Done.
-parsing GTF file: /tmp/nxf.ZB9XBvOyXZ/tih_rna_sample_00669_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.ZB9XBvOyXZ/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.ZB9XBvOyXZ/tih_rna_sample_00669_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.ZB9XBvOyXZ/tih_rna_sample_00669_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.ZB9XBvOyXZ/fi_workdir/tih_rna_sample_00669_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.ZB9XBvOyXZ/fi_workdir/tih_rna_sample_00669_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00669_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00669_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:03:46 : INFO : Done.
-parsing GTF file: /tmp/nxf.ZB9XBvOyXZ/fi_workdir/tih_rna_sample_00669_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.ZB9XBvOyXZ/fi_workdir/tih_rna_sample_00669_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[1060000]   -done parsing /tmp/nxf.ZB9XBvOyXZ/fi_workdir/tih_rna_sample_00669_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num genes matched < 2' => 15,
          'low complexity anchor region' => 12,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 166,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'excessive soft clipping' => 5852,
          'seq-similar region overlap' => 8,
          'per_id < 96' => 4372,
          ' ** passed ** ' => 2821,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
          'exons hit < 2' => 4,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 9
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.ZB9XBvOyXZ/fi_workdir/tih_rna_sample_00669_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[126000]   
[127000]   -fusion SPANNING read extraction for scaff: ACACA--LGMN

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[105000]   -fusion SPANNING read extraction for scaff: AP000873.1--PCF11

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[87000]   -fusion SPANNING read extraction for scaff: CLTA--RASA2

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[8000]   -fusion SPANNING read extraction for scaff: LINC01002--ZCCHC7

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[228000]   -fusion SPANNING read extraction for scaff: NCOA1--RBKS

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

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[13000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

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[13000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

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[6000]   -fusion SPANNING read extraction for scaff: PPIL3--CFLAR-AS1

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[94000]   -fusion SPANNING read extraction for scaff: PUM2--B3GNTL1

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[209000]   -fusion SPANNING read extraction for scaff: ST14--ARHGAP32

