Done.
-parsing GTF file: /tmp/nxf.ijKyWHNdWq/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.ijKyWHNdWq/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.ijKyWHNdWq/aih-tih-sc-d963a2-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.ijKyWHNdWq/aih-tih-sc-d963a2-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.ijKyWHNdWq/fi_workdir/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.ijKyWHNdWq/fi_workdir/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-d963a2-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-d963a2-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
22:22:52 : INFO : Done.
-parsing GTF file: /tmp/nxf.ijKyWHNdWq/fi_workdir/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.ijKyWHNdWq/fi_workdir/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[1010000]   -done parsing /tmp/nxf.ijKyWHNdWq/fi_workdir/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num genes matched < 2' => 51,
          'low complexity anchor region' => 7,
          'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 8,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 48,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 65,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4,
          ' ** passed ** ' => 4315,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 5,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'per_id < 96' => 2821,
          'excessive soft clipping' => 4101
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.ijKyWHNdWq/fi_workdir/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[3000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

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[15000]   -fusion SPANNING read extraction for scaff: AC026150.1--GOLGA6L10

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[330000]   
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[334000]   
[335000]   -fusion SPANNING read extraction for scaff: AC136431.1--PKD1P5

[1000]   
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[4000]   
[5000]   -fusion SPANNING read extraction for scaff: AL162574.2--SYPL2

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[34000]   
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[39000]   -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B

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[5000]   
[6000]   -fusion SPANNING read extraction for scaff: FAM102B--AC092506.1

[1000]   
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[5000]   
[6000]   -fusion SPANNING read extraction for scaff: FAM102B--AL591888.1

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[56000]   -fusion SPANNING read extraction for scaff: GUSBP13--NAIP

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[5000]   -fusion SPANNING read extraction for scaff: LINC00381--SYPL2

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[42000]   -fusion SPANNING read extraction for scaff: NPHP3--ACAD11

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[20000]   -fusion SPANNING read extraction for scaff: NRXN3--SYPL2

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[27000]   -fusion SPANNING read extraction for scaff: PMS2P6--CCDC146

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[5000]   -fusion SPANNING read extraction for scaff: PPIAP24--SYPL2

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[170000]   -fusion SPANNING read extraction for scaff: RBM14--RBM4

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[212000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[27000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

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[17000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[15000]   -fusion SPANNING read extraction for scaff: UBE2Q2P1--GOLGA6L10
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 15361
        };
EM: Starting log likelihood: -6283.112175
EM: Round [1] log likelihood: -6263.664932
EM: Round [2] log likelihood: -6255.865762
EM: Round [3] log likelihood: -6252.653941
EM: Round [4] log likelihood: -6251.379542
EM: Round [5] log likelihood: -6250.896505
EM: Round [6] log likelihood: -6250.718304
EM: Round [7] log likelihood: -6250.652653
EM: Round [8] log likelihood: -6250.628121
EM: Round [9] log likelihood: -6250.618793
EM: Round [10] log likelihood: -6250.615195
EM: Round [11] log likelihood: -6250.613792
EM: Round [12] log likelihood: -6250.613242
EM: Round [13] log likelihood: -6250.613026
EM: Round [14] log likelihood: -6250.612940
EM: Stopping iterations at round 14 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.ijKyWHNdWq/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.ijKyWHNdWq/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.ijKyWHNdWq/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.ijKyWHNdWq/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.ijKyWHNdWq/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.ijKyWHNdWq/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.ijKyWHNdWq/aih-tih-sc-d963a2-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.ijKyWHNdWq/fi_workdir/aih-tih-sc-d963a2-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.ijKyWHNdWq/fi_workdir/aih-tih-sc-d963a2-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.ijKyWHNdWq/fi_workdir/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.ijKyWHNdWq/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.ijKyWHNdWq/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -6140.172743
EM: Round [1] log likelihood: -6124.157017
EM: Round [2] log likelihood: -6117.515601
EM: Round [3] log likelihood: -6114.732791
EM: Round [4] log likelihood: -6113.621248
EM: Round [5] log likelihood: -6113.200549
EM: Round [6] log likelihood: -6113.046279
EM: Round [7] log likelihood: -6112.989826
EM: Round [8] log likelihood: -6112.968831
EM: Round [9] log likelihood: -6112.960863
EM: Round [10] log likelihood: -6112.957788
EM: Round [11] log likelihood: -6112.956587
EM: Round [12] log likelihood: -6112.956114
EM: Round [13] log likelihood: -6112.955927
EM: Round [14] log likelihood: -6112.955853
EM: Stopping iterations at round 14 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.ijKyWHNdWq/aih-tih-sc-d963a2-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296352227
Warning - not locating file: /tmp/nxf.ijKyWHNdWq/aih-tih-sc-d963a2-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000189136.9]
WARNING, no entry stored in dbm for [ENSG00000198237.8]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000260126.2]
WARNING, no entry stored in dbm for [ENSG00000254681.6]
WARNING, no entry stored in dbm for [ENSG00000260693.1]
WARNING, no entry stored in dbm for [ENSG00000226240.2]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
ls: cannot access 'IGV_inputs': No such file or directory