Done.
-parsing GTF file: /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.uxAJ9Mobh9/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.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:25:45 : INFO : Done.
-parsing GTF file: /tmp/nxf.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[800000]   -done parsing /tmp/nxf.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'excessive soft clipping' => 19454,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
          'per_id < 96' => 6365,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 5,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 7496,
          'seq-similar region overlap' => 673,
          'low complexity anchor region' => 15,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 60,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 20,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 129,
          ' ** passed ** ' => 2219,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 14,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 424,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 322,
          'num genes matched < 2' => 16,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 436
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[83000]   -fusion SPANNING read extraction for scaff: ATP9A--KIF3B

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[223000]   -fusion SPANNING read extraction for scaff: IGL-@-ext--AC097110.1

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[11000]   -fusion SPANNING read extraction for scaff: MAP1LC3A--TTLL9

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[65000]   
[66000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[60000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[70000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[15000]   -fusion SPANNING read extraction for scaff: RPRD1A--MOCOS

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[90000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[7000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[64000]   -fusion SPANNING read extraction for scaff: TOX2--TSHZ2

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[42000]   -fusion SPANNING read extraction for scaff: TOX2--AL109930.1

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[26000]   -fusion SPANNING read extraction for scaff: TTC39C--CABLES1

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[16000]   -fusion SPANNING read extraction for scaff: TTLL9--CABLES1

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[21000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 19859,
          'seq similar region alignment' => 54545
        };
EM: Starting log likelihood: -1899.187716
EM: Round [1] log likelihood: -1899.184567
EM: Round [2] log likelihood: -1899.181447
EM: Round [3] log likelihood: -1899.178357
EM: Round [4] log likelihood: -1899.175296
EM: Round [5] log likelihood: -1899.172264
EM: Round [6] log likelihood: -1899.169260
EM: Round [7] log likelihood: -1899.166284
EM: Round [8] log likelihood: -1899.163336
EM: Round [9] log likelihood: -1899.160415
EM: Round [10] log likelihood: -1899.157522
EM: Round [11] log likelihood: -1899.154655
EM: Round [12] log likelihood: -1899.151814
EM: Round [13] log likelihood: -1899.149000
EM: Round [14] log likelihood: -1899.146211
EM: Round [15] log likelihood: -1899.143447
EM: Round [16] log likelihood: -1899.140709
EM: Round [17] log likelihood: -1899.137996
EM: Round [18] log likelihood: -1899.135307
EM: Round [19] log likelihood: -1899.132642
EM: Round [20] log likelihood: -1899.130002
EM: Round [21] log likelihood: -1899.127385
EM: Round [22] log likelihood: -1899.124792
EM: Round [23] log likelihood: -1899.122221
EM: Round [24] log likelihood: -1899.119674
EM: Round [25] log likelihood: -1899.117149
EM: Round [26] log likelihood: -1899.114647
EM: Round [27] log likelihood: -1899.112167
EM: Round [28] log likelihood: -1899.109708
EM: Round [29] log likelihood: -1899.107272
EM: Round [30] log likelihood: -1899.104856
EM: Round [31] log likelihood: -1899.102462
EM: Round [32] log likelihood: -1899.100089
EM: Round [33] log likelihood: -1899.097736
EM: Round [34] log likelihood: -1899.095404
EM: Round [35] log likelihood: -1899.093092
EM: Round [36] log likelihood: -1899.090800
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EM: Round [480] log likelihood: -1898.800971
EM: Round [481] log likelihood: -1898.800871
EM: Stopping iterations at round 481 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-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.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-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.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-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.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1863.820188
EM: Round [1] log likelihood: -1863.820188
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296445688
Warning - not locating file: /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-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]
ls: cannot access 'IGV_inputs': No such file or directory