Done.
-parsing GTF file: /tmp/nxf.cSkHntQf4x/aih-tih-sc-804b22-R1_A23WJ53LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.cSkHntQf4x/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.cSkHntQf4x/aih-tih-sc-804b22-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.cSkHntQf4x/aih-tih-sc-804b22-R1_A23WJ53LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.cSkHntQf4x/fi_workdir/aih-tih-sc-804b22-R1_A23WJ53LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.cSkHntQf4x/fi_workdir/aih-tih-sc-804b22-R1_A23WJ53LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-804b22-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-804b22-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
11:57:07 : INFO : Done.
-parsing GTF file: /tmp/nxf.cSkHntQf4x/fi_workdir/aih-tih-sc-804b22-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.cSkHntQf4x/fi_workdir/aih-tih-sc-804b22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam

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[1110000]   -done parsing /tmp/nxf.cSkHntQf4x/fi_workdir/aih-tih-sc-804b22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num genes matched < 2' => 3,
          'seq-similar region overlap' => 86,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 214,
          'exons hit < 2' => 1,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 4,
          'low complexity anchor region' => 3,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 228,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 124,
          ' ** passed ** ' => 6279,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
          'per_id < 96' => 3404,
          'excessive soft clipping' => 6905,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 654,
          'small anchor length' => 12
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.cSkHntQf4x/fi_workdir/aih-tih-sc-804b22-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[4000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[15000]   -fusion SPANNING read extraction for scaff: ANKFN1--IKZF3

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[25000]   -fusion SPANNING read extraction for scaff: ANKIB1--RUNDC3B

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[62000]   -fusion SPANNING read extraction for scaff: CISD3--AC011447.3

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[126000]   -fusion SPANNING read extraction for scaff: CRTC1--TEKT4P2

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[126000]   -fusion SPANNING read extraction for scaff: CRTC1--CR381653.1

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[63000]   -fusion SPANNING read extraction for scaff: DOCK8--PGM5P3-AS1

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[63000]   -fusion SPANNING read extraction for scaff: DOCK8--PGM5P4-AS1

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[12000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[6000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1

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[6000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2

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[6000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

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[13000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

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[13000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

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[9000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

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[13000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

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[73000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

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[95000]   -fusion SPANNING read extraction for scaff: PCGF2--AC011447.3

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[57000]   -fusion SPANNING read extraction for scaff: TEX2--STRADA

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[23000]   -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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[20000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[62000]   -fusion SPANNING read extraction for scaff: UPF1--AC011474.1

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[24000]   -fusion SPANNING read extraction for scaff: YIPF2--VN1R7P

