Done.
-parsing GTF file: /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.3Kz68mZ8J3/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.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
22:25:55 : INFO : Done.
-parsing GTF file: /tmp/nxf.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

[10000]   
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[720000]   -done parsing /tmp/nxf.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'seq-similar region overlap' => 110,
          ' ** passed ** ' => 8761,
          'per_id < 96' => 2384,
          'low complexity anchor region' => 10,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 2,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 18,
          'num genes matched < 2' => 15,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 18,
          'excessive soft clipping' => 3477,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 8,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 8,
          'small anchor length' => 46,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 21
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

[1000]   
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[6000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: AP001347.1--ANKRD20A11P

[1000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

[1000]   
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[5000]   
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[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
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[9000]   
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[11000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
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[8000]   
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[11000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
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[6000]   
[7000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

[1000]   
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[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

[1000]   
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[5000]   
[6000]   
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[8000]   
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[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

[1000]   
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[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

[1000]   
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[7000]   
[8000]   
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[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

[1000]   
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[11000]   
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[14000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

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[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8

[1000]   
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[6000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4

[1000]   
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[7000]   
[8000]   
[9000]   
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[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10

[1000]   
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[3000]   
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[7000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5

[1000]   
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[10000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11

[1000]   
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[11000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6

[1000]   
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[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3

[1000]   
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[3000]   
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[12000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9

[1000]   
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[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7

[1000]   
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[16000]   
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[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12

[1000]   
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[3000]   
[4000]   
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[6000]   
[7000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
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[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
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[13000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
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[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[1000]   
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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[44000]   
[45000]   
[46000]   
[47000]   
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[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[14000]   
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[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
[2000]   
[3000]   
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[30000]   
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[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
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[67000]   
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[73000]   
[74000]   
[75000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[8000]   
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[16000]   
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[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

[1000]   
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[5000]   
[6000]   
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[8000]   
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[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 33639,
          'lacks exon overlap' => 2645
        };
EM: Starting log likelihood: -3555.675454
EM: Round [1] log likelihood: -3554.541146
EM: Round [2] log likelihood: -3553.766733
EM: Round [3] log likelihood: -3553.098799
EM: Round [4] log likelihood: -3552.516180
EM: Round [5] log likelihood: -3552.002671
EM: Round [6] log likelihood: -3551.545651
EM: Round [7] log likelihood: -3551.135175
EM: Round [8] log likelihood: -3550.763340
EM: Round [9] log likelihood: -3550.423811
EM: Round [10] log likelihood: -3550.111487
EM: Round [11] log likelihood: -3549.822232
EM: Round [12] log likelihood: -3549.552682
EM: Round [13] log likelihood: -3549.300090
EM: Round [14] log likelihood: -3549.062203
EM: Round [15] log likelihood: -3548.837168
EM: Round [16] log likelihood: -3548.623457
EM: Round [17] log likelihood: -3548.419806
EM: Round [18] log likelihood: -3548.225164
EM: Round [19] log likelihood: -3548.038658
EM: Round [20] log likelihood: -3547.859557
EM: Round [21] log likelihood: -3547.687248
EM: Round [22] log likelihood: -3547.521215
EM: Round [23] log likelihood: -3547.361018
EM: Round [24] log likelihood: -3547.206286
EM: Round [25] log likelihood: -3547.056699
EM: Round [26] log likelihood: -3546.911979
EM: Round [27] log likelihood: -3546.771887
EM: Round [28] log likelihood: -3546.636211
EM: Round [29] log likelihood: -3546.504765
EM: Round [30] log likelihood: -3546.377382
EM: Round [31] log likelihood: -3546.253910
EM: Round [32] log likelihood: -3546.134213
EM: Round [33] log likelihood: -3546.018164
EM: Round [34] log likelihood: -3545.905647
EM: Round [35] log likelihood: -3545.796552
EM: Round [36] log likelihood: -3545.690775
EM: Round [37] log likelihood: -3545.588219
EM: Round [38] log likelihood: -3545.488791
EM: Round [39] log likelihood: -3545.392401
EM: Round [40] log likelihood: -3545.298963
EM: Round [41] log likelihood: -3545.208394
EM: Round [42] log likelihood: -3545.120612
EM: Round [43] log likelihood: -3545.035539
EM: Round [44] log likelihood: -3544.953099
EM: Round [45] log likelihood: -3544.873216
EM: Round [46] log likelihood: -3544.795818
EM: Round [47] log likelihood: -3544.720834
EM: Round [48] log likelihood: -3544.648194
EM: Round [49] log likelihood: -3544.577829
EM: Round [50] log likelihood: -3544.509674
EM: Round [51] log likelihood: -3544.443663
EM: Round [52] log likelihood: -3544.379732
EM: Round [53] log likelihood: -3544.317819
EM: Round [54] log likelihood: -3544.257863
EM: Round [55] log likelihood: -3544.199804
EM: Round [56] log likelihood: -3544.143586
EM: Round [57] log likelihood: -3544.089150
EM: Round [58] log likelihood: -3544.036442
EM: Round [59] log likelihood: -3543.985407
EM: Round [60] log likelihood: -3543.935994
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EM: Round [516] log likelihood: -3542.131868
EM: Stopping iterations at round 516 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-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.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-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.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-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.3Kz68mZ8J3/fi_workdir/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2340.175499
EM: Round [1] log likelihood: -2339.953691
EM: Round [2] log likelihood: -2339.953628
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296655419
Warning - not locating file: /tmp/nxf.3Kz68mZ8J3/aih-tih-sc-fe8311-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 [ENSG00000282057.1]
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 [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
ls: cannot access 'IGV_inputs': No such file or directory