Done.
-parsing GTF file: /tmp/nxf.XlnH4YHSaN/659_bhK-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.XlnH4YHSaN/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.XlnH4YHSaN/659_bhK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.XlnH4YHSaN/659_bhK-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.XlnH4YHSaN/fi_workdir/659_bhK-T1-TRNA-1_B23MHV2LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.XlnH4YHSaN/fi_workdir/659_bhK-T1-TRNA-1_B23MHV2LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bhK-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bhK-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
11:22:59 : INFO : Done.
-parsing GTF file: /tmp/nxf.XlnH4YHSaN/fi_workdir/659_bhK-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.XlnH4YHSaN/fi_workdir/659_bhK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

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[550000]   -done parsing /tmp/nxf.XlnH4YHSaN/fi_workdir/659_bhK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'low complexity anchor region' => 1,
          'small anchor length' => 47,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 23,
          'excessive soft clipping' => 3666,
          'seq-similar region overlap' => 39,
          'per_id < 96' => 2736,
          ' ** passed ** ' => 5490,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 25,
          'num genes matched < 2' => 24,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.XlnH4YHSaN/fi_workdir/659_bhK-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[8000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[176000]   -fusion SPANNING read extraction for scaff: CCDC6--RET

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[10000]   -fusion SPANNING read extraction for scaff: DNAJC1--C10orf143

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[13000]   -fusion SPANNING read extraction for scaff: ECHS1--NEBL

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[3000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

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[7000]   -fusion SPANNING read extraction for scaff: NEBL--CDK1

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[7000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10

[1000]   
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[4000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6

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[5000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5

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[7000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11

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[7000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7

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[66000]   
[67000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3

[1000]   
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[6000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12

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[15000]   -fusion SPANNING read extraction for scaff: PMS2P5--CCDC146

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[25000]   -fusion SPANNING read extraction for scaff: PRSS27--TPSB2

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[66000]   
[67000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

[1000]   
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[24000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[24000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

[1000]   
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[4000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
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[17000]   -fusion SPANNING read extraction for scaff: TRIM59--IFT80

[1000]   
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[8000]   
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[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 2243,
          'seq similar region alignment' => 7629
        };
EM: Starting log likelihood: -4143.081468
EM: Round [1] log likelihood: -4136.797454
EM: Round [2] log likelihood: -4136.440193
EM: Round [3] log likelihood: -4136.152397
EM: Round [4] log likelihood: -4135.912829
EM: Round [5] log likelihood: -4135.712568
EM: Round [6] log likelihood: -4135.544527
EM: Round [7] log likelihood: -4135.403019
EM: Round [8] log likelihood: -4135.283448
EM: Round [9] log likelihood: -4135.182083
EM: Round [10] log likelihood: -4135.095880
EM: Round [11] log likelihood: -4135.022347
EM: Round [12] log likelihood: -4134.959433
EM: Round [13] log likelihood: -4134.905447
EM: Round [14] log likelihood: -4134.858991
EM: Round [15] log likelihood: -4134.818902
EM: Round [16] log likelihood: -4134.784214
EM: Round [17] log likelihood: -4134.754121
EM: Round [18] log likelihood: -4134.727946
EM: Round [19] log likelihood: -4134.705123
EM: Round [20] log likelihood: -4134.685175
EM: Round [21] log likelihood: -4134.667701
EM: Round [22] log likelihood: -4134.652359
EM: Round [23] log likelihood: -4134.638861
EM: Round [24] log likelihood: -4134.626962
EM: Round [25] log likelihood: -4134.616453
EM: Round [26] log likelihood: -4134.607155
EM: Round [27] log likelihood: -4134.598914
EM: Round [28] log likelihood: -4134.591598
EM: Round [29] log likelihood: -4134.585094
EM: Round [30] log likelihood: -4134.579304
EM: Round [31] log likelihood: -4134.574143
EM: Round [32] log likelihood: -4134.569537
EM: Round [33] log likelihood: -4134.565422
EM: Round [34] log likelihood: -4134.561741
EM: Round [35] log likelihood: -4134.558445
EM: Round [36] log likelihood: -4134.555492
EM: Round [37] log likelihood: -4134.552844
EM: Round [38] log likelihood: -4134.550467
EM: Round [39] log likelihood: -4134.548333
EM: Round [40] log likelihood: -4134.546414
EM: Round [41] log likelihood: -4134.544689
EM: Round [42] log likelihood: -4134.543137
EM: Round [43] log likelihood: -4134.541739
EM: Round [44] log likelihood: -4134.540481
EM: Round [45] log likelihood: -4134.539346
EM: Round [46] log likelihood: -4134.538324
EM: Round [47] log likelihood: -4134.537402
EM: Round [48] log likelihood: -4134.536571
EM: Round [49] log likelihood: -4134.535820
EM: Round [50] log likelihood: -4134.535143
EM: Round [51] log likelihood: -4134.534531
EM: Round [52] log likelihood: -4134.533978
EM: Round [53] log likelihood: -4134.533479
EM: Round [54] log likelihood: -4134.533027
EM: Round [55] log likelihood: -4134.532619
EM: Round [56] log likelihood: -4134.532250
EM: Round [57] log likelihood: -4134.531917
EM: Round [58] log likelihood: -4134.531614
EM: Round [59] log likelihood: -4134.531341
EM: Round [60] log likelihood: -4134.531094
EM: Round [61] log likelihood: -4134.530869
EM: Round [62] log likelihood: -4134.530666
EM: Round [63] log likelihood: -4134.530482
EM: Round [64] log likelihood: -4134.530315
EM: Round [65] log likelihood: -4134.530164
EM: Round [66] log likelihood: -4134.530027
EM: Round [67] log likelihood: -4134.529902
EM: Round [68] log likelihood: -4134.529789
EM: Round [69] log likelihood: -4134.529686
EM: Round [70] log likelihood: -4134.529592
EM: Stopping iterations at round 70 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.XlnH4YHSaN/659_bhK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.XlnH4YHSaN/659_bhK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.XlnH4YHSaN/659_bhK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.XlnH4YHSaN/659_bhK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.XlnH4YHSaN/659_bhK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.XlnH4YHSaN/659_bhK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.XlnH4YHSaN/659_bhK-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.XlnH4YHSaN/fi_workdir/659_bhK-T1-TRNA-1_B23MHV2LT4_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.XlnH4YHSaN/fi_workdir/659_bhK-T1-TRNA-1_B23MHV2LT4_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.XlnH4YHSaN/fi_workdir/659_bhK-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.XlnH4YHSaN/659_bhK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.XlnH4YHSaN/659_bhK-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3989.955327
EM: Round [1] log likelihood: -3988.815094
EM: Round [2] log likelihood: -3988.807019
EM: Round [3] log likelihood: -3988.806942
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.XlnH4YHSaN/659_bhK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295280014
Warning - not locating file: /tmp/nxf.XlnH4YHSaN/659_bhK-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000123965.13]
WARNING, no entry stored in dbm for [ENSG00000123965.13]
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 [ENSG00000280136.2]
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