Done.
-parsing GTF file: /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.hsK8Wg1IOC/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.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00434_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00434_B23WHTKLT4_1.star.sortedByCoord.out.bam
11:28:17 : INFO : Done.
-parsing GTF file: /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

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[540000]   -done parsing /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'per_id < 96' => 2031,
          'num genes matched < 2' => 2,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8,
          'seq-similar region overlap' => 30,
          'exons hit < 2' => 1,
          'excessive soft clipping' => 3626,
          'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 18,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 22,
          'small anchor length' => 36,
          ' ** passed ** ' => 14838,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 28
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[63000]   -fusion SPANNING read extraction for scaff: AC006008.1--DPP6

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[64000]   -fusion SPANNING read extraction for scaff: AC092666.1--DPP6

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[11000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[17000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[17000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[19000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[15000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[15000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[24000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[84000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[28000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[36000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 2222,
          'seq similar region alignment' => 37886
        };
EM: Starting log likelihood: -2036.217615
EM: Round [1] log likelihood: -2036.102224
EM: Round [2] log likelihood: -2036.064765
EM: Round [3] log likelihood: -2036.028771
EM: Round [4] log likelihood: -2035.994167
EM: Round [5] log likelihood: -2035.960887
EM: Round [6] log likelihood: -2035.928864
EM: Round [7] log likelihood: -2035.898039
EM: Round [8] log likelihood: -2035.868356
EM: Round [9] log likelihood: -2035.839761
EM: Round [10] log likelihood: -2035.812206
EM: Round [11] log likelihood: -2035.785642
EM: Round [12] log likelihood: -2035.760027
EM: Round [13] log likelihood: -2035.735318
EM: Round [14] log likelihood: -2035.711477
EM: Round [15] log likelihood: -2035.688467
EM: Round [16] log likelihood: -2035.666252
EM: Round [17] log likelihood: -2035.644800
EM: Round [18] log likelihood: -2035.624079
EM: Round [19] log likelihood: -2035.604059
EM: Round [20] log likelihood: -2035.584713
EM: Round [21] log likelihood: -2035.566014
EM: Round [22] log likelihood: -2035.547935
EM: Round [23] log likelihood: -2035.530454
EM: Round [24] log likelihood: -2035.513546
EM: Round [25] log likelihood: -2035.497191
EM: Round [26] log likelihood: -2035.481366
EM: Round [27] log likelihood: -2035.466053
EM: Round [28] log likelihood: -2035.451232
EM: Round [29] log likelihood: -2035.436885
EM: Round [30] log likelihood: -2035.422996
EM: Round [31] log likelihood: -2035.409546
EM: Round [32] log likelihood: -2035.396521
EM: Round [33] log likelihood: -2035.383904
EM: Round [34] log likelihood: -2035.371683
EM: Round [35] log likelihood: -2035.359843
EM: Round [36] log likelihood: -2035.348370
EM: Round [37] log likelihood: -2035.337252
EM: Round [38] log likelihood: -2035.326477
EM: Round [39] log likelihood: -2035.316032
EM: Round [40] log likelihood: -2035.305907
EM: Round [41] log likelihood: -2035.296091
EM: Round [42] log likelihood: -2035.286574
EM: Round [43] log likelihood: -2035.277345
