Done.
-parsing GTF file: /tmp/nxf.7hzIZZLTPS/aih-tih-sc-13d441-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.7hzIZZLTPS/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.7hzIZZLTPS/aih-tih-sc-13d441-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.7hzIZZLTPS/aih-tih-sc-13d441-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.7hzIZZLTPS/fi_workdir/aih-tih-sc-13d441-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.7hzIZZLTPS/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
11:13:03 : INFO : Done.
-parsing GTF file: /tmp/nxf.7hzIZZLTPS/fi_workdir/aih-tih-sc-13d441-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.7hzIZZLTPS/fi_workdir/aih-tih-sc-13d441-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[740000]   -done parsing /tmp/nxf.7hzIZZLTPS/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 ' => 45,
          'excessive soft clipping' => 3328,
          'low complexity anchor region' => 6,
          'exons hit < 2' => 5,
          ' ** passed ** ' => 10576,
          'num genes matched < 2' => 21,
          'small anchor length' => 63,
          'seq-similar region overlap' => 143,
          'per_id < 96' => 2461,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 36
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.7hzIZZLTPS/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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[7000]   -fusion SPANNING read extraction for scaff: BMS1P7--AGAP13P

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

[1000]   
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[3000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

[1000]   
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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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[73000]   
[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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[6000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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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' => 5247
        };
EM: Starting log likelihood: -3468.332451
EM: Round [1] log likelihood: -3466.855701
EM: Round [2] log likelihood: -3466.394156
EM: Round [3] log likelihood: -3465.984941
EM: Round [4] log likelihood: -3465.619852
EM: Round [5] log likelihood: -3465.293509
EM: Round [6] log likelihood: -3465.001290
EM: Round [7] log likelihood: -3464.739208
EM: Round [8] log likelihood: -3464.503803
EM: Round [9] log likelihood: -3464.292066
EM: Round [10] log likelihood: -3464.101369
EM: Round [11] log likelihood: -3463.929411
EM: Round [12] log likelihood: -3463.774169
EM: Round [13] log likelihood: -3463.633866
EM: Round [14] log likelihood: -3463.506930
EM: Round [15] log likelihood: -3463.391974
EM: Round [16] log likelihood: -3463.287766
EM: Round [17] log likelihood: -3463.193216
EM: Round [18] log likelihood: -3463.107352
EM: Round [19] log likelihood: -3463.029311
EM: Round [20] log likelihood: -3462.958321
EM: Round [21] log likelihood: -3462.893695
EM: Round [22] log likelihood: -3462.834817
EM: Round [23] log likelihood: -3462.781137
EM: Round [24] log likelihood: -3462.732159
EM: Round [25] log likelihood: -3462.687443
EM: Round [26] log likelihood: -3462.646589
EM: Round [27] log likelihood: -3462.609240
EM: Round [28] log likelihood: -3462.575074
EM: Round [29] log likelihood: -3462.543800
EM: Round [30] log likelihood: -3462.515157
EM: Round [31] log likelihood: -3462.488908
EM: Round [32] log likelihood: -3462.464841
EM: Round [33] log likelihood: -3462.442762
EM: Round [34] log likelihood: -3462.422496
EM: Round [35] log likelihood: -3462.403886
EM: Round [36] log likelihood: -3462.386788
EM: Round [37] log likelihood: -3462.371071
EM: Round [38] log likelihood: -3462.356618
EM: Round [39] log likelihood: -3462.343321
EM: Round [40] log likelihood: -3462.331082
EM: Round [41] log likelihood: -3462.319814
EM: Round [42] log likelihood: -3462.309434
EM: Round [43] log likelihood: -3462.299870
EM: Round [44] log likelihood: -3462.291054
