Done.
-parsing GTF file: /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.L2BqxZvgea/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.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00457_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00457_B23WHTKLT4_1.star.sortedByCoord.out.bam
11:07:30 : INFO : Done.
-parsing GTF file: /tmp/nxf.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

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[720000]   -done parsing /tmp/nxf.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 12,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 34,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'small anchor length' => 130,
          'num genes matched < 2' => 9,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 9,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 148,
          'excessive soft clipping' => 6298,
          'seq-similar region overlap' => 77,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
          'per_id < 96' => 5453,
          ' ** passed ** ' => 21366,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 9,
          'exons hit < 2' => 2
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[15000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[58000]   
[59000]   -fusion SPANNING read extraction for scaff: CSNK1D--AC131274.3

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[57000]   
[58000]   
[59000]   -fusion SPANNING read extraction for scaff: CSNK1D--AC069061.1

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[32000]   -fusion SPANNING read extraction for scaff: JPT1--C17orf58

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

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[12000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[11000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[11000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[91000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[70000]   -fusion SPANNING read extraction for scaff: PRSS27--TPSB2

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[120000]   
[121000]   
[122000]   -fusion SPANNING read extraction for scaff: PSMD12--BPTF

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[17000]   -fusion SPANNING read extraction for scaff: SLC39A11--LINC00511

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[18000]   -fusion SPANNING read extraction for scaff: SOCS7--DBF4B

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[24000]   -fusion SPANNING read extraction for scaff: SOCS7--ADAM11

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[45000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[13000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 22779,
          'lacks exon overlap' => 2632
        };
EM: Starting log likelihood: -1951.837462
EM: Round [1] log likelihood: -1951.557139
EM: Round [2] log likelihood: -1951.380350
EM: Round [3] log likelihood: -1951.225798
EM: Round [4] log likelihood: -1951.090103
EM: Round [5] log likelihood: -1950.970545
EM: Round [6] log likelihood: -1950.864889
EM: Round [7] log likelihood: -1950.771276
EM: Round [8] log likelihood: -1950.688147
EM: Round [9] log likelihood: -1950.614181
EM: Round [10] log likelihood: -1950.548257
EM: Round [11] log likelihood: -1950.489409
EM: Round [12] log likelihood: -1950.436810
EM: Round [13] log likelihood: -1950.389740
EM: Round [14] log likelihood: -1950.347574
EM: Round [15] log likelihood: -1950.309765
EM: Round [16] log likelihood: -1950.275837
EM: Round [17] log likelihood: -1950.245367
EM: Round [18] log likelihood: -1950.217986
EM: Round [19] log likelihood: -1950.193367
EM: Round [20] log likelihood: -1950.171218
EM: Round [21] log likelihood: -1950.151283
EM: Round [22] log likelihood: -1950.133333
EM: Round [23] log likelihood: -1950.117165
EM: Round [24] log likelihood: -1950.102595
EM: Round [25] log likelihood: -1950.089464
EM: Round [26] log likelihood: -1950.077624
EM: Round [27] log likelihood: -1950.066947
EM: Round [28] log likelihood: -1950.057316
EM: Round [29] log likelihood: -1950.048627
EM: Round [30] log likelihood: -1950.040787
EM: Round [31] log likelihood: -1950.033711
EM: Round [32] log likelihood: -1950.027324
EM: Round [33] log likelihood: -1950.021558
EM: Round [34] log likelihood: -1950.016352
EM: Round [35] log likelihood: -1950.011652
EM: Round [36] log likelihood: -1950.007407
EM: Round [37] log likelihood: -1950.003573
EM: Round [38] log likelihood: -1950.000111
EM: Round [39] log likelihood: -1949.996984
EM: Round [40] log likelihood: -1949.994159
EM: Round [41] log likelihood: -1949.991607
EM: Round [42] log likelihood: -1949.989301
EM: Round [43] log likelihood: -1949.987218
EM: Round [44] log likelihood: -1949.985336
EM: Round [45] log likelihood: -1949.983636
EM: Round [46] log likelihood: -1949.982100
EM: Round [47] log likelihood: -1949.980711
EM: Round [48] log likelihood: -1949.979457
EM: Round [49] log likelihood: -1949.978324
EM: Round [50] log likelihood: -1949.977299
EM: Round [51] log likelihood: -1949.976374
EM: Round [52] log likelihood: -1949.975537
EM: Round [53] log likelihood: -1949.974781
EM: Round [54] log likelihood: -1949.974098
EM: Round [55] log likelihood: -1949.973481
EM: Round [56] log likelihood: -1949.972923
EM: Round [57] log likelihood: -1949.972419
EM: Round [58] log likelihood: -1949.971963
EM: Round [59] log likelihood: -1949.971551
EM: Round [60] log likelihood: -1949.971179
EM: Round [61] log likelihood: -1949.970842
EM: Round [62] log likelihood: -1949.970538
EM: Round [63] log likelihood: -1949.970264
EM: Round [64] log likelihood: -1949.970015
EM: Round [65] log likelihood: -1949.969791
EM: Round [66] log likelihood: -1949.969588
EM: Round [67] log likelihood: -1949.969405
EM: Round [68] log likelihood: -1949.969239
EM: Round [69] log likelihood: -1949.969089
EM: Round [70] log likelihood: -1949.968954
EM: Round [71] log likelihood: -1949.968831
EM: Round [72] log likelihood: -1949.968721
EM: Round [73] log likelihood: -1949.968621
EM: Stopping iterations at round 73 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_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.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_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.L2BqxZvgea/fi_workdir/tih_rna_sample_00457_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1793.315190
EM: Round [1] log likelihood: -1793.243426
EM: Round [2] log likelihood: -1793.243377
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_1_1.fastp.fastq.gz: 295627857
Warning - not locating file: /tmp/nxf.L2BqxZvgea/tih_rna_sample_00457_B23WHTKLT4_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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000227036.8]
WARNING, no entry stored in dbm for [ENSG00000227036.8]
ls: cannot access 'IGV_inputs': No such file or directory