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[38000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[7000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[17000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[97000]   -fusion SPANNING read extraction for scaff: ZMYND8--GSG1L
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 5250,
          'lacks exon overlap' => 5759
        };
EM: Starting log likelihood: -3754.731252
EM: Round [1] log likelihood: -3753.930595
EM: Round [2] log likelihood: -3753.921951
EM: Round [3] log likelihood: -3753.914001
EM: Round [4] log likelihood: -3753.906251
EM: Round [5] log likelihood: -3753.898693
EM: Round [6] log likelihood: -3753.891321
EM: Round [7] log likelihood: -3753.884128
EM: Round [8] log likelihood: -3753.877109
EM: Round [9] log likelihood: -3753.870259
EM: Round [10] log likelihood: -3753.863572
EM: Round [11] log likelihood: -3753.857044
EM: Round [12] log likelihood: -3753.850670
EM: Round [13] log likelihood: -3753.844445
EM: Round [14] log likelihood: -3753.838364
EM: Round [15] log likelihood: -3753.832425
EM: Round [16] log likelihood: -3753.826622
EM: Round [17] log likelihood: -3753.820952
EM: Round [18] log likelihood: -3753.815410
EM: Round [19] log likelihood: -3753.809994
EM: Round [20] log likelihood: -3753.804700
EM: Round [21] log likelihood: -3753.799524
EM: Round [22] log likelihood: -3753.794463
EM: Round [23] log likelihood: -3753.789515
EM: Round [24] log likelihood: -3753.784675
EM: Round [25] log likelihood: -3753.779942
EM: Round [26] log likelihood: -3753.775312
EM: Round [27] log likelihood: -3753.770783
EM: Round [28] log likelihood: -3753.766351
EM: Round [29] log likelihood: -3753.762015
EM: Round [30] log likelihood: -3753.757772
EM: Round [31] log likelihood: -3753.753620
EM: Round [32] log likelihood: -3753.749556
EM: Round [33] log likelihood: -3753.745578
EM: Round [34] log likelihood: -3753.741684
EM: Round [35] log likelihood: -3753.737872
EM: Round [36] log likelihood: -3753.734140
EM: Round [37] log likelihood: -3753.730486
EM: Round [38] log likelihood: -3753.726907
EM: Round [39] log likelihood: -3753.723403
EM: Round [40] log likelihood: -3753.719971
EM: Round [41] log likelihood: -3753.716609
EM: Round [42] log likelihood: -3753.713317
EM: Round [43] log likelihood: -3753.710092
EM: Round [44] log likelihood: -3753.706932
EM: Round [45] log likelihood: -3753.703837
EM: Round [46] log likelihood: -3753.700805
EM: Round [47] log likelihood: -3753.697833
EM: Round [48] log likelihood: -3753.694922
EM: Round [49] log likelihood: -3753.692069
EM: Round [50] log likelihood: -3753.689273
EM: Round [51] log likelihood: -3753.686532
EM: Round [52] log likelihood: -3753.683847
EM: Round [53] log likelihood: -3753.681214
EM: Round [54] log likelihood: -3753.678634
EM: Round [55] log likelihood: -3753.676105
EM: Round [56] log likelihood: -3753.673625
EM: Round [57] log likelihood: -3753.671195
EM: Round [58] log likelihood: -3753.668811
EM: Round [59] log likelihood: -3753.666475
EM: Round [60] log likelihood: -3753.664184
EM: Round [61] log likelihood: -3753.661938
EM: Round [62] log likelihood: -3753.659735
EM: Round [63] log likelihood: -3753.657575
EM: Round [64] log likelihood: -3753.655457
EM: Round [65] log likelihood: -3753.653380
EM: Round [66] log likelihood: -3753.651342
EM: Round [67] log likelihood: -3753.649344
EM: Round [68] log likelihood: -3753.647385
EM: Round [69] log likelihood: -3753.645462
EM: Round [70] log likelihood: -3753.643577
EM: Round [71] log likelihood: -3753.641727
EM: Round [72] log likelihood: -3753.639913
EM: Round [73] log likelihood: -3753.638133
EM: Round [74] log likelihood: -3753.636387
EM: Round [75] log likelihood: -3753.634674
EM: Round [76] log likelihood: -3753.632993
EM: Round [77] log likelihood: -3753.631344
EM: Round [78] log likelihood: -3753.629726
EM: Round [79] log likelihood: -3753.628139
EM: Round [80] log likelihood: -3753.626581
EM: Round [81] log likelihood: -3753.625053
EM: Round [82] log likelihood: -3753.623553
EM: Round [83] log likelihood: -3753.622082
EM: Round [84] log likelihood: -3753.620637
EM: Round [85] log likelihood: -3753.619220
EM: Round [86] log likelihood: -3753.617829
