Done.
-parsing GTF file: /tmp/nxf.wWZEvZazNS/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.wWZEvZazNS/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.wWZEvZazNS/659_bGW-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.wWZEvZazNS/659_bGW-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.wWZEvZazNS/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.wWZEvZazNS/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
11:58:28 : INFO : Done.
-parsing GTF file: /tmp/nxf.wWZEvZazNS/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.wWZEvZazNS/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

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[2140000]   -done parsing /tmp/nxf.wWZEvZazNS/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'per_id < 96' => 11107,
          'low complexity anchor region' => 3,
          'exons hit < 2' => 53,
          'small anchor length' => 6,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 14,
          ' ** passed ** ' => 5098,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 5,
          'num genes matched < 2' => 157,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 36,
          'seq-similar region overlap' => 29,
          'excessive soft clipping' => 11690,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 149
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.wWZEvZazNS/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[23000]   -fusion SPANNING read extraction for scaff: ANKRD24--KEAP1

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[115000]   -fusion SPANNING read extraction for scaff: BORCS5--LIMA1

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[25000]   -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B

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[59000]   -fusion SPANNING read extraction for scaff: DIP2B--PTRHD1

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[492000]   -fusion SPANNING read extraction for scaff: DLG5--KCNMA1

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[108000]   -fusion SPANNING read extraction for scaff: GPRC5A--RFC1

[1000]   
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[4000]   
[5000]   -fusion SPANNING read extraction for scaff: GTF2A1L--STON1-GTF2A1L

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[97000]   
[98000]   -fusion SPANNING read extraction for scaff: JMJD1C--LINC00841

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[97000]   
[98000]   -fusion SPANNING read extraction for scaff: JMJD1C--AL137026.2

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[114000]   
[115000]   
[116000]   -fusion SPANNING read extraction for scaff: MRPS6--RUNX1

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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: NDUFA9--C12orf4

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[27000]   
[28000]   
[29000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
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[6000]   
[7000]   
[8000]   
[9000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

[1000]   
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[8000]   
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[53000]   
[54000]   -fusion SPANNING read extraction for scaff: PKP2--ASS1P14

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[73000]   
[74000]   -fusion SPANNING read extraction for scaff: POLR2E--KEAP1

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[130000]   
[131000]   -fusion SPANNING read extraction for scaff: PTPRK--RSPO3

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[107000]   
[108000]   -fusion SPANNING read extraction for scaff: RFC1--GPRC5A

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[132000]   
[133000]   -fusion SPANNING read extraction for scaff: SLC5A3--RUNX1

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[61000]   
[62000]   -fusion SPANNING read extraction for scaff: SULT1B1--TBC1D1

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[12000]   
[13000]   -fusion SPANNING read extraction for scaff: SULT1B1--AC098680.2

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[184000]   -fusion SPANNING read extraction for scaff: TYK2--SBNO2

