Done.
-parsing GTF file: /tmp/nxf.Oac3XwDIj7/tih_rna_sample_00451_B23WHTKLT4_2.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.Oac3XwDIj7/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.Oac3XwDIj7/tih_rna_sample_00451_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.Oac3XwDIj7/tih_rna_sample_00451_B23WHTKLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.Oac3XwDIj7/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.Oac3XwDIj7/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00451_B23WHTKLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00451_B23WHTKLT4_2.star.sortedByCoord.out.bam
09:48:31 : INFO : Done.
-parsing GTF file: /tmp/nxf.Oac3XwDIj7/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_2.gtf
-parsing /tmp/nxf.Oac3XwDIj7/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_2.star.cSorted.dupsMarked.bam

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[580000]   -done parsing /tmp/nxf.Oac3XwDIj7/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'seq-similar region overlap' => 509,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'per_id < 96' => 2330,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 27,
          'num genes matched < 2' => 1,
          'excessive soft clipping' => 3753,
          'low complexity anchor region' => 14,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 39,
          ' ** passed ** ' => 4210,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 18,
          'small anchor length' => 14,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 9,
          'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 50
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.Oac3XwDIj7/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[41000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[33000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[37000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[43000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13

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[47000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1

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[39000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2

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[47000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

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[51000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[43000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[12000]   -fusion SPANNING read extraction for scaff: PTPN20--BMS1P7

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[97000]   -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408

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[39000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[23000]   -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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[11000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 968,
          'seq similar region alignment' => 29639
        };
EM: Starting log likelihood: -3569.073662
EM: Round [1] log likelihood: -3568.523735
EM: Round [2] log likelihood: -3568.217449
EM: Round [3] log likelihood: -3567.953950
EM: Round [4] log likelihood: -3567.726043
EM: Round [5] log likelihood: -3567.528112
EM: Round [6] log likelihood: -3567.355618
EM: Round [7] log likelihood: -3567.204849
EM: Round [8] log likelihood: -3567.072735
EM: Round [9] log likelihood: -3566.956716
EM: Round [10] log likelihood: -3566.854641
EM: Round [11] log likelihood: -3566.764687
EM: Round [12] log likelihood: -3566.685302
EM: Round [13] log likelihood: -3566.615158
EM: Round [14] log likelihood: -3566.553112
EM: Round [15] log likelihood: -3566.498176
EM: Round [16] log likelihood: -3566.449496
EM: Round [17] log likelihood: -3566.406327
EM: Round [18] log likelihood: -3566.368020
EM: Round [19] log likelihood: -3566.334009
EM: Round [20] log likelihood: -3566.303796
EM: Round [21] log likelihood: -3566.276946
EM: Round [22] log likelihood: -3566.253074
EM: Round [23] log likelihood: -3566.231842
EM: Round [24] log likelihood: -3566.212954
EM: Round [25] log likelihood: -3566.196145
EM: Round [26] log likelihood: -3566.181182
EM: Round [27] log likelihood: -3566.167861
EM: Round [28] log likelihood: -3566.155999
EM: Round [29] log likelihood: -3566.145434
EM: Round [30] log likelihood: -3566.136023
EM: Round [31] log likelihood: -3566.127639
EM: Round [32] log likelihood: -3566.120168
EM: Round [33] log likelihood: -3566.113511
EM: Round [34] log likelihood: -3566.107578
EM: Round [35] log likelihood: -3566.102291
EM: Round [36] log likelihood: -3566.097578
EM: Round [37] log likelihood: -3566.093377
EM: Round [38] log likelihood: -3566.089631
EM: Round [39] log likelihood: -3566.086293
EM: Round [40] log likelihood: -3566.083316
EM: Round [41] log likelihood: -3566.080662
EM: Round [42] log likelihood: -3566.078296
EM: Round [43] log likelihood: -3566.076186
EM: Round [44] log likelihood: -3566.074305
EM: Round [45] log likelihood: -3566.072627
EM: Round [46] log likelihood: -3566.071131
EM: Round [47] log likelihood: -3566.069797
EM: Round [48] log likelihood: -3566.068608
EM: Round [49] log likelihood: -3566.067547
EM: Round [50] log likelihood: -3566.066601
EM: Round [51] log likelihood: -3566.065757
EM: Round [52] log likelihood: -3566.065005
EM: Round [53] log likelihood: -3566.064334
EM: Round [54] log likelihood: -3566.063736
EM: Round [55] log likelihood: -3566.063202
EM: Round [56] log likelihood: -3566.062726
EM: Round [57] log likelihood: -3566.062302
EM: Round [58] log likelihood: -3566.061923
EM: Round [59] log likelihood: -3566.061585
EM: Round [60] log likelihood: -3566.061284
EM: Round [61] log likelihood: -3566.061016
EM: Round [62] log likelihood: -3566.060776
EM: Round [63] log likelihood: -3566.060563
EM: Round [64] log likelihood: -3566.060372
EM: Round [65] log likelihood: -3566.060202
EM: Round [66] log likelihood: -3566.060051
EM: Round [67] log likelihood: -3566.059916
EM: Round [68] log likelihood: -3566.059795
EM: Round [69] log likelihood: -3566.059688
EM: Round [70] log likelihood: -3566.059592
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.Oac3XwDIj7/tih_rna_sample_00451_B23WHTKLT4_2.consolidated.bam into /tmp/nxf.Oac3XwDIj7/tih_rna_sample_00451_B23WHTKLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.Oac3XwDIj7/tih_rna_sample_00451_B23WHTKLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Oac3XwDIj7/tih_rna_sample_00451_B23WHTKLT4_2.consolidated.bam.read_coords > /tmp/nxf.Oac3XwDIj7/tih_rna_sample_00451_B23WHTKLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Oac3XwDIj7/tih_rna_sample_00451_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.Oac3XwDIj7/tih_rna_sample_00451_B23WHTKLT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Oac3XwDIj7/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_2.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.Oac3XwDIj7/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_2.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.Oac3XwDIj7/fi_workdir/tih_rna_sample_00451_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Oac3XwDIj7/tih_rna_sample_00451_B23WHTKLT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.Oac3XwDIj7/tih_rna_sample_00451_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2209.369475
EM: Round [1] log likelihood: -2209.363222
EM: Round [2] log likelihood: -2209.363198
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.Oac3XwDIj7/tih_rna_sample_00451_B23WHTKLT4_2_1.fastp.fastq.gz: 172562915
Warning - not locating file: /tmp/nxf.Oac3XwDIj7/tih_rna_sample_00451_B23WHTKLT4_2.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
ls: cannot access 'IGV_inputs': No such file or directory