Done.
-parsing GTF file: /tmp/nxf.VxeCOiKRWK/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.VxeCOiKRWK/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.VxeCOiKRWK/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.VxeCOiKRWK/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.VxeCOiKRWK/fi_workdir/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.VxeCOiKRWK/fi_workdir/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
22:18:11 : INFO : Done.
-parsing GTF file: /tmp/nxf.VxeCOiKRWK/fi_workdir/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.VxeCOiKRWK/fi_workdir/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[1160000]   -done parsing /tmp/nxf.VxeCOiKRWK/fi_workdir/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 105,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 30,
          'excessive soft clipping' => 8736,
          'small anchor length' => 3,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 42,
          ' ** passed ** ' => 2329,
          'low complexity anchor region' => 9,
          'exons hit < 2' => 6,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 37,
          'num genes matched < 2' => 80,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 200,
          'per_id < 96' => 4241,
          'seq-similar region overlap' => 108
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.VxeCOiKRWK/fi_workdir/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[102000]   -fusion SPANNING read extraction for scaff: ABAT--GSG1L

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[13000]   
[14000]   -fusion SPANNING read extraction for scaff: AKAP10--KCNU1

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[13000]   -fusion SPANNING read extraction for scaff: AKAP10--AC090453.1

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[17000]   -fusion SPANNING read extraction for scaff: AP3M2--NRG1

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[3000]   -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2

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[155000]   -fusion SPANNING read extraction for scaff: CCDC189--MROH1

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[21000]   -fusion SPANNING read extraction for scaff: CMTM8--RN7SL120P

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[21000]   -fusion SPANNING read extraction for scaff: CMTM8--CNTN6

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[39000]   
[40000]   -fusion SPANNING read extraction for scaff: CUL1--RBMS3

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[66000]   -fusion SPANNING read extraction for scaff: EZH1--TBC1D16

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[64000]   -fusion SPANNING read extraction for scaff: GBE1--FOXP1

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[3000]   -fusion SPANNING read extraction for scaff: GSG1L--AJ003147.2

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[14000]   -fusion SPANNING read extraction for scaff: HSD17B7P2--RAD18

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[17000]   -fusion SPANNING read extraction for scaff: IKZF2--LINC01953

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[31000]   -fusion SPANNING read extraction for scaff: LRMDA--ADK

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[75000]   -fusion SPANNING read extraction for scaff: N4BP2L2--LITAFD

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[9000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[9000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[10000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[9000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1

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[9000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2

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[10000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13

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[70000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[48000]   -fusion SPANNING read extraction for scaff: SUCLG2--CNTN3

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[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   -fusion SPANNING read extraction for scaff: SUCLG2--NIPA2P2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   -fusion SPANNING read extraction for scaff: SUCLG2-AS1--PTPRG

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[26000]   
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[30000]   
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[39000]   
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[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   -fusion SPANNING read extraction for scaff: TCF4--HNRNPA1P57

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: TDRD1--HECTD2

[1000]   -fusion SPANNING read extraction for scaff: TDRD1--RPS27P1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
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[13000]   
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[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[30000]   
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[34000]   
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[40000]   
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[42000]   
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[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   -fusion SPANNING read extraction for scaff: XRN2--GRM7

[1000]   
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[6000]   
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[8000]   
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[30000]   
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[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   -fusion SPANNING read extraction for scaff: ZC3HAV1--CNTNAP2

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
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[8000]   
[9000]   
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[30000]   
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[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   -fusion SPANNING read extraction for scaff: ZNF267--SPECC1
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 8757,
          'lacks exon overlap' => 17158
        };
EM: Starting log likelihood: -3602.548504
EM: Round [1] log likelihood: -3602.289413
EM: Round [2] log likelihood: -3602.166643
EM: Round [3] log likelihood: -3602.062654
EM: Round [4] log likelihood: -3601.974033
EM: Round [5] log likelihood: -3601.898155
EM: Round [6] log likelihood: -3601.832933
EM: Round [7] log likelihood: -3601.776689
EM: Round [8] log likelihood: -3601.728051
EM: Round [9] log likelihood: -3601.685892
EM: Round [10] log likelihood: -3601.649276
EM: Round [11] log likelihood: -3601.617420
EM: Round [12] log likelihood: -3601.589664
EM: Round [13] log likelihood: -3601.565449
EM: Round [14] log likelihood: -3601.544300
EM: Round [15] log likelihood: -3601.525812
EM: Round [16] log likelihood: -3601.509636
EM: Round [17] log likelihood: -3601.495472
EM: Round [18] log likelihood: -3601.483064
EM: Round [19] log likelihood: -3601.472187
EM: Round [20] log likelihood: -3601.462647
EM: Round [21] log likelihood: -3601.454278
EM: Round [22] log likelihood: -3601.446932
EM: Round [23] log likelihood: -3601.440482
EM: Round [24] log likelihood: -3601.434818
EM: Round [25] log likelihood: -3601.429842
EM: Round [26] log likelihood: -3601.425470
EM: Round [27] log likelihood: -3601.421629
EM: Round [28] log likelihood: -3601.418252
EM: Round [29] log likelihood: -3601.415283
EM: Round [30] log likelihood: -3601.412673
EM: Round [31] log likelihood: -3601.410379
EM: Round [32] log likelihood: -3601.408361
EM: Round [33] log likelihood: -3601.406586
EM: Round [34] log likelihood: -3601.405025
EM: Round [35] log likelihood: -3601.403652
EM: Round [36] log likelihood: -3601.402445
EM: Round [37] log likelihood: -3601.401382
EM: Round [38] log likelihood: -3601.400448
EM: Round [39] log likelihood: -3601.399626
EM: Round [40] log likelihood: -3601.398903
EM: Round [41] log likelihood: -3601.398266
EM: Round [42] log likelihood: -3601.397706
EM: Round [43] log likelihood: -3601.397214
EM: Round [44] log likelihood: -3601.396780
EM: Round [45] log likelihood: -3601.396399
EM: Round [46] log likelihood: -3601.396063
EM: Round [47] log likelihood: -3601.395768
EM: Round [48] log likelihood: -3601.395508
EM: Round [49] log likelihood: -3601.395280
EM: Round [50] log likelihood: -3601.395079
EM: Round [51] log likelihood: -3601.394902
EM: Round [52] log likelihood: -3601.394746
EM: Round [53] log likelihood: -3601.394609
EM: Round [54] log likelihood: -3601.394488
EM: Round [55] log likelihood: -3601.394382
EM: Round [56] log likelihood: -3601.394289
EM: Stopping iterations at round 56 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.VxeCOiKRWK/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.VxeCOiKRWK/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.VxeCOiKRWK/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.VxeCOiKRWK/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.VxeCOiKRWK/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.VxeCOiKRWK/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.VxeCOiKRWK/aih-tih-sc-b6a2e8-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.VxeCOiKRWK/fi_workdir/aih-tih-sc-b6a2e8-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.VxeCOiKRWK/fi_workdir/aih-tih-sc-b6a2e8-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.VxeCOiKRWK/fi_workdir/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.VxeCOiKRWK/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.VxeCOiKRWK/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3252.638888
EM: Round [1] log likelihood: -3252.610421
EM: Round [2] log likelihood: -3252.610419
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.VxeCOiKRWK/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296820409
Warning - not locating file: /tmp/nxf.VxeCOiKRWK/aih-tih-sc-b6a2e8-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000262668.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000237442.3]
WARNING, no entry stored in dbm for [ENSG00000241316.8]
WARNING, no entry stored in dbm for [ENSG00000241316.8]
ls: cannot access 'IGV_inputs': No such file or directory