Done.
-parsing GTF file: /tmp/nxf.vFikEdS7Kl/tih_rna_sample_00619_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.vFikEdS7Kl/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.vFikEdS7Kl/tih_rna_sample_00619_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.vFikEdS7Kl/tih_rna_sample_00619_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.vFikEdS7Kl/fi_workdir/tih_rna_sample_00619_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.vFikEdS7Kl/fi_workdir/tih_rna_sample_00619_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00619_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00619_B23MVV7LT4_1.star.sortedByCoord.out.bam
10:46:29 : INFO : Done.
-parsing GTF file: /tmp/nxf.vFikEdS7Kl/fi_workdir/tih_rna_sample_00619_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.vFikEdS7Kl/fi_workdir/tih_rna_sample_00619_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[140000]   -done parsing /tmp/nxf.vFikEdS7Kl/fi_workdir/tih_rna_sample_00619_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          ' ** passed ** ' => 1117,
          'seq-similar region overlap' => 295,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1,
          'per_id < 96' => 508,
          'num genes matched < 2' => 13,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 7,
          'excessive soft clipping' => 1768,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 17
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.vFikEdS7Kl/fi_workdir/tih_rna_sample_00619_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[14000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 296,
          'seq similar region alignment' => 13143
        };
EM: Starting log likelihood: -677.406070
EM: Round [1] log likelihood: -677.376483
EM: Round [2] log likelihood: -677.348231
EM: Round [3] log likelihood: -677.321237
EM: Round [4] log likelihood: -677.295430
EM: Round [5] log likelihood: -677.270744
EM: Round [6] log likelihood: -677.247115
EM: Round [7] log likelihood: -677.224488
EM: Round [8] log likelihood: -677.202810
EM: Round [9] log likelihood: -677.182031
EM: Round [10] log likelihood: -677.162105
EM: Round [11] log likelihood: -677.142989
EM: Round [12] log likelihood: -677.124644
EM: Round [13] log likelihood: -677.107030
EM: Round [14] log likelihood: -677.090114
EM: Round [15] log likelihood: -677.073861
EM: Round [16] log likelihood: -677.058242
EM: Round [17] log likelihood: -677.043226
EM: Round [18] log likelihood: -677.028786
EM: Round [19] log likelihood: -677.014896
EM: Round [20] log likelihood: -677.001531
EM: Round [21] log likelihood: -676.988669
EM: Round [22] log likelihood: -676.976287
EM: Round [23] log likelihood: -676.964364
EM: Round [24] log likelihood: -676.952882
EM: Round [25] log likelihood: -676.941821
EM: Round [26] log likelihood: -676.931163
EM: Round [27] log likelihood: -676.920893
EM: Round [28] log likelihood: -676.910993
EM: Round [29] log likelihood: -676.901450
EM: Round [30] log likelihood: -676.892247
EM: Round [31] log likelihood: -676.883373
EM: Round [32] log likelihood: -676.874813
EM: Round [33] log likelihood: -676.866556
EM: Round [34] log likelihood: -676.858589
EM: Round [35] log likelihood: -676.850901
EM: Round [36] log likelihood: -676.843481
EM: Round [37] log likelihood: -676.836320
EM: Round [38] log likelihood: -676.829406
EM: Round [39] log likelihood: -676.822732
EM: Round [40] log likelihood: -676.816287
EM: Round [41] log likelihood: -676.810063
EM: Round [42] log likelihood: -676.804052
EM: Round [43] log likelihood: -676.798246
EM: Round [44] log likelihood: -676.792638
EM: Round [45] log likelihood: -676.787220
EM: Round [46] log likelihood: -676.781985
EM: Round [47] log likelihood: -676.776927
EM: Round [48] log likelihood: -676.772039
EM: Round [49] log likelihood: -676.767315
EM: Round [50] log likelihood: -676.762749
EM: Round [51] log likelihood: -676.758336
EM: Round [52] log likelihood: -676.754070
EM: Round [53] log likelihood: -676.749946
EM: Round [54] log likelihood: -676.745959
EM: Round [55] log likelihood: -676.742105
EM: Round [56] log likelihood: -676.738377
EM: Round [57] log likelihood: -676.734773
EM: Round [58] log likelihood: -676.731288
EM: Round [59] log likelihood: -676.727917
EM: Round [60] log likelihood: -676.724657
EM: Round [61] log likelihood: -676.721504
EM: Round [62] log likelihood: -676.718455
EM: Round [63] log likelihood: -676.715505
EM: Round [64] log likelihood: -676.712651
EM: Round [65] log likelihood: -676.709890
EM: Round [66] log likelihood: -676.707220
EM: Round [67] log likelihood: -676.704636
EM: Round [68] log likelihood: -676.702136
EM: Round [69] log likelihood: -676.699717
EM: Round [70] log likelihood: -676.697377
EM: Round [71] log likelihood: -676.695112
EM: Round [72] log likelihood: -676.692920
EM: Round [73] log likelihood: -676.690800
EM: Round [74] log likelihood: -676.688747
EM: Round [75] log likelihood: -676.686761
EM: Round [76] log likelihood: -676.684839
EM: Round [77] log likelihood: -676.682979
EM: Round [78] log likelihood: -676.681178
EM: Round [79] log likelihood: -676.679435
EM: Round [80] log likelihood: -676.677748
EM: Round [81] log likelihood: -676.676115
EM: Round [82] log likelihood: -676.674535
EM: Round [83] log likelihood: -676.673005
