Done.
-parsing GTF file: /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.BAl7gZ6CTL/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.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:37:08 : INFO : Done.
-parsing GTF file: /tmp/nxf.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[780000]   -done parsing /tmp/nxf.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'seq-similar region overlap' => 232,
          'num genes matched < 2' => 12,
          'small anchor length' => 3,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 6,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 33,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 46,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 24,
          ' ** passed ** ' => 2339,
          'per_id < 96' => 2928,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3,
          'excessive soft clipping' => 4891,
          'low complexity anchor region' => 31,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[10000]   -fusion SPANNING read extraction for scaff: AC020899.1--FLT3LG

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[4000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[4000]   -fusion SPANNING read extraction for scaff: ASAH2B--PRKG1

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[100000]   
[101000]   
[102000]   
[103000]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   -fusion SPANNING read extraction for scaff: CSMD3--RNU4-37P

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[108000]   -fusion SPANNING read extraction for scaff: CSMD3--LINC02237

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[102000]   
[103000]   
[104000]   
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[107000]   
[108000]   
[109000]   -fusion SPANNING read extraction for scaff: GDPD1--SETD2

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[66000]   
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[68000]   
[69000]   
[70000]   
[71000]   
[72000]   -fusion SPANNING read extraction for scaff: GUSBP13--NAIP

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

[1000]   
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[40000]   
[41000]   -fusion SPANNING read extraction for scaff: PARD6B--RASSF2

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[29000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[30000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[31000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[79000]   
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[86000]   
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[103000]   
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[105000]   
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[109000]   
[110000]   
[111000]   -fusion SPANNING read extraction for scaff: SETD2--CA4

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[20000]   
[21000]   -fusion SPANNING read extraction for scaff: SFMBT1--RFT1

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: SORCS1--AL353740.1

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: SORCS1--LINC02661

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[4000]   -fusion SPANNING read extraction for scaff: SREK1IP1--RGS7BP

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[2000]   
[3000]   -fusion SPANNING read extraction for scaff: SREK1IP1--MRPL49P1

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[32000]   
[33000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[5000]   
[6000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[15000]   
[16000]   -fusion SPANNING read extraction for scaff: TTC39C--ISM1

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[12000]   
[13000]   -fusion SPANNING read extraction for scaff: TTC39C--AL121782.1

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[17000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 3446,
          'seq similar region alignment' => 25791
        };
EM: Starting log likelihood: -2751.836266
EM: Round [1] log likelihood: -2751.064566
EM: Round [2] log likelihood: -2750.426526
EM: Round [3] log likelihood: -2749.882730
EM: Round [4] log likelihood: -2749.416482
EM: Round [5] log likelihood: -2749.014938
EM: Round [6] log likelihood: -2748.667828
EM: Round [7] log likelihood: -2748.366831
EM: Round [8] log likelihood: -2748.105122
EM: Round [9] log likelihood: -2747.877056
EM: Round [10] log likelihood: -2747.677917
EM: Round [11] log likelihood: -2747.503744
EM: Round [12] log likelihood: -2747.351186
EM: Round [13] log likelihood: -2747.217391
EM: Round [14] log likelihood: -2747.099922
EM: Round [15] log likelihood: -2746.996689
EM: Round [16] log likelihood: -2746.905892
EM: Round [17] log likelihood: -2746.825974
EM: Round [18] log likelihood: -2746.755586
EM: Round [19] log likelihood: -2746.693557
EM: Round [20] log likelihood: -2746.638868
EM: Round [21] log likelihood: -2746.590630
EM: Round [22] log likelihood: -2746.548066
EM: Round [23] log likelihood: -2746.510495
EM: Round [24] log likelihood: -2746.477322
EM: Round [25] log likelihood: -2746.448025
EM: Round [26] log likelihood: -2746.422145
EM: Round [27] log likelihood: -2746.399279
EM: Round [28] log likelihood: -2746.379072
EM: Round [29] log likelihood: -2746.361212
EM: Round [30] log likelihood: -2746.345425
EM: Round [31] log likelihood: -2746.331468
EM: Round [32] log likelihood: -2746.319127
EM: Round [33] log likelihood: -2746.308215
EM: Round [34] log likelihood: -2746.298566
EM: Round [35] log likelihood: -2746.290031
EM: Round [36] log likelihood: -2746.282484
EM: Round [37] log likelihood: -2746.275807
EM: Round [38] log likelihood: -2746.269902
EM: Round [39] log likelihood: -2746.264678
EM: Round [40] log likelihood: -2746.260057
EM: Round [41] log likelihood: -2746.255969
EM: Round [42] log likelihood: -2746.252353
EM: Round [43] log likelihood: -2746.249153
EM: Round [44] log likelihood: -2746.246322
EM: Round [45] log likelihood: -2746.243818
EM: Round [46] log likelihood: -2746.241602
EM: Round [47] log likelihood: -2746.239641
EM: Round [48] log likelihood: -2746.237906
EM: Round [49] log likelihood: -2746.236372
EM: Round [50] log likelihood: -2746.235014
EM: Round [51] log likelihood: -2746.233812
EM: Round [52] log likelihood: -2746.232749
EM: Round [53] log likelihood: -2746.231808
EM: Round [54] log likelihood: -2746.230975
EM: Round [55] log likelihood: -2746.230239
EM: Round [56] log likelihood: -2746.229587
EM: Round [57] log likelihood: -2746.229010
EM: Round [58] log likelihood: -2746.228500
EM: Round [59] log likelihood: -2746.228048
EM: Round [60] log likelihood: -2746.227649
EM: Round [61] log likelihood: -2746.227295
EM: Round [62] log likelihood: -2746.226982
EM: Round [63] log likelihood: -2746.226705
EM: Round [64] log likelihood: -2746.226460
EM: Round [65] log likelihood: -2746.226244
EM: Round [66] log likelihood: -2746.226052
EM: Round [67] log likelihood: -2746.225882
EM: Round [68] log likelihood: -2746.225732
EM: Round [69] log likelihood: -2746.225599
EM: Round [70] log likelihood: -2746.225481
EM: Round [71] log likelihood: -2746.225377
EM: Round [72] log likelihood: -2746.225285
EM: Stopping iterations at round 72 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-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.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-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.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-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.BAl7gZ6CTL/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2574.397102
EM: Round [1] log likelihood: -2574.377943
EM: Round [2] log likelihood: -2574.377526
EM: Round [3] log likelihood: -2574.377517
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296382314
Warning - not locating file: /tmp/nxf.BAl7gZ6CTL/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000242858.1]
WARNING, no entry stored in dbm for [ENSG00000198237.8]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
ls: cannot access 'IGV_inputs': No such file or directory