log likelihood: -3052.642005
EM: Round [100] log likelihood: -3052.641882
EM: Round [101] log likelihood: -3052.641767
EM: Round [102] log likelihood: -3052.641660
EM: Round [103] log likelihood: -3052.641561
EM: Stopping iterations at round 103 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.yOtAvc2Emi/aih-tih-sc-13d441-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.yOtAvc2Emi/aih-tih-sc-13d441-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.yOtAvc2Emi/aih-tih-sc-13d441-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.yOtAvc2Emi/aih-tih-sc-13d441-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.yOtAvc2Emi/aih-tih-sc-13d441-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.yOtAvc2Emi/aih-tih-sc-13d441-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.yOtAvc2Emi/aih-tih-sc-13d441-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.yOtAvc2Emi/fi_workdir/aih-tih-sc-13d441-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.yOtAvc2Emi/fi_workdir/aih-tih-sc-13d441-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.yOtAvc2Emi/fi_workdir/aih-tih-sc-13d441-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.yOtAvc2Emi/aih-tih-sc-13d441-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.yOtAvc2Emi/aih-tih-sc-13d441-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2832.216430
EM: Round [1] log likelihood: -2832.085570
EM: Round [2] log likelihood: -2832.085559
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.yOtAvc2Emi/aih-tih-sc-13d441-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 257719664
Warning - not locating file: /tmp/nxf.yOtAvc2Emi/aih-tih-sc-13d441-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000232386.9]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
ls: cannot access 'IGV_inputs': No such file or directory