Done.
-parsing GTF file: /tmp/nxf.K3w4JnSYAS/tih_rna_sample_00636_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.K3w4JnSYAS/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.K3w4JnSYAS/tih_rna_sample_00636_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.K3w4JnSYAS/tih_rna_sample_00636_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.K3w4JnSYAS/fi_workdir/tih_rna_sample_00636_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.K3w4JnSYAS/fi_workdir/tih_rna_sample_00636_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00636_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00636_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:57:45 : INFO : Done.
-parsing GTF file: /tmp/nxf.K3w4JnSYAS/fi_workdir/tih_rna_sample_00636_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.K3w4JnSYAS/fi_workdir/tih_rna_sample_00636_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[830000]   -done parsing /tmp/nxf.K3w4JnSYAS/fi_workdir/tih_rna_sample_00636_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 10,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 51,
          'small anchor length' => 1,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
          'exons hit < 2' => 1,
          ' ** passed ** ' => 7245,
          'excessive soft clipping' => 4374,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 29,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 248,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 9,
          'per_id < 96' => 2096,
          'low complexity anchor region' => 3,
          'num genes matched < 2' => 12,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 30,
          'seq-similar region overlap' => 114
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.K3w4JnSYAS/fi_workdir/tih_rna_sample_00636_B23MVV7LT4_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: AC079781.4--ASNS

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[9000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[92000]   -fusion SPANNING read extraction for scaff: ARHGEF35-AS1--ARHGEF35

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[168000]   
[169000]   -fusion SPANNING read extraction for scaff: FOXP1--ITPR1

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[19000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1

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[19000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2

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[23000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13

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[17000]   -fusion SPANNING read extraction for scaff: PCDHA5--PCDHAC1

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[17000]   -fusion SPANNING read extraction for scaff: PCDHA5--PCDHAC2

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[21000]   -fusion SPANNING read extraction for scaff: PCDHA5--PCDHA13

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8

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

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5

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[7000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4

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[41000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9

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[88000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[27000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[28000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

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[6000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[92000]   -fusion SPANNING read extraction for scaff: TPRA1--FOXP1

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[23000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 10808,
          'seq similar region alignment' => 20349
        };
EM: Starting log likelihood: -4089.845449
EM: Round [1] log likelihood: -4087.765484
EM: Round [2] log likelihood: -4086.875296
EM: Round [3] log likelihood: -4086.177311
EM: Round [4] log likelihood: -4085.603521
EM: Round [5] log likelihood: -4085.125987
EM: Round [6] log likelihood: -4084.726649
EM: Round [7] log likelihood: -4084.391684
EM: Round [8] log likelihood: -4084.110013
EM: Round [9] log likelihood: -4083.872629
EM: Round [10] log likelihood: -4083.672159
EM: Round [11] log likelihood: -4083.502542
EM: Round [12] log likelihood: -4083.358774
EM: Round [13] log likelihood: -4083.236710
EM: Round [14] log likelihood: -4083.132909
EM: Round [15] log likelihood: -4083.044504
EM: Round [16] log likelihood: -4082.969102
EM: Round [17] log likelihood: -4082.904701
EM: Round [18] log likelihood: -4082.849621
EM: Round [19] log likelihood: -4082.802453
EM: Round [20] log likelihood: -4082.762009
EM: Round [21] log likelihood: -4082.727290
EM: Round [22] log likelihood: -4082.697450
EM: Round [23] log likelihood: -4082.671775
EM: Round [24] log likelihood: -4082.649660
EM: Round [25] log likelihood: -4082.630591
EM: Round [26] log likelihood: -4082.614132
EM: Round [27] log likelihood: -4082.599912
EM: Round [28] log likelihood: -4082.587615
EM: Round [29] log likelihood: -4082.576971
EM: Round [30] log likelihood: -4082.567750
EM: Round [31] log likelihood: -4082.559756
EM: Round [32] log likelihood: -4082.552819
EM: Round [33] log likelihood: -4082.546796
EM: Round [34] log likelihood: -4082.541561
EM: Round [35] log likelihood: -4082.537009
EM: Round [36] log likelihood: -4082.533048
EM: Round [37] log likelihood: -4082.529599
EM: Round [38] log likelihood: -4082.526594
EM: Round [39] log likelihood: -4082.523974
EM: Round [40] log likelihood: -4082.521689
EM: Round [41] log likelihood: -4082.519694
EM: Round [42] log likelihood: -4082.517952
EM: Round [43] log likelihood: -4082.516431
EM: Round [44] log likelihood: -4082.515100
EM: Round [45] log likelihood: -4082.513937
EM: Round [46] log likelihood: -4082.512920
EM: Round [47] log likelihood: -4082.512029
EM: Round [48] log likelihood: -4082.511249
EM: Round [49] log likelihood: -4082.510565
EM: Round [50] log likelihood: -4082.509967
EM: Round [51] log likelihood: -4082.509442
EM: Round [52] log likelihood: -4082.508981
EM: Round [53] log likelihood: -4082.508577
EM: Round [54] log likelihood: -4082.508222
EM: Round [55] log likelihood: -4082.507910
EM: Round [56] log likelihood: -4082.507637
EM: Round [57] log likelihood: -4082.507396
EM: Round [58] log likelihood: -4082.507184
EM: Round [59] log likelihood: -4082.506998
EM: Round [60] log likelihood: -4082.506834
EM: Round [61] log likelihood: -4082.506690
EM: Round [62] log likelihood: -4082.506562
EM: Round [63] log likelihood: -4082.506450
EM: Round [64] log likelihood: -4082.506351
EM: Stopping iterations at round 64 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.K3w4JnSYAS/tih_rna_sample_00636_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.K3w4JnSYAS/tih_rna_sample_00636_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.K3w4JnSYAS/tih_rna_sample_00636_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.K3w4JnSYAS/tih_rna_sample_00636_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.K3w4JnSYAS/tih_rna_sample_00636_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.K3w4JnSYAS/tih_rna_sample_00636_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.K3w4JnSYAS/tih_rna_sample_00636_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.K3w4JnSYAS/fi_workdir/tih_rna_sample_00636_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.K3w4JnSYAS/fi_workdir/tih_rna_sample_00636_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.K3w4JnSYAS/fi_workdir/tih_rna_sample_00636_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.K3w4JnSYAS/tih_rna_sample_00636_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.K3w4JnSYAS/tih_rna_sample_00636_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3481.463000
EM: Round [1] log likelihood: -3481.057729
EM: Round [2] log likelihood: -3481.057420
EM: Round [3] log likelihood: -3481.057419
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.K3w4JnSYAS/tih_rna_sample_00636_B23MVV7LT4_1_1.fastp.fastq.gz: 278298367
Warning - not locating file: /tmp/nxf.K3w4JnSYAS/tih_rna_sample_00636_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000244198.7]
WARNING, no entry stored in dbm for [ENSG00000244198.7]
WARNING, no entry stored in dbm for [ENSG00000244198.7]
ls: cannot access 'IGV_inputs': No such file or directory