EM: Round [84] log likelihood: -676.671524
EM: Round [85] log likelihood: -676.670090
EM: Round [86] log likelihood: -676.668702
EM: Round [87] log likelihood: -676.667359
EM: Round [88] log likelihood: -676.666058
EM: Round [89] log likelihood: -676.664799
EM: Round [90] log likelihood: -676.663580
EM: Round [91] log likelihood: -676.662399
EM: Round [92] log likelihood: -676.661256
EM: Round [93] log likelihood: -676.660150
EM: Round [94] log likelihood: -676.659079
EM: Round [95] log likelihood: -676.658041
EM: Round [96] log likelihood: -676.657037
EM: Round [97] log likelihood: -676.656064
EM: Round [98] log likelihood: -676.655123
EM: Round [99] log likelihood: -676.654211
EM: Round [100] log likelihood: -676.653328
EM: Round [101] log likelihood: -676.652473
EM: Round [102] log likelihood: -676.651645
EM: Round [103] log likelihood: -676.650843
EM: Round [104] log likelihood: -676.650067
EM: Round [105] log likelihood: -676.649315
EM: Round [106] log likelihood: -676.648587
EM: Round [107] log likelihood: -676.647882
EM: Round [108] log likelihood: -676.647199
EM: Round [109] log likelihood: -676.646538
EM: Round [110] log likelihood: -676.645898
EM: Round [111] log likelihood: -676.645278
EM: Round [112] log likelihood: -676.644677
EM: Round [113] log likelihood: -676.644095
EM: Round [114] log likelihood: -676.643532
EM: Round [115] log likelihood: -676.642987
EM: Round [116] log likelihood: -676.642458
EM: Round [117] log likelihood: -676.641947
EM: Round [118] log likelihood: -676.641451
EM: Round [119] log likelihood: -676.640971
EM: Round [120] log likelihood: -676.640506
EM: Round [121] log likelihood: -676.640056
EM: Round [122] log likelihood: -676.639620
EM: Round [123] log likelihood: -676.639197
EM: Round [124] log likelihood: -676.638788
EM: Round [125] log likelihood: -676.638392
EM: Round [126] log likelihood: -676.638008
EM: Round [127] log likelihood: -676.637637
EM: Round [128] log likelihood: -676.637277
EM: Round [129] log likelihood: -676.636928
EM: Round [130] log likelihood: -676.636590
EM: Round [131] log likelihood: -676.636263
EM: Round [132] log likelihood: -676.635946
EM: Round [133] log likelihood: -676.635639
EM: Round [134] log likelihood: -676.635342
EM: Round [135] log likelihood: -676.635054
EM: Round [136] log likelihood: -676.634775
EM: Round [137] log likelihood: -676.634505
EM: Round [138] log likelihood: -676.634243
EM: Round [139] log likelihood: -676.633990
EM: Round [140] log likelihood: -676.633744
EM: Round [141] log likelihood: -676.633507
EM: Round [142] log likelihood: -676.633276
EM: Round [143] log likelihood: -676.633053
EM: Round [144] log likelihood: -676.632837
EM: Round [145] log likelihood: -676.632628
EM: Round [146] log likelihood: -676.632425
EM: Round [147] log likelihood: -676.632228
EM: Round [148] log likelihood: -676.632038
EM: Round [149] log likelihood: -676.631854
EM: Round [150] log likelihood: -676.631675
EM: Round [151] log likelihood: -676.631502
EM: Round [152] log likelihood: -676.631335
EM: Round [153] log likelihood: -676.631173
EM: Round [154] log likelihood: -676.631015
EM: Round [155] log likelihood: -676.630863
EM: Round [156] log likelihood: -676.630716
EM: Round [157] log likelihood: -676.630573
EM: Round [158] log likelihood: -676.630434
EM: Round [159] log likelihood: -676.630300
EM: Round [160] log likelihood: -676.630170
EM: Round [161] log likelihood: -676.630045
EM: Round [162] log likelihood: -676.629923
EM: Round [163] log likelihood: -676.629805
EM: Round [164] log likelihood: -676.629690
EM: Round [165] log likelihood: -676.629580
EM: Round [166] log likelihood: -676.629472
EM: Round [167] log likelihood: -676.629368
EM: Round [168] log likelihood: -676.629268
EM: Round [169] log likelihood: -676.629170
EM: Stopping iterations at round 169 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.vFikEdS7Kl/tih_rna_sample_00619_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.vFikEdS7Kl/tih_rna_sample_00619_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.vFikEdS7Kl/tih_rna_sample_00619_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.vFikEdS7Kl/tih_rna_sample_00619_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.vFikEdS7Kl/tih_rna_sample_00619_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.vFikEdS7Kl/tih_rna_sample_00619_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.vFikEdS7Kl/tih_rna_sample_00619_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.vFikEdS7Kl/fi_workdir/tih_rna_sample_00619_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.vFikEdS7Kl/fi_workdir/tih_rna_sample_00619_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.vFikEdS7Kl/fi_workdir/tih_rna_sample_00619_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.vFikEdS7Kl/tih_rna_sample_00619_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.vFikEdS7Kl/tih_rna_sample_00619_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -601.338526
EM: Round [1] log likelihood: -601.338526
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.vFikEdS7Kl/tih_rna_sample_00619_B23MVV7LT4_1_1.fastp.fastq.gz: 241794911
Warning - not locating file: /tmp/nxf.vFikEdS7Kl/tih_rna_sample_00619_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
ls: cannot access 'IGV_inputs': No such file or directory