EM: Round [44] log likelihood: -2035.268394
EM: Round [45] log likelihood: -2035.259714
EM: Round [46] log likelihood: -2035.251294
EM: Round [47] log likelihood: -2035.243126
EM: Round [48] log likelihood: -2035.235202
EM: Round [49] log likelihood: -2035.227515
EM: Round [50] log likelihood: -2035.220056
EM: Round [51] log likelihood: -2035.212818
EM: Round [52] log likelihood: -2035.205795
EM: Round [53] log likelihood: -2035.198978
EM: Round [54] log likelihood: -2035.192362
EM: Round [55] log likelihood: -2035.185941
EM: Round [56] log likelihood: -2035.179708
EM: Round [57] log likelihood: -2035.173658
EM: Round [58] log likelihood: -2035.167784
EM: Round [59] log likelihood: -2035.162081
EM: Round [60] log likelihood: -2035.156544
EM: Round [61] log likelihood: -2035.151168
EM: Round [62] log likelihood: -2035.145948
EM: Round [63] log likelihood: -2035.140879
EM: Round [64] log likelihood: -2035.135957
EM: Round [65] log likelihood: -2035.131176
EM: Round [66] log likelihood: -2035.126533
EM: Round [67] log likelihood: -2035.122024
EM: Round [68] log likelihood: -2035.117644
EM: Round [69] log likelihood: -2035.113389
EM: Round [70] log likelihood: -2035.109257
EM: Round [71] log likelihood: -2035.105242
EM: Round [72] log likelihood: -2035.101342
EM: Round [73] log likelihood: -2035.097554
EM: Round [74] log likelihood: -2035.093873
EM: Round [75] log likelihood: -2035.090297
EM: Round [76] log likelihood: -2035.086823
EM: Round [77] log likelihood: -2035.083447
EM: Round [78] log likelihood: -2035.080167
EM: Round [79] log likelihood: -2035.076980
EM: Round [80] log likelihood: -2035.073883
EM: Round [81] log likelihood: -2035.070874
EM: Round [82] log likelihood: -2035.067949
EM: Round [83] log likelihood: -2035.065107
EM: Round [84] log likelihood: -2035.062345
EM: Round [85] log likelihood: -2035.059661
EM: Round [86] log likelihood: -2035.057053
EM: Round [87] log likelihood: -2035.054517
EM: Round [88] log likelihood: -2035.052053
EM: Round [89] log likelihood: -2035.049658
EM: Round [90] log likelihood: -2035.047330
EM: Round [91] log likelihood: -2035.045068
EM: Round [92] log likelihood: -2035.042869
EM: Round [93] log likelihood: -2035.040731
EM: Round [94] log likelihood: -2035.038653
EM: Round [95] log likelihood: -2035.036633
EM: Round [96] log likelihood: -2035.034670
EM: Round [97] log likelihood: -2035.032761
EM: Round [98] log likelihood: -2035.030905
EM: Round [99] log likelihood: -2035.029101
EM: Round [100] log likelihood: -2035.027348
EM: Round [101] log likelihood: -2035.025643
EM: Round [102] log likelihood: -2035.023986
EM: Round [103] log likelihood: -2035.022375
EM: Round [104] log likelihood: -2035.020808
EM: Round [105] log likelihood: -2035.019285
EM: Round [106] log likelihood: -2035.017804
EM: Round [107] log likelihood: -2035.016365
EM: Round [108] log likelihood: -2035.014965
EM: Round [109] log likelihood: -2035.013604
EM: Round [110] log likelihood: -2035.012281
EM: Round [111] log likelihood: -2035.010994
EM: Round [112] log likelihood: -2035.009744
EM: Round [113] log likelihood: -2035.008527
EM: Round [114] log likelihood: -2035.007345
EM: Round [115] log likelihood: -2035.006195
EM: Round [116] log likelihood: -2035.005076
EM: Round [117] log likelihood: -2035.003989
EM: Round [118] log likelihood: -2035.002932
EM: Round [119] log likelihood: -2035.001904
EM: Round [120] log likelihood: -2035.000904
EM: Round [121] log likelihood: -2034.999932
EM: Round [122] log likelihood: -2034.998987
EM: Round [123] log likelihood: -2034.998068
EM: Round [124] log likelihood: -2034.997174
EM: Round [125] log likelihood: -2034.996304
EM: Round [126] log likelihood: -2034.995459
EM: Round [127] log likelihood: -2034.994637
EM: Round [128] log likelihood: -2034.993838
EM: Round [129] log likelihood: -2034.993060
EM: Round [130] log likelihood: -2034.992304
EM: Round [131] log likelihood: -2034.991569
