Done.
-parsing GTF file: /tmp/nxf.9iPmgMNlDq/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.9iPmgMNlDq/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.9iPmgMNlDq/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.9iPmgMNlDq/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.9iPmgMNlDq/fi_workdir/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.9iPmgMNlDq/fi_workdir/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
10:39:45 : INFO : Done.
-parsing GTF file: /tmp/nxf.9iPmgMNlDq/fi_workdir/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.9iPmgMNlDq/fi_workdir/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam

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[390000]   -done parsing /tmp/nxf.9iPmgMNlDq/fi_workdir/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'per_id < 96' => 1080,
          'seq-similar region overlap' => 111,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 20,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 5,
          ' ** passed ** ' => 2059,
          'small anchor length' => 3,
          'excessive soft clipping' => 2170,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 18,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 23,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 6,
          'low complexity anchor region' => 1
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.9iPmgMNlDq/fi_workdir/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[36000]   -fusion SPANNING read extraction for scaff: ATE1--WAPL

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[11000]   -fusion SPANNING read extraction for scaff: C1QTNF3--AMACR
-fusion SPANNING read extraction for scaff: CCDC169--SOHLH2

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[46000]   -fusion SPANNING read extraction for scaff: CDK11A--SLC35E2B

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[135000]   -fusion SPANNING read extraction for scaff: EP300--PVALB

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[8000]   -fusion SPANNING read extraction for scaff: PAPSS2--AL157400.3

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[13000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[13000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[15000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[10000]   -fusion SPANNING read extraction for scaff: PCDHA5--PCDHAC1

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[10000]   -fusion SPANNING read extraction for scaff: PCDHA5--PCDHAC2

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[12000]   -fusion SPANNING read extraction for scaff: PCDHA5--PCDHA13

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[14000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[14000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[16000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

