Done.
-parsing GTF file: /tmp/nxf.C5fLO8d1BZ/tih_rna_sample_00604_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.C5fLO8d1BZ/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.C5fLO8d1BZ/tih_rna_sample_00604_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.C5fLO8d1BZ/tih_rna_sample_00604_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.C5fLO8d1BZ/fi_workdir/tih_rna_sample_00604_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.C5fLO8d1BZ/fi_workdir/tih_rna_sample_00604_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00604_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00604_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:26:36 : INFO : Done.
-parsing GTF file: /tmp/nxf.C5fLO8d1BZ/fi_workdir/tih_rna_sample_00604_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.C5fLO8d1BZ/fi_workdir/tih_rna_sample_00604_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[870000]   -done parsing /tmp/nxf.C5fLO8d1BZ/fi_workdir/tih_rna_sample_00604_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'small anchor length' => 29,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 7,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 5,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 48,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 6,
          'num genes matched < 2' => 41,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 24,
          'per_id < 96' => 2009,
          'seq-similar region overlap' => 18,
          ' ** passed ** ' => 5093,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 121,
          'excessive soft clipping' => 3882
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.C5fLO8d1BZ/fi_workdir/tih_rna_sample_00604_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[11000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

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[17000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   -fusion SPANNING read extraction for scaff: ATG12--NSUN2

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[20000]   
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[27000]   
[28000]   -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B

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[6000]   
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[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   -fusion SPANNING read extraction for scaff: FARP2--ANO7

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[28000]   -fusion SPANNING read extraction for scaff: HS2ST1--COL24A1

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[11000]   -fusion SPANNING read extraction for scaff: HS2ST1--AL691520.1

[1000]   
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[4000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: MDM2--RERG

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[61000]   
[62000]   -fusion SPANNING read extraction for scaff: MON2--OLR1

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[120000]   
[121000]   
[122000]   
[123000]   -fusion SPANNING read extraction for scaff: NSUN2--KDM3B

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

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

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

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: PCDHA8--PCDHA13

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: PCDHA8--PCDHAC1

[1000]   
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[3000]   -fusion SPANNING read extraction for scaff: PCDHA8--PCDHAC2

[1000]   
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[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[9000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[23000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[13000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[41000]   
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[47000]   
[48000]   
[49000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[12000]   
[13000]   -fusion SPANNING read extraction for scaff: RAB40C--RBFOX1

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[8000]   -fusion SPANNING read extraction for scaff: RAB40C--CACNG2

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[55000]   
[56000]   -fusion SPANNING read extraction for scaff: RASA1--FAM53C

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[20000]   
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[23000]   
[24000]   -fusion SPANNING read extraction for scaff: SELENOF--AL033530.1

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[21000]   
[22000]   -fusion SPANNING read extraction for scaff: SNORC--NGEF

