Done.
-parsing GTF file: /tmp/nxf.gXp9MDBVBB/tih_rna_sample_00652_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.gXp9MDBVBB/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.gXp9MDBVBB/tih_rna_sample_00652_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.gXp9MDBVBB/tih_rna_sample_00652_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.gXp9MDBVBB/fi_workdir/tih_rna_sample_00652_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.gXp9MDBVBB/fi_workdir/tih_rna_sample_00652_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00652_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00652_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:45:16 : INFO : Done.
-parsing GTF file: /tmp/nxf.gXp9MDBVBB/fi_workdir/tih_rna_sample_00652_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.gXp9MDBVBB/fi_workdir/tih_rna_sample_00652_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[670000]   -done parsing /tmp/nxf.gXp9MDBVBB/fi_workdir/tih_rna_sample_00652_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'low complexity anchor region' => 7,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 30,
          'exons hit < 2' => 1,
          'seq-similar region overlap' => 38,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          ' ** passed ** ' => 3873,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 7,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 14,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 196,
          'per_id < 96' => 2126,
          'small anchor length' => 19,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 34,
          'num genes matched < 2' => 6,
          'excessive soft clipping' => 5167
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.gXp9MDBVBB/fi_workdir/tih_rna_sample_00652_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[17000]   -fusion SPANNING read extraction for scaff: AC012174.1--TTLL5

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[18000]   -fusion SPANNING read extraction for scaff: AGAP14P--FRMPD2

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[24000]   -fusion SPANNING read extraction for scaff: CUL3--UNC80

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[38000]   
[39000]   -fusion SPANNING read extraction for scaff: FAM13A--TMEM65

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[37000]   
[38000]   -fusion SPANNING read extraction for scaff: FAM13A--TRMT12

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[124000]   -fusion SPANNING read extraction for scaff: KIAA1217--RET

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[11000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[10000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[13000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[12000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

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[11000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

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[14000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[5000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[5000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[154000]   -fusion SPANNING read extraction for scaff: PDLIM5--KIAA1217

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[8000]   -fusion SPANNING read extraction for scaff: RRM2B--BMPR1B

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[15000]   -fusion SPANNING read extraction for scaff: SLC30A9--RASSF6

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[17000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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