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[14000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[3000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[13000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 1121,
          'seq similar region alignment' => 12897
        };
EM: Starting log likelihood: -1708.223449
EM: Round [1] log likelihood: -1707.950701
EM: Round [2] log likelihood: -1707.713285
EM: Round [3] log likelihood: -1707.505406
EM: Round [4] log likelihood: -1707.322467
EM: Round [5] log likelihood: -1707.160763
EM: Round [6] log likelihood: -1707.017270
EM: Round [7] log likelihood: -1706.889492
EM: Round [8] log likelihood: -1706.775347
EM: Round [9] log likelihood: -1706.673084
EM: Round [10] log likelihood: -1706.581219
EM: Round [11] log likelihood: -1706.498487
EM: Round [12] log likelihood: -1706.423803
EM: Round [13] log likelihood: -1706.356230
EM: Round [14] log likelihood: -1706.294958
EM: Round [15] log likelihood: -1706.239280
EM: Round [16] log likelihood: -1706.188580
EM: Round [17] log likelihood: -1706.142320
EM: Round [18] log likelihood: -1706.100025
EM: Round [19] log likelihood: -1706.061278
EM: Round [20] log likelihood: -1706.025711
EM: Round [21] log likelihood: -1705.992997
EM: Round [22] log likelihood: -1705.962847
EM: Round [23] log likelihood: -1705.935006
EM: Round [24] log likelihood: -1705.909244
EM: Round [25] log likelihood: -1705.885360
EM: Round [26] log likelihood: -1705.863170
EM: Round [27] log likelihood: -1705.842515
EM: Round [28] log likelihood: -1705.823249
EM: Round [29] log likelihood: -1705.805242
EM: Round [30] log likelihood: -1705.788379
EM: Round [31] log likelihood: -1705.772556
EM: Round [32] log likelihood: -1705.757680
EM: Round [33] log likelihood: -1705.743667
EM: Round [34] log likelihood: -1705.730442
EM: Round [35] log likelihood: -1705.717937
EM: Round [36] log likelihood: -1705.706091
EM: Round [37] log likelihood: -1705.694849
EM: Round [38] log likelihood: -1705.684162
EM: Round [39] log likelihood: -1705.673985
EM: Round [40] log likelihood: -1705.664278
EM: Round [41] log likelihood: -1705.655005
EM: Round [42] log likelihood: -1705.646132
EM: Round [43] log likelihood: -1705.637630
EM: Round [44] log likelihood: -1705.629471
EM: Round [45] log likelihood: -1705.621632
EM: Round [46] log likelihood: -1705.614090
EM: Round [47] log likelihood: -1705.606825
EM: Round [48] log likelihood: -1705.599818
EM: Round [49] log likelihood: -1705.593054
EM: Round [50] log likelihood: -1705.586516
EM: Round [51] log likelihood: -1705.580191
EM: Round [52] log likelihood: -1705.574067
EM: Round [53] log likelihood: -1705.568132
EM: Round [54] log likelihood: -1705.562374
EM: Round [55] log likelihood: -1705.556786
EM: Round [56] log likelihood: -1705.551357
EM: Round [57] log likelihood: -1705.546080
EM: Round [58] log likelihood: -1705.540947
EM: Round [59] log likelihood: -1705.535951
EM: Round [60] log likelihood: -1705.531086
EM: Round [61] log likelihood: -1705.526346
EM: Round [62] log likelihood: -1705.521725
EM: Round [63] log likelihood: -1705.517219
EM: Round [64] log likelihood: -1705.512823
EM: Round [65] log likelihood: -1705.508533
EM: Round [66] log likelihood: -1705.504344
EM: Round [67] log likelihood: -1705.500252
EM: Round [68] log likelihood: -1705.496255
EM: Round [69] log likelihood: -1705.492349
EM: Round [70] log likelihood: -1705.488530
EM: Round [71] log likelihood: -1705.484796
EM: Round [72] log likelihood: -1705.481144
EM: Round [73] log likelihood: -1705.477572
EM: Round [74] log likelihood: -1705.474077
EM: Round [75] log likelihood: -1705.470656
EM: Round [76] log likelihood: -1705.467308
EM: Round [77] log likelihood: -1705.464031
EM: Round [78] log likelihood: -1705.460822
EM: Round [79] log likelihood: -1705.457680
EM: Round [80] log likelihood: -1705.454602
EM: Round [81] log likelihood: -1705.451588
EM: Round [82] log likelihood: -1705.448635
EM: Round [83] log likelihood: -1705.445743
EM: Round [84] log likelihood: -1705.442908
EM: Round [85] log likelihood: -1705.440131
EM: Round [86] log likelihood: -1705.437409
EM: Round [87] log likelihood: -1705.434741
EM: Round [88] log likelihood: -1705.432127
EM: Round [89] log likelihood: -1705.429564
EM: Round [90] log likelihood: -1705.427052
EM: Round [91] log likelihood: -1705.424589
EM: Round [92] log likelihood: -1705.422174
EM: Round [93] log likelihood: -1705.419807
EM: Round [94] log likelihood: -1705.417486
EM: Round [95] log likelihood: -1705.415209