EM: Round [87] log likelihood: -3753.616464
EM: Round [88] log likelihood: -3753.615124
EM: Round [89] log likelihood: -3753.613810
EM: Round [90] log likelihood: -3753.612519
EM: Round [91] log likelihood: -3753.611252
EM: Round [92] log likelihood: -3753.610009
EM: Round [93] log likelihood: -3753.608789
EM: Round [94] log likelihood: -3753.607591
EM: Round [95] log likelihood: -3753.606415
EM: Round [96] log likelihood: -3753.605261
EM: Round [97] log likelihood: -3753.604128
EM: Round [98] log likelihood: -3753.603016
EM: Round [99] log likelihood: -3753.601924
EM: Round [100] log likelihood: -3753.600853
EM: Round [101] log likelihood: -3753.599800
EM: Round [102] log likelihood: -3753.598768
EM: Round [103] log likelihood: -3753.597753
EM: Round [104] log likelihood: -3753.596758
EM: Round [105] log likelihood: -3753.595780
EM: Round [106] log likelihood: -3753.594821
EM: Round [107] log likelihood: -3753.593878
EM: Round [108] log likelihood: -3753.592953
EM: Round [109] log likelihood: -3753.592045
EM: Round [110] log likelihood: -3753.591153
EM: Round [111] log likelihood: -3753.590277
EM: Round [112] log likelihood: -3753.589417
EM: Round [113] log likelihood: -3753.588573
EM: Round [114] log likelihood: -3753.587744
EM: Round [115] log likelihood: -3753.586929
EM: Round [116] log likelihood: -3753.586130
EM: Round [117] log likelihood: -3753.585345
EM: Round [118] log likelihood: -3753.584574
EM: Round [119] log likelihood: -3753.583817
EM: Round [120] log likelihood: -3753.583073
EM: Round [121] log likelihood: -3753.582343
EM: Round [122] log likelihood: -3753.581626
EM: Round [123] log likelihood: -3753.580922
EM: Round [124] log likelihood: -3753.580231
EM: Round [125] log likelihood: -3753.579552
EM: Round [126] log likelihood: -3753.578885
EM: Round [127] log likelihood: -3753.578230
EM: Round [128] log likelihood: -3753.577586
EM: Round [129] log likelihood: -3753.576954
EM: Round [130] log likelihood: -3753.576334
EM: Round [131] log likelihood: -3753.575724
EM: Round [132] log likelihood: -3753.575126
EM: Round [133] log likelihood: -3753.574538
EM: Round [134] log likelihood: -3753.573960
EM: Round [135] log likelihood: -3753.573393
EM: Round [136] log likelihood: -3753.572836
EM: Round [137] log likelihood: -3753.572289
EM: Round [138] log likelihood: -3753.571752
EM: Round [139] log likelihood: -3753.571224
EM: Round [140] log likelihood: -3753.570705
EM: Round [141] log likelihood: -3753.570196
EM: Round [142] log likelihood: -3753.569696
EM: Round [143] log likelihood: -3753.569204
EM: Round [144] log likelihood: -3753.568721
EM: Round [145] log likelihood: -3753.568247
EM: Round [146] log likelihood: -3753.567781
EM: Round [147] log likelihood: -3753.567324
EM: Round [148] log likelihood: -3753.566875
EM: Round [149] log likelihood: -3753.566433
EM: Round [150] log likelihood: -3753.565999
EM: Round [151] log likelihood: -3753.565573
EM: Round [152] log likelihood: -3753.565155
EM: Round [153] log likelihood: -3753.564744
EM: Round [154] log likelihood: -3753.564340
EM: Round [155] log likelihood: -3753.563943
EM: Round [156] log likelihood: -3753.563553
EM: Round [157] log likelihood: -3753.563170
EM: Round [158] log likelihood: -3753.562794
EM: Round [159] log likelihood: -3753.562425
EM: Round [160] log likelihood: -3753.562062
EM: Round [161] log likelihood: -3753.561705
EM: Round [162] log likelihood: -3753.561355
EM: Round [163] log likelihood: -3753.561011
EM: Round [164] log likelihood: -3753.560672
EM: Round [165] log likelihood: -3753.560340
EM: Round [166] log likelihood: -3753.560014
EM: Round [167] log likelihood: -3753.559693
EM: Round [168] log likelihood: -3753.559378
EM: Round [169] log likelihood: -3753.559069
EM: Round [170] log likelihood: -3753.558765
EM: Round [171] log likelihood: -3753.558466
EM: Round [172] log likelihood: -3753.558173
EM: Round [173] log likelihood: -3753.557884
EM: Round [174] log likelihood: -3753.557601
EM: Round [175] log likelihood: -3753.557323
EM: Round [176] log likelihood: -3753.557049
EM: Round [177] log likelihood: -3753.556780
EM: Round [178] log likelihood: -3753.556517
EM: Round [179] log likelihood: -3753.556257
EM: Round [180] log likelihood: -3753.556002
EM: Round [181] log likelihood: -3753.555752