EM: Round [45] log likelihood: -3462.282924
EM: Round [46] log likelihood: -3462.275425
EM: Round [47] log likelihood: -3462.268506
EM: Round [48] log likelihood: -3462.262120
EM: Round [49] log likelihood: -3462.256223
EM: Round [50] log likelihood: -3462.250778
EM: Round [51] log likelihood: -3462.245747
EM: Round [52] log likelihood: -3462.241099
EM: Round [53] log likelihood: -3462.236803
EM: Round [54] log likelihood: -3462.232831
EM: Round [55] log likelihood: -3462.229158
EM: Round [56] log likelihood: -3462.225761
EM: Round [57] log likelihood: -3462.222619
EM: Round [58] log likelihood: -3462.219711
EM: Round [59] log likelihood: -3462.217021
EM: Round [60] log likelihood: -3462.214530
EM: Round [61] log likelihood: -3462.212224
EM: Round [62] log likelihood: -3462.210089
EM: Round [63] log likelihood: -3462.208111
EM: Round [64] log likelihood: -3462.206280
EM: Round [65] log likelihood: -3462.204583
EM: Round [66] log likelihood: -3462.203011
EM: Round [67] log likelihood: -3462.201554
EM: Round [68] log likelihood: -3462.200204
EM: Round [69] log likelihood: -3462.198953
EM: Round [70] log likelihood: -3462.197793
EM: Round [71] log likelihood: -3462.196718
EM: Round [72] log likelihood: -3462.195721
EM: Round [73] log likelihood: -3462.194796
EM: Round [74] log likelihood: -3462.193939
EM: Round [75] log likelihood: -3462.193143
EM: Round [76] log likelihood: -3462.192406
EM: Round [77] log likelihood: -3462.191721
EM: Round [78] log likelihood: -3462.191087
EM: Round [79] log likelihood: -3462.190498
EM: Round [80] log likelihood: -3462.189951
EM: Round [81] log likelihood: -3462.189444
EM: Round [82] log likelihood: -3462.188974
EM: Round [83] log likelihood: -3462.188537
EM: Round [84] log likelihood: -3462.188132
EM: Round [85] log likelihood: -3462.187756
EM: Round [86] log likelihood: -3462.187407
EM: Round [87] log likelihood: -3462.187083
EM: Round [88] log likelihood: -3462.186782
EM: Round [89] log likelihood: -3462.186503
EM: Round [90] log likelihood: -3462.186244
EM: Round [91] log likelihood: -3462.186003
EM: Round [92] log likelihood: -3462.185779
EM: Round [93] log likelihood: -3462.185572
EM: Round [94] log likelihood: -3462.185379
EM: Round [95] log likelihood: -3462.185200
EM: Round [96] log likelihood: -3462.185034
EM: Round [97] log likelihood: -3462.184880
EM: Round [98] log likelihood: -3462.184737
EM: Round [99] log likelihood: -3462.184604
EM: Round [100] log likelihood: -3462.184480
EM: Round [101] log likelihood: -3462.184366
EM: Round [102] log likelihood: -3462.184259
EM: Round [103] log likelihood: -3462.184160
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.7hzIZZLTPS/aih-tih-sc-13d441-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.7hzIZZLTPS/aih-tih-sc-13d441-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.7hzIZZLTPS/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.7hzIZZLTPS/aih-tih-sc-13d441-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.7hzIZZLTPS/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.7hzIZZLTPS/aih-tih-sc-13d441-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.7hzIZZLTPS/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.7hzIZZLTPS/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.7hzIZZLTPS/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.7hzIZZLTPS/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.7hzIZZLTPS/aih-tih-sc-13d441-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.7hzIZZLTPS/aih-tih-sc-13d441-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3239.563328
EM: Round [1] log likelihood: -3239.412247
EM: Round [2] log likelihood: -3239.412093
EM: Round [3] log likelihood: -3239.412092
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.7hzIZZLTPS/aih-tih-sc-13d441-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 257719664
Warning - not locating file: /tmp/nxf.7hzIZZLTPS/aih-tih-sc-13d441-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 [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000243289.1]
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