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[63000]   -fusion SPANNING read extraction for scaff: WDR19--ATP8A1
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 23028,
          'seq similar region alignment' => 23004
        };
EM: Starting log likelihood: -2937.921463
EM: Round [1] log likelihood: -2933.674342
EM: Round [2] log likelihood: -2933.501213
EM: Round [3] log likelihood: -2933.391085
EM: Round [4] log likelihood: -2933.293244
EM: Round [5] log likelihood: -2933.205778
EM: Round [6] log likelihood: -2933.127397
EM: Round [7] log likelihood: -2933.057012
EM: Round [8] log likelihood: -2932.993694
EM: Round [9] log likelihood: -2932.936645
EM: Round [10] log likelihood: -2932.885172
EM: Round [11] log likelihood: -2932.838675
EM: Round [12] log likelihood: -2932.796628
EM: Round [13] log likelihood: -2932.758567
EM: Round [14] log likelihood: -2932.724086
EM: Round [15] log likelihood: -2932.692824
EM: Round [16] log likelihood: -2932.664461
EM: Round [17] log likelihood: -2932.638710
EM: Round [18] log likelihood: -2932.615320
EM: Round [19] log likelihood: -2932.594061
EM: Round [20] log likelihood: -2932.574730
EM: Round [21] log likelihood: -2932.557145
EM: Round [22] log likelihood: -2932.541141
EM: Round [23] log likelihood: -2932.526571
EM: Round [24] log likelihood: -2932.513302
EM: Round [25] log likelihood: -2932.501213
EM: Round [26] log likelihood: -2932.490197
EM: Round [27] log likelihood: -2932.480154
EM: Round [28] log likelihood: -2932.470997
EM: Round [29] log likelihood: -2932.462645
EM: Round [30] log likelihood: -2932.455026
EM: Round [31] log likelihood: -2932.448074
EM: Round [32] log likelihood: -2932.441729
EM: Round [33] log likelihood: -2932.435936
EM: Round [34] log likelihood: -2932.430647
EM: Round [35] log likelihood: -2932.425817
EM: Round [36] log likelihood: -2932.421406
EM: Round [37] log likelihood: -2932.417375
EM: Round [38] log likelihood: -2932.413692
EM: Round [39] log likelihood: -2932.410327
EM: Round [40] log likelihood: -2932.407251
EM: Round [41] log likelihood: -2932.404439
EM: Round [42] log likelihood: -2932.401868
EM: Round [43] log likelihood: -2932.399516
EM: Round [44] log likelihood: -2932.397366
EM: Round [45] log likelihood: -2932.395399
EM: Round [46] log likelihood: -2932.393600
EM: Round [47] log likelihood: -2932.391954
EM: Round [48] log likelihood: -2932.390448
EM: Round [49] log likelihood: -2932.389069
EM: Round [50] log likelihood: -2932.387807
EM: Round [51] log likelihood: -2932.386652
EM: Round [52] log likelihood: -2932.385595
EM: Round [53] log likelihood: -2932.384626
EM: Round [54] log likelihood: -2932.383740
EM: Round [55] log likelihood: -2932.382928
EM: Round [56] log likelihood: -2932.382184
EM: Round [57] log likelihood: -2932.381503
EM: Round [58] log likelihood: -2932.380878
EM: Round [59] log likelihood: -2932.380307
EM: Round [60] log likelihood: -2932.379782
EM: Round [61] log likelihood: -2932.379302
EM: Round [62] log likelihood: -2932.378862
EM: Round [63] log likelihood: -2932.378459
EM: Round [64] log likelihood: -2932.378089
EM: Round [65] log likelihood: -2932.377750
EM: Round [66] log likelihood: -2932.377439
EM: Round [67] log likelihood: -2932.377154
EM: Round [68] log likelihood: -2932.376893
EM: Round [69] log likelihood: -2932.376653
EM: Round [70] log likelihood: -2932.376433
EM: Round [71] log likelihood: -2932.376231
EM: Round [72] log likelihood: -2932.376046
EM: Round [73] log likelihood: -2932.375877
EM: Round [74] log likelihood: -2932.375721
EM: Round [75] log likelihood: -2932.375578
EM: Round [76] log likelihood: -2932.375447
EM: Round [77] log likelihood: -2932.375327
EM: Round [78] log likelihood: -2932.375216
EM: Round [79] log likelihood: -2932.375115
EM: Round [80] log likelihood: -2932.375022
EM: Stopping iterations at round 80 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.wWZEvZazNS/659_bGW-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.wWZEvZazNS/659_bGW-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.wWZEvZazNS/659_bGW-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.wWZEvZazNS/659_bGW-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.wWZEvZazNS/659_bGW-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.wWZEvZazNS/659_bGW-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.wWZEvZazNS/659_bGW-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.wWZEvZazNS/fi_workdir/659_bGW-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.wWZEvZazNS/fi_workdir/659_bGW-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.wWZEvZazNS/fi_workdir/659_bGW-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.wWZEvZazNS/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.wWZEvZazNS/659_bGW-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2634.090592
EM: Round [1] log likelihood: -2633.177333
EM: Round [2] log likelihood: -2633.177301
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.wWZEvZazNS/659_bGW-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295604466
Warning - not locating file: /tmp/nxf.wWZEvZazNS/659_bGW-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000068781.21]
WARNING, no entry stored in dbm for [ENSG00000068781.21]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
ls: cannot access 'IGV_inputs': No such file or directory