Done.
-parsing GTF file: /tmp/nxf.BeuoTtRGkb/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.BeuoTtRGkb/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.BeuoTtRGkb/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.BeuoTtRGkb/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.BeuoTtRGkb/fi_workdir/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.BeuoTtRGkb/fi_workdir/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:14:04 : INFO : Done.
-parsing GTF file: /tmp/nxf.BeuoTtRGkb/fi_workdir/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.BeuoTtRGkb/fi_workdir/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

[10000]   
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[430000]   -done parsing /tmp/nxf.BeuoTtRGkb/fi_workdir/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'exons hit < 2' => 4,
          'small anchor length' => 37,
          'excessive soft clipping' => 2239,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 52,
          'per_id < 96' => 1893,
          'seq-similar region overlap' => 108,
          ' ** passed ** ' => 6190,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.BeuoTtRGkb/fi_workdir/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[27000]   -fusion SPANNING read extraction for scaff: AC013268.1--MALL

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[13000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[5000]   -fusion SPANNING read extraction for scaff: GTF2A1L--STON1-GTF2A1L

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[12000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[14000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[12000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[49000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[9000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[22000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[25000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[23000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[21000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[41000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[23000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[13000]   -fusion SPANNING read extraction for scaff: PRSS27--TPSB2

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[31000]   -fusion SPANNING read extraction for scaff: STON1--GTF2A1L

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[28000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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

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[21000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 34175,
          'lacks exon overlap' => 1353
        };
EM: Starting log likelihood: -2791.944583
EM: Round [1] log likelihood: -2791.538389
EM: Round [2] log likelihood: -2791.217715
EM: Round [3] log likelihood: -2790.955041
EM: Round [4] log likelihood: -2790.738224
EM: Round [5] log likelihood: -2790.558200
EM: Round [6] log likelihood: -2790.408013
EM: Round [7] log likelihood: -2790.282231
EM: Round [8] log likelihood: -2790.176554
EM: Round [9] log likelihood: -2790.087534
EM: Round [10] log likelihood: -2790.012383
EM: Round [11] log likelihood: -2789.948824
EM: Round [12] log likelihood: -2789.894987
EM: Round [13] log likelihood: -2789.849327
EM: Round [14] log likelihood: -2789.810561
EM: Round [15] log likelihood: -2789.777617
EM: Round [16] log likelihood: -2789.749599
EM: Round [17] log likelihood: -2789.725756
EM: Round [18] log likelihood: -2789.705454
EM: Round [19] log likelihood: -2789.688160
EM: Round [20] log likelihood: -2789.673421
EM: Round [21] log likelihood: -2789.660856
EM: Round [22] log likelihood: -2789.650142
EM: Round [23] log likelihood: -2789.641002
EM: Round [24] log likelihood: -2789.633206
EM: Round [25] log likelihood: -2789.626553
EM: Round [26] log likelihood: -2789.620875
EM: Round [27] log likelihood: -2789.616029
EM: Round [28] log likelihood: -2789.611892
EM: Round [29] log likelihood: -2789.608361
EM: Round [30] log likelihood: -2789.605345
EM: Round [31] log likelihood: -2789.602771
EM: Round [32] log likelihood: -2789.600573
EM: Round [33] log likelihood: -2789.598696
EM: Round [34] log likelihood: -2789.597093
EM: Round [35] log likelihood: -2789.595724
EM: Round [36] log likelihood: -2789.594555
EM: Round [37] log likelihood: -2789.593557
EM: Round [38] log likelihood: -2789.592704
EM: Round [39] log likelihood: -2789.591976
EM: Round [40] log likelihood: -2789.591354
EM: Round [41] log likelihood: -2789.590822
EM: Round [42] log likelihood: -2789.590369
EM: Round [43] log likelihood: -2789.589981
EM: Round [44] log likelihood: -2789.589650
EM: Round [45] log likelihood: -2789.589367
EM: Round [46] log likelihood: -2789.589126
EM: Round [47] log likelihood: -2789.588920
EM: Round [48] log likelihood: -2789.588744
EM: Round [49] log likelihood: -2789.588593
EM: Round [50] log likelihood: -2789.588465
EM: Round [51] log likelihood: -2789.588355
EM: Round [52] log likelihood: -2789.588261
EM: Stopping iterations at round 52 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.BeuoTtRGkb/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.BeuoTtRGkb/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.BeuoTtRGkb/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.BeuoTtRGkb/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.BeuoTtRGkb/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.BeuoTtRGkb/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.BeuoTtRGkb/aih-tih-sc-d1f1a3-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.BeuoTtRGkb/fi_workdir/aih-tih-sc-d1f1a3-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.BeuoTtRGkb/fi_workdir/aih-tih-sc-d1f1a3-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.BeuoTtRGkb/fi_workdir/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.BeuoTtRGkb/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.BeuoTtRGkb/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2576.127962
EM: Round [1] log likelihood: -2576.117774
EM: Round [2] log likelihood: -2576.117694
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.BeuoTtRGkb/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 297220257
Warning - not locating file: /tmp/nxf.BeuoTtRGkb/aih-tih-sc-d1f1a3-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
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 [ENSG00000068781.21]
WARNING, no entry stored in dbm for [ENSG00000068781.21]
ls: cannot access 'IGV_inputs': No such file or directory