EM: Round [96] log likelihood: -1705.412978
EM: Round [97] log likelihood: -1705.410789
EM: Round [98] log likelihood: -1705.408642
EM: Round [99] log likelihood: -1705.406537
EM: Round [100] log likelihood: -1705.404473
EM: Round [101] log likelihood: -1705.402448
EM: Round [102] log likelihood: -1705.400461
EM: Round [103] log likelihood: -1705.398513
EM: Round [104] log likelihood: -1705.396602
EM: Round [105] log likelihood: -1705.394728
EM: Round [106] log likelihood: -1705.392889
EM: Round [107] log likelihood: -1705.391085
EM: Round [108] log likelihood: -1705.389315
EM: Round [109] log likelihood: -1705.387579
EM: Round [110] log likelihood: -1705.385876
EM: Round [111] log likelihood: -1705.384205
EM: Round [112] log likelihood: -1705.382566
EM: Round [113] log likelihood: -1705.380957
EM: Round [114] log likelihood: -1705.379379
EM: Round [115] log likelihood: -1705.377831
EM: Round [116] log likelihood: -1705.376312
EM: Round [117] log likelihood: -1705.374821
EM: Round [118] log likelihood: -1705.373358
EM: Round [119] log likelihood: -1705.371923
EM: Round [120] log likelihood: -1705.370515
EM: Round [121] log likelihood: -1705.369133
EM: Round [122] log likelihood: -1705.367777
EM: Round [123] log likelihood: -1705.366446
EM: Round [124] log likelihood: -1705.365140
EM: Round [125] log likelihood: -1705.363859
EM: Round [126] log likelihood: -1705.362602
EM: Round [127] log likelihood: -1705.361367
EM: Round [128] log likelihood: -1705.360156
EM: Round [129] log likelihood: -1705.358968
EM: Round [130] log likelihood: -1705.357801
EM: Round [131] log likelihood: -1705.356657
EM: Round [132] log likelihood: -1705.355533
EM: Round [133] log likelihood: -1705.354431
EM: Round [134] log likelihood: -1705.353349
EM: Round [135] log likelihood: -1705.352287
EM: Round [136] log likelihood: -1705.351244
EM: Round [137] log likelihood: -1705.350221
EM: Round [138] log likelihood: -1705.349217
EM: Round [139] log likelihood: -1705.348232
EM: Round [140] log likelihood: -1705.347264
EM: Round [141] log likelihood: -1705.346315
EM: Round [142] log likelihood: -1705.345383
EM: Round [143] log likelihood: -1705.344469
EM: Round [144] log likelihood: -1705.343571
EM: Round [145] log likelihood: -1705.342690
EM: Round [146] log likelihood: -1705.341825
EM: Round [147] log likelihood: -1705.340976
EM: Round [148] log likelihood: -1705.340143
EM: Round [149] log likelihood: -1705.339325
EM: Round [150] log likelihood: -1705.338522
EM: Round [151] log likelihood: -1705.337734
EM: Round [152] log likelihood: -1705.336960
EM: Round [153] log likelihood: -1705.336201
EM: Round [154] log likelihood: -1705.335456
EM: Round [155] log likelihood: -1705.334724
EM: Round [156] log likelihood: -1705.334006
EM: Round [157] log likelihood: -1705.333301
EM: Round [158] log likelihood: -1705.332609
EM: Round [159] log likelihood: -1705.331929
EM: Round [160] log likelihood: -1705.331262
EM: Round [161] log likelihood: -1705.330608
EM: Round [162] log likelihood: -1705.329965
EM: Round [163] log likelihood: -1705.329334
EM: Round [164] log likelihood: -1705.328715
EM: Round [165] log likelihood: -1705.328107
EM: Round [166] log likelihood: -1705.327510
EM: Round [167] log likelihood: -1705.326924
EM: Round [168] log likelihood: -1705.326349
EM: Round [169] log likelihood: -1705.325784
EM: Round [170] log likelihood: -1705.325230
EM: Round [171] log likelihood: -1705.324685
EM: Round [172] log likelihood: -1705.324151
EM: Round [173] log likelihood: -1705.323627
EM: Round [174] log likelihood: -1705.323112
EM: Round [175] log likelihood: -1705.322606
EM: Round [176] log likelihood: -1705.322110
EM: Round [177] log likelihood: -1705.321623
EM: Round [178] log likelihood: -1705.321144
EM: Round [179] log likelihood: -1705.320675
EM: Round [180] log likelihood: -1705.320214
EM: Round [181] log likelihood: -1705.319761
EM: Round [182] log likelihood: -1705.319317
EM: Round [183] log likelihood: -1705.318881
EM: Round [184] log likelihood: -1705.318452
EM: Round [185] log likelihood: -1705.318032
EM: Round [186] log likelihood: -1705.317619
EM: Round [187] log likelihood: -1705.317214
EM: Round [188] log likelihood: -1705.316816
EM: Round [189] log likelihood: -1705.316425
EM: Round [190] log likelihood: -1705.316041
EM: Round [191] log likelihood: -1705.315665
EM: Round [192] log likelihood: -1705.315295
EM: Round [193] log likelihood: -1705.314932
EM: Round [194] log likelihood: -1705.314576
EM: Round [195] log likelihood: -1705.314226