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[17000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 2729,
          'seq similar region alignment' => 26570
        };
EM: Starting log likelihood: -2427.915482
EM: Round [1] log likelihood: -2427.707599
EM: Round [2] log likelihood: -2427.541445
EM: Round [3] log likelihood: -2427.399892
EM: Round [4] log likelihood: -2427.277660
EM: Round [5] log likelihood: -2427.171030
EM: Round [6] log likelihood: -2427.077266
EM: Round [7] log likelihood: -2426.994306
EM: Round [8] log likelihood: -2426.920551
EM: Round [9] log likelihood: -2426.854731
EM: Round [10] log likelihood: -2426.795814
EM: Round [11] log likelihood: -2426.742944
EM: Round [12] log likelihood: -2426.695398
EM: Round [13] log likelihood: -2426.652560
EM: Round [14] log likelihood: -2426.613893
EM: Round [15] log likelihood: -2426.578931
EM: Round [16] log likelihood: -2426.547266
EM: Round [17] log likelihood: -2426.518535
EM: Round [18] log likelihood: -2426.492420
EM: Round [19] log likelihood: -2426.468639
EM: Round [20] log likelihood: -2426.446940
EM: Round [21] log likelihood: -2426.427103
EM: Round [22] log likelihood: -2426.408930
EM: Round [23] log likelihood: -2426.392246
EM: Round [24] log likelihood: -2426.376896
EM: Round [25] log likelihood: -2426.362744
EM: Round [26] log likelihood: -2426.349667
EM: Round [27] log likelihood: -2426.337557
EM: Round [28] log likelihood: -2426.326319
EM: Round [29] log likelihood: -2426.315868
EM: Round [30] log likelihood: -2426.306129
EM: Round [31] log likelihood: -2426.297035
EM: Round [32] log likelihood: -2426.288527
EM: Round [33] log likelihood: -2426.280552
EM: Round [34] log likelihood: -2426.273064
EM: Round [35] log likelihood: -2426.266021
EM: Round [36] log likelihood: -2426.259385
EM: Round [37] log likelihood: -2426.253125
EM: Round [38] log likelihood: -2426.247210
EM: Round [39] log likelihood: -2426.241614
EM: Round [40] log likelihood: -2426.236313
EM: Round [41] log likelihood: -2426.231286
EM: Round [42] log likelihood: -2426.226513
EM: Round [43] log likelihood: -2426.221978
EM: Round [44] log likelihood: -2426.217664
EM: Round [45] log likelihood: -2426.213557
EM: Round [46] log likelihood: -2426.209644
EM: Round [47] log likelihood: -2426.205914
EM: Round [48] log likelihood: -2426.202355
EM: Round [49] log likelihood: -2426.198958
EM: Round [50] log likelihood: -2426.195713
EM: Round [51] log likelihood: -2426.192612
EM: Round [52] log likelihood: -2426.189648
EM: Round [53] log likelihood: -2426.186813
EM: Round [54] log likelihood: -2426.184100
EM: Round [55] log likelihood: -2426.181503
EM: Round [56] log likelihood: -2426.179017
EM: Round [57] log likelihood: -2426.176636
EM: Round [58] log likelihood: -2426.174355
EM: Round [59] log likelihood: -2426.172170
EM: Round [60] log likelihood: -2426.170075
EM: Round [61] log likelihood: -2426.168066
EM: Round [62] log likelihood: -2426.166141
EM: Round [63] log likelihood: -2426.164294
EM: Round [64] log likelihood: -2426.162523
EM: Round [65] log likelihood: -2426.160824
EM: Round [66] log likelihood: -2426.159194
EM: Round [67] log likelihood: -2426.157629
EM: Round [68] log likelihood: -2426.156128
EM: Round [69] log likelihood: -2426.154687
EM: Round [70] log likelihood: -2426.153304
EM: Round [71] log likelihood: -2426.151977
EM: Round [72] log likelihood: -2426.150702
EM: Round [73] log likelihood: -2426.149478
EM: Round [74] log likelihood: -2426.148303
EM: Round [75] log likelihood: -2426.147175
EM: Round [76] log likelihood: -2426.146091
EM: Round [77] log likelihood: -2426.145051
EM: Round [78] log likelihood: -2426.144051
EM: Round [79] log likelihood: -2426.143091
EM: Round [80] log likelihood: -2426.142169
EM: Round [81] log likelihood: -2426.141283
EM: Round [82] log likelihood: -2426.140433
EM: Round [83] log likelihood: -2426.139615
EM: Round [84] log likelihood: -2426.138830
EM: Round [85] log likelihood: -2426.138075
EM: Round [86] log likelihood: -2426.137350
EM: Round [87] log likelihood: -2426.136654
EM: Round [88] log likelihood: -2426.135985
EM: Round [89] log likelihood: -2426.135342
EM: Round [90] log likelihood: -2426.134724
EM: Round [91] log likelihood: -2426.134130
EM: Round [92] log likelihood: -2426.133559
EM: Round [93] log likelihood: -2426.133011
EM: Round [94] log likelihood: -2426.132484
EM: Round [95] log likelihood: -2426.131978
EM: Round [96] log likelihood: -2426.131491
EM: Round [97] log likelihood: -2426.131023
EM: Round [98] log likelihood: -2426.130574
EM: Round [99] log likelihood: -2426.130142
EM: Round [100] log likelihood: -2426.129726
EM: Round [101] log likelihood: -2426.129327
EM: Round [102] log likelihood: -2426.128944
EM: Round [103] log likelihood: -2426.128575
EM: Round [104] log likelihood: -2426.128220
EM: Round [105] log likelihood: -2426.127880
EM: Round [106] log likelihood: -2426.127552
EM: Round [107] log likelihood: -2426.127238
EM: Round [108] log likelihood: -2426.126935
EM: Round [109] log likelihood: -2426.126644
EM: Round [110] log likelihood: -2426.126365
EM: Round [111] log likelihood: -2426.126096
EM: Round [112] log likelihood: -2426.125838
EM: Round [113] log likelihood: -2426.125589
EM: Round [114] log likelihood: -2426.125350
EM: Round [115] log likelihood: -2426.125121
EM: Round [116] log likelihood: -2426.124900
EM: Round [117] log likelihood: -2426.124688
EM: Round [118] log likelihood: -2426.124484
EM: Round [119] log likelihood: -2426.124288
EM: Round [120] log likelihood: -2426.124100
EM: Round [121] log likelihood: -2426.123919
EM: Round [122] log likelihood: -2426.123745
EM: Round [123] log likelihood: -2426.123577
EM: Round [124] log likelihood: -2426.123416
EM: Round [125] log likelihood: -2426.123262
EM: Round [126] log likelihood: -2426.123113
EM: Round [127] log likelihood: -2426.122970
EM: Round [128] log likelihood: -2426.122832
EM: Round [129] log likelihood: -2426.122700
EM: Round [130] log likelihood: -2426.122573
EM: Round [131] log likelihood: -2426.122451
EM: Round [132] log likelihood: -2426.122333
EM: Round [133] log likelihood: -2426.122220
EM: Round [134] log likelihood: -2426.122112
EM: Round [135] log likelihood: -2426.122007
EM: Round [136] log likelihood: -2426.121907
EM: Round [137] log likelihood: -2426.121810
EM: Stopping iterations at round 137 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.gXp9MDBVBB/tih_rna_sample_00652_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.gXp9MDBVBB/tih_rna_sample_00652_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.gXp9MDBVBB/tih_rna_sample_00652_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.gXp9MDBVBB/tih_rna_sample_00652_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.gXp9MDBVBB/tih_rna_sample_00652_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.gXp9MDBVBB/tih_rna_sample_00652_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.gXp9MDBVBB/tih_rna_sample_00652_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.gXp9MDBVBB/fi_workdir/tih_rna_sample_00652_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.gXp9MDBVBB/fi_workdir/tih_rna_sample_00652_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.gXp9MDBVBB/fi_workdir/tih_rna_sample_00652_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.gXp9MDBVBB/tih_rna_sample_00652_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.gXp9MDBVBB/tih_rna_sample_00652_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2026.099102
EM: Round [1] log likelihood: -2026.089288
EM: Round [2] log likelihood: -2026.089208
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.gXp9MDBVBB/tih_rna_sample_00652_B23MVV7LT4_1_1.fastp.fastq.gz: 295852739
Warning - not locating file: /tmp/nxf.gXp9MDBVBB/tih_rna_sample_00652_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000279058.2]
WARNING, no entry stored in dbm for [ENSG00000279058.2]
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 [ENSG00000260115.1]
ls: cannot access 'IGV_inputs': No such file or directory