EM: Round [132] log likelihood: -2034.990854
EM: Round [133] log likelihood: -2034.990159
EM: Round [134] log likelihood: -2034.989483
EM: Round [135] log likelihood: -2034.988825
EM: Round [136] log likelihood: -2034.988186
EM: Round [137] log likelihood: -2034.987564
EM: Round [138] log likelihood: -2034.986959
EM: Round [139] log likelihood: -2034.986371
EM: Round [140] log likelihood: -2034.985798
EM: Round [141] log likelihood: -2034.985242
EM: Round [142] log likelihood: -2034.984701
EM: Round [143] log likelihood: -2034.984175
EM: Round [144] log likelihood: -2034.983663
EM: Round [145] log likelihood: -2034.983165
EM: Round [146] log likelihood: -2034.982681
EM: Round [147] log likelihood: -2034.982210
EM: Round [148] log likelihood: -2034.981752
EM: Round [149] log likelihood: -2034.981307
EM: Round [150] log likelihood: -2034.980874
EM: Round [151] log likelihood: -2034.980452
EM: Round [152] log likelihood: -2034.980043
EM: Round [153] log likelihood: -2034.979644
EM: Round [154] log likelihood: -2034.979257
EM: Round [155] log likelihood: -2034.978880
EM: Round [156] log likelihood: -2034.978513
EM: Round [157] log likelihood: -2034.978156
EM: Round [158] log likelihood: -2034.977809
EM: Round [159] log likelihood: -2034.977472
EM: Round [160] log likelihood: -2034.977144
EM: Round [161] log likelihood: -2034.976825
EM: Round [162] log likelihood: -2034.976514
EM: Round [163] log likelihood: -2034.976213
EM: Round [164] log likelihood: -2034.975919
EM: Round [165] log likelihood: -2034.975633
EM: Round [166] log likelihood: -2034.975356
EM: Round [167] log likelihood: -2034.975085
EM: Round [168] log likelihood: -2034.974823
EM: Round [169] log likelihood: -2034.974567
EM: Round [170] log likelihood: -2034.974318
EM: Round [171] log likelihood: -2034.974077
EM: Round [172] log likelihood: -2034.973841
EM: Round [173] log likelihood: -2034.973613
EM: Round [174] log likelihood: -2034.973390
EM: Round [175] log likelihood: -2034.973174
EM: Round [176] log likelihood: -2034.972963
EM: Round [177] log likelihood: -2034.972758
EM: Round [178] log likelihood: -2034.972559
EM: Round [179] log likelihood: -2034.972366
EM: Round [180] log likelihood: -2034.972177
EM: Round [181] log likelihood: -2034.971994
EM: Round [182] log likelihood: -2034.971816
EM: Round [183] log likelihood: -2034.971642
EM: Round [184] log likelihood: -2034.971474
EM: Round [185] log likelihood: -2034.971310
EM: Round [186] log likelihood: -2034.971150
EM: Round [187] log likelihood: -2034.970995
EM: Round [188] log likelihood: -2034.970844
EM: Round [189] log likelihood: -2034.970697
EM: Round [190] log likelihood: -2034.970554
EM: Round [191] log likelihood: -2034.970415
EM: Round [192] log likelihood: -2034.970280
EM: Round [193] log likelihood: -2034.970149
EM: Round [194] log likelihood: -2034.970021
EM: Round [195] log likelihood: -2034.969897
EM: Round [196] log likelihood: -2034.969776
EM: Round [197] log likelihood: -2034.969658
EM: Round [198] log likelihood: -2034.969544
EM: Round [199] log likelihood: -2034.969432
EM: Round [200] log likelihood: -2034.969324
EM: Round [201] log likelihood: -2034.969219
EM: Round [202] log likelihood: -2034.969116
EM: Round [203] log likelihood: -2034.969017
EM: Stopping iterations at round 203 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_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.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_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.hsK8Wg1IOC/fi_workdir/tih_rna_sample_00434_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1498.743054
EM: Round [1] log likelihood: -1498.743054
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1_1.fastp.fastq.gz: 295645013
Warning - not locating file: /tmp/nxf.hsK8Wg1IOC/tih_rna_sample_00434_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000282057.1]
ls: cannot access 'IGV_inputs': No such file or directory