EM: Round [196] log likelihood: -1705.313882
EM: Round [197] log likelihood: -1705.313545
EM: Round [198] log likelihood: -1705.313214
EM: Round [199] log likelihood: -1705.312889
EM: Round [200] log likelihood: -1705.312569
EM: Round [201] log likelihood: -1705.312256
EM: Round [202] log likelihood: -1705.311948
EM: Round [203] log likelihood: -1705.311646
EM: Round [204] log likelihood: -1705.311349
EM: Round [205] log likelihood: -1705.311058
EM: Round [206] log likelihood: -1705.310772
EM: Round [207] log likelihood: -1705.310491
EM: Round [208] log likelihood: -1705.310216
EM: Round [209] log likelihood: -1705.309945
EM: Round [210] log likelihood: -1705.309679
EM: Round [211] log likelihood: -1705.309418
EM: Round [212] log likelihood: -1705.309162
EM: Round [213] log likelihood: -1705.308910
EM: Round [214] log likelihood: -1705.308663
EM: Round [215] log likelihood: -1705.308421
EM: Round [216] log likelihood: -1705.308183
EM: Round [217] log likelihood: -1705.307949
EM: Round [218] log likelihood: -1705.307719
EM: Round [219] log likelihood: -1705.307494
EM: Round [220] log likelihood: -1705.307273
EM: Round [221] log likelihood: -1705.307055
EM: Round [222] log likelihood: -1705.306842
EM: Round [223] log likelihood: -1705.306633
EM: Round [224] log likelihood: -1705.306427
EM: Round [225] log likelihood: -1705.306225
EM: Round [226] log likelihood: -1705.306026
EM: Round [227] log likelihood: -1705.305832
EM: Round [228] log likelihood: -1705.305641
EM: Round [229] log likelihood: -1705.305453
EM: Round [230] log likelihood: -1705.305268
EM: Round [231] log likelihood: -1705.305087
EM: Round [232] log likelihood: -1705.304910
EM: Round [233] log likelihood: -1705.304735
EM: Round [234] log likelihood: -1705.304564
EM: Round [235] log likelihood: -1705.304396
EM: Round [236] log likelihood: -1705.304230
EM: Round [237] log likelihood: -1705.304068
EM: Round [238] log likelihood: -1705.303909
EM: Round [239] log likelihood: -1705.303753
EM: Round [240] log likelihood: -1705.303599
EM: Round [241] log likelihood: -1705.303448
EM: Round [242] log likelihood: -1705.303300
EM: Round [243] log likelihood: -1705.303155
EM: Round [244] log likelihood: -1705.303012
EM: Round [245] log likelihood: -1705.302872
EM: Round [246] log likelihood: -1705.302734
EM: Round [247] log likelihood: -1705.302599
EM: Round [248] log likelihood: -1705.302466
EM: Round [249] log likelihood: -1705.302336
EM: Round [250] log likelihood: -1705.302208
EM: Round [251] log likelihood: -1705.302083
EM: Round [252] log likelihood: -1705.301959
EM: Round [253] log likelihood: -1705.301838
EM: Round [254] log likelihood: -1705.301719
EM: Round [255] log likelihood: -1705.301602
EM: Round [256] log likelihood: -1705.301488
EM: Round [257] log likelihood: -1705.301375
EM: Round [258] log likelihood: -1705.301264
EM: Round [259] log likelihood: -1705.301156
EM: Round [260] log likelihood: -1705.301049
EM: Round [261] log likelihood: -1705.300945
EM: Round [262] log likelihood: -1705.300842
EM: Round [263] log likelihood: -1705.300741
EM: Round [264] log likelihood: -1705.300642
EM: Stopping iterations at round 264 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.9iPmgMNlDq/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.9iPmgMNlDq/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.9iPmgMNlDq/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.9iPmgMNlDq/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.9iPmgMNlDq/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.9iPmgMNlDq/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.9iPmgMNlDq/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.9iPmgMNlDq/fi_workdir/aih-tih-sc-f29b4f-R1_A23WJ53LT4_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.9iPmgMNlDq/fi_workdir/aih-tih-sc-f29b4f-R1_A23WJ53LT4_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.9iPmgMNlDq/fi_workdir/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.9iPmgMNlDq/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.9iPmgMNlDq/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1309.983693
EM: Round [1] log likelihood: -1309.983693
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.9iPmgMNlDq/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 187053789
Warning - not locating file: /tmp/nxf.9iPmgMNlDq/aih-tih-sc-f29b4f-R1_A23WJ53LT4_1.gmap_trinity_GG.fusions.gff3.bed
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]
ls: cannot access 'IGV_inputs': No such file or directory