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[86000]   
[87000]   
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[102000]   
[103000]   
[104000]   
[105000]   
[106000]   
[107000]   
[108000]   
[109000]   
[110000]   
[111000]   
[112000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[8000]   
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[11000]   
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[18000]   
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[20000]   
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[23000]   
[24000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[5000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[18000]   
[19000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 21443,
          'lacks exon overlap' => 10233
        };
EM: Starting log likelihood: -5839.430402
EM: Round [1] log likelihood: -5835.677788
EM: Round [2] log likelihood: -5835.644089
EM: Round [3] log likelihood: -5835.622612
EM: Round [4] log likelihood: -5835.602758
EM: Round [5] log likelihood: -5835.584363
EM: Round [6] log likelihood: -5835.567296
EM: Round [7] log likelihood: -5835.551439
EM: Round [8] log likelihood: -5835.536691
EM: Round [9] log likelihood: -5835.522959
EM: Round [10] log likelihood: -5835.510161
EM: Round [11] log likelihood: -5835.498223
EM: Round [12] log likelihood: -5835.487077
EM: Round [13] log likelihood: -5835.476663
EM: Round [14] log likelihood: -5835.466926
EM: Round [15] log likelihood: -5835.457817
EM: Round [16] log likelihood: -5835.449289
EM: Round [17] log likelihood: -5835.441301
EM: Round [18] log likelihood: -5835.433815
EM: Round [19] log likelihood: -5835.426796
EM: Round [20] log likelihood: -5835.420212
EM: Round [21] log likelihood: -5835.414033
EM: Round [22] log likelihood: -5835.408233
EM: Round [23] log likelihood: -5835.402785
EM: Round [24] log likelihood: -5835.397667
EM: Round [25] log likelihood: -5835.392857
EM: Round [26] log likelihood: -5835.388336
EM: Round [27] log likelihood: -5835.384085
EM: Round [28] log likelihood: -5835.380086
EM: Round [29] log likelihood: -5835.376324
EM: Round [30] log likelihood: -5835.372784
EM: Round [31] log likelihood: -5835.369452
EM: Round [32] log likelihood: -5835.366315
EM: Round [33] log likelihood: -5835.363362
EM: Round [34] log likelihood: -5835.360581
EM: Round [35] log likelihood: -5835.357961
EM: Round [36] log likelihood: -5835.355493
EM: Round [37] log likelihood: -5835.353168
EM: Round [38] log likelihood: -5835.350977
EM: Round [39] log likelihood: -5835.348912
EM: Round [40] log likelihood: -5835.346966
EM: Round [41] log likelihood: -5835.345131
EM: Round [42] log likelihood: -5835.343402
EM: Round [43] log likelihood: -5835.341771
EM: Round [44] log likelihood: -5835.340233
EM: Round [45] log likelihood: -5835.338783
EM: Round [46] log likelihood: -5835.337415
EM: Round [47] log likelihood: -5835.336125
EM: Round [48] log likelihood: -5835.334908
EM: Round [49] log likelihood: -5835.333760
EM: Round [50] log likelihood: -5835.332677
EM: Round [51] log likelihood: -5835.331656
EM: Round [52] log likelihood: -5835.330692
EM: Round [53] log likelihood: -5835.329782
EM: Round [54] log likelihood: -5835.328924
EM: Round [55] log likelihood: -5835.328114
EM: Round [56] log likelihood: -5835.327350
EM: Round [57] log likelihood: -5835.326629
EM: Round [58] log likelihood: -5835.325948
EM: Round [59] log likelihood: -5835.325305
EM: Round [60] log likelihood: -5835.324699
EM: Round [61] log likelihood: -5835.324127
EM: Round [62] log likelihood: -5835.323586
EM: Round [63] log likelihood: -5835.323076
EM: Round [64] log likelihood: -5835.322595
EM: Round [65] log likelihood: -5835.322140
EM: Round [66] log likelihood: -5835.321711
EM: Round [67] log likelihood: -5835.321306
EM: Round [68] log likelihood: -5835.320924
EM: Round [69] log likelihood: -5835.320563
EM: Round [70] log likelihood: -5835.320222
EM: Round [71] log likelihood: -5835.319900
EM: Round [72] log likelihood: -5835.319596
EM: Round [73] log likelihood: -5835.319310
EM: Round [74] log likelihood: -5835.319039
EM: Round [75] log likelihood: -5835.318783
EM: Round [76] log likelihood: -5835.318542
EM: Round [77] log likelihood: -5835.318314
EM: Round [78] log likelihood: -5835.318098
EM: Round [79] log likelihood: -5835.317895
EM: Round [80] log likelihood: -5835.317703
EM: Round [81] log likelihood: -5835.317522
EM: Round [82] log likelihood: -5835.317351
EM: Round [83] log likelihood: -5835.317189
EM: Round [84] log likelihood: -5835.317036
EM: Round [85] log likelihood: -5835.316892
EM: Round [86] log likelihood: -5835.316756
EM: Round [87] log likelihood: -5835.316628
EM: Round [88] log likelihood: -5835.316506
EM: Round [89] log likelihood: -5835.316392
EM: Round [90] log likelihood: -5835.316284
EM: Round [91] log likelihood: -5835.316181
EM: Round [92] log likelihood: -5835.316085
EM: Stopping iterations at round 92 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.C5fLO8d1BZ/tih_rna_sample_00604_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.C5fLO8d1BZ/tih_rna_sample_00604_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.C5fLO8d1BZ/tih_rna_sample_00604_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.C5fLO8d1BZ/tih_rna_sample_00604_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.C5fLO8d1BZ/tih_rna_sample_00604_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.C5fLO8d1BZ/tih_rna_sample_00604_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.C5fLO8d1BZ/tih_rna_sample_00604_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.C5fLO8d1BZ/fi_workdir/tih_rna_sample_00604_B23MVV7LT4_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.C5fLO8d1BZ/fi_workdir/tih_rna_sample_00604_B23MVV7LT4_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.C5fLO8d1BZ/fi_workdir/tih_rna_sample_00604_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.C5fLO8d1BZ/tih_rna_sample_00604_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.C5fLO8d1BZ/tih_rna_sample_00604_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -5527.902564
EM: Round [1] log likelihood: -5526.344345
EM: Round [2] log likelihood: -5526.340643
EM: Round [3] log likelihood: -5526.340634
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.C5fLO8d1BZ/tih_rna_sample_00604_B23MVV7LT4_1_1.fastp.fastq.gz: 296342511
Warning - not locating file: /tmp/nxf.C5fLO8d1BZ/tih_rna_sample_00604_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000285407.1]
WARNING, no entry stored in dbm for [ENSG00000285407.1]
WARNING, no entry stored in dbm for [ENSG00000285407.1]
WARNING, no entry stored in dbm for [ENSG00000285407.1]
WARNING, no entry stored in dbm for [ENSG00000285407.1]
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]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
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]
WARNING, no entry stored in dbm for [ENSG00000285473.1]
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 [ENSG00000242193.11]
ls: cannot access 'IGV_inputs': No such file or directory