EM: Round [182] log likelihood: -3753.555506
EM: Round [183] log likelihood: -3753.555264
EM: Round [184] log likelihood: -3753.555027
EM: Round [185] log likelihood: -3753.554794
EM: Round [186] log likelihood: -3753.554564
EM: Round [187] log likelihood: -3753.554339
EM: Round [188] log likelihood: -3753.554118
EM: Round [189] log likelihood: -3753.553901
EM: Round [190] log likelihood: -3753.553687
EM: Round [191] log likelihood: -3753.553477
EM: Round [192] log likelihood: -3753.553271
EM: Round [193] log likelihood: -3753.553068
EM: Round [194] log likelihood: -3753.552869
EM: Round [195] log likelihood: -3753.552673
EM: Round [196] log likelihood: -3753.552481
EM: Round [197] log likelihood: -3753.552292
EM: Round [198] log likelihood: -3753.552107
EM: Round [199] log likelihood: -3753.551924
EM: Round [200] log likelihood: -3753.551745
EM: Round [201] log likelihood: -3753.551569
EM: Round [202] log likelihood: -3753.551396
EM: Round [203] log likelihood: -3753.551226
EM: Round [204] log likelihood: -3753.551059
EM: Round [205] log likelihood: -3753.550895
EM: Round [206] log likelihood: -3753.550734
EM: Round [207] log likelihood: -3753.550575
EM: Round [208] log likelihood: -3753.550420
EM: Round [209] log likelihood: -3753.550267
EM: Round [210] log likelihood: -3753.550116
EM: Round [211] log likelihood: -3753.549969
EM: Round [212] log likelihood: -3753.549823
EM: Round [213] log likelihood: -3753.549681
EM: Round [214] log likelihood: -3753.549541
EM: Round [215] log likelihood: -3753.549403
EM: Round [216] log likelihood: -3753.549268
EM: Round [217] log likelihood: -3753.549135
EM: Round [218] log likelihood: -3753.549004
EM: Round [219] log likelihood: -3753.548876
EM: Round [220] log likelihood: -3753.548750
EM: Round [221] log likelihood: -3753.548626
EM: Round [222] log likelihood: -3753.548504
EM: Round [223] log likelihood: -3753.548384
EM: Round [224] log likelihood: -3753.548266
EM: Round [225] log likelihood: -3753.548151
EM: Round [226] log likelihood: -3753.548037
EM: Round [227] log likelihood: -3753.547926
EM: Round [228] log likelihood: -3753.547816
EM: Round [229] log likelihood: -3753.547708
EM: Round [230] log likelihood: -3753.547602
EM: Round [231] log likelihood: -3753.547498
EM: Round [232] log likelihood: -3753.547396
EM: Round [233] log likelihood: -3753.547296
EM: Round [234] log likelihood: -3753.547197
EM: Stopping iterations at round 234 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.ZB9XBvOyXZ/tih_rna_sample_00669_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.ZB9XBvOyXZ/tih_rna_sample_00669_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.ZB9XBvOyXZ/tih_rna_sample_00669_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.ZB9XBvOyXZ/tih_rna_sample_00669_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.ZB9XBvOyXZ/tih_rna_sample_00669_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.ZB9XBvOyXZ/tih_rna_sample_00669_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.ZB9XBvOyXZ/tih_rna_sample_00669_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.ZB9XBvOyXZ/fi_workdir/tih_rna_sample_00669_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.ZB9XBvOyXZ/fi_workdir/tih_rna_sample_00669_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.ZB9XBvOyXZ/fi_workdir/tih_rna_sample_00669_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.ZB9XBvOyXZ/tih_rna_sample_00669_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.ZB9XBvOyXZ/tih_rna_sample_00669_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3607.690341
EM: Round [1] log likelihood: -3607.065249
EM: Round [2] log likelihood: -3607.064724
EM: Round [3] log likelihood: -3607.064722
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.ZB9XBvOyXZ/tih_rna_sample_00669_B23MVV7LT4_1_1.fastp.fastq.gz: 272885379
Warning - not locating file: /tmp/nxf.ZB9XBvOyXZ/tih_rna_sample_00669_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000247137.9]
WARNING, no entry stored in dbm for [ENSG00000247137.9]
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 [ENSG00000282508.2]
WARNING, no entry stored in dbm for [ENSG00000226312.7]
WARNING, no entry stored in dbm for [ENSG00000226312.7]
ls: cannot access 'IGV_inputs': No such file or directory