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[24000]   -fusion SPANNING read extraction for scaff: YIPF2--AF254983.2
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 12811,
          'lacks exon overlap' => 14881
        };
EM: Starting log likelihood: -2337.176500
EM: Round [1] log likelihood: -2336.795516
EM: Round [2] log likelihood: -2336.557471
EM: Round [3] log likelihood: -2336.344513
EM: Round [4] log likelihood: -2336.153762
EM: Round [5] log likelihood: -2335.982721
EM: Round [6] log likelihood: -2335.829196
EM: Round [7] log likelihood: -2335.691263
EM: Round [8] log likelihood: -2335.567225
EM: Round [9] log likelihood: -2335.455584
EM: Round [10] log likelihood: -2335.355015
EM: Round [11] log likelihood: -2335.264344
EM: Round [12] log likelihood: -2335.182529
EM: Round [13] log likelihood: -2335.108644
EM: Round [14] log likelihood: -2335.041864
EM: Round [15] log likelihood: -2334.981456
EM: Round [16] log likelihood: -2334.926764
EM: Round [17] log likelihood: -2334.877204
EM: Round [18] log likelihood: -2334.832254
EM: Round [19] log likelihood: -2334.791447
EM: Round [20] log likelihood: -2334.754364
EM: Round [21] log likelihood: -2334.720633
EM: Round [22] log likelihood: -2334.689917
EM: Round [23] log likelihood: -2334.661917
EM: Round [24] log likelihood: -2334.636363
EM: Round [25] log likelihood: -2334.613014
EM: Round [26] log likelihood: -2334.591653
EM: Round [27] log likelihood: -2334.572086
EM: Round [28] log likelihood: -2334.554137
EM: Round [29] log likelihood: -2334.537650
EM: Round [30] log likelihood: -2334.522484
EM: Round [31] log likelihood: -2334.508511
EM: Round [32] log likelihood: -2334.495618
EM: Round [33] log likelihood: -2334.483703
EM: Round [34] log likelihood: -2334.472672
EM: Round [35] log likelihood: -2334.462443
EM: Round [36] log likelihood: -2334.452940
EM: Round [37] log likelihood: -2334.444098
EM: Round [38] log likelihood: -2334.435855
EM: Round [39] log likelihood: -2334.428156
EM: Round [40] log likelihood: -2334.420953
EM: Round [41] log likelihood: -2334.414200
EM: Round [42] log likelihood: -2334.407858
EM: Round [43] log likelihood: -2334.401891
EM: Round [44] log likelihood: -2334.396267
EM: Round [45] log likelihood: -2334.390955
EM: Round [46] log likelihood: -2334.385930
EM: Round [47] log likelihood: -2334.381167
EM: Round [48] log likelihood: -2334.376644
EM: Round [49] log likelihood: -2334.372343
EM: Round [50] log likelihood: -2334.368246
EM: Round [51] log likelihood: -2334.364336
EM: Round [52] log likelihood: -2334.360599
EM: Round [53] log likelihood: -2334.357022
EM: Round [54] log likelihood: -2334.353593
EM: Round [55] log likelihood: -2334.350301
EM: Round [56] log likelihood: -2334.347137
EM: Round [57] log likelihood: -2334.344091
EM: Round [58] log likelihood: -2334.341155
EM: Round [59] log likelihood: -2334.338323
EM: Round [60] log likelihood: -2334.335587
EM: Round [61] log likelihood: -2334.332942
EM: Round [62] log likelihood: -2334.330381
EM: Round [63] log likelihood: -2334.327900
EM: Round [64] log likelihood: -2334.325494
EM: Round [65] log likelihood: -2334.323159
EM: Round [66] log likelihood: -2334.320891
EM: Round [67] log likelihood: -2334.318687
EM: Round [68] log likelihood: -2334.316543
EM: Round [69] log likelihood: -2334.314456
EM: Round [70] log likelihood: -2334.312424
EM: Round [71] log likelihood: -2334.310443
EM: Round [72] log likelihood: -2334.308512
EM: Round [73] log likelihood: -2334.306629
EM: Round [74] log likelihood: -2334.304791
EM: Round [75] log likelihood: -2334.302996
EM: Round [76] log likelihood: -2334.301243
EM: Round [77] log likelihood: -2334.299531
EM: Round [78] log likelihood: -2334.297857
EM: Round [79] log likelihood: -2334.296221
EM: Round [80] log likelihood: -2334.294620
EM: Round [81] log likelihood: -2334.293055
EM: Round [82] log likelihood: -2334.291523
EM: Round [83] log likelihood: -2334.290024
EM: Round [84] log likelihood: -2334.288556
EM: Round [85] log likelihood: -2334.287119
EM: Round [86] log likelihood: -2334.285711
EM: Round [87] log likelihood: -2334.284333
EM: Round [88] log likelihood: -2334.282982
EM: Round [89] log likelihood: -2334.281659
EM: Round [90] log likelihood: -2334.280362
EM: Round [91] log likelihood: -2334.279091
EM: Round [92] log likelihood: -2334.277845
EM: Round [93] log likelihood: -2334.276624
EM: Round [94] log likelihood: -2334.275427
EM: Round [95] log likelihood: -2334.274253
EM: Round [96] log likelihood: -2334.273102
EM: Round [97] log likelihood: -2334.271973
EM: Round [98] log likelihood: -2334.270865
EM: Round [99] log likelihood: -2334.269779
EM: Round [100] log likelihood: -2334.268714
EM: Round [101] log likelihood: -2334.267669
EM: Round [102] log likelihood: -2334.266643
EM: Round [103] log likelihood: -2334.265637
EM: Round [104] log likelihood: -2334.264650
EM: Round [105] log likelihood: -2334.263682
EM: Round [106] log likelihood: -2334.262732
EM: Round [107] log likelihood: -2334.261799
EM: Round [108] log likelihood: -2334.260884
EM: Round [109] log likelihood: -2334.259986
EM: Round [110] log likelihood: -2334.259104
EM: Round [111] log likelihood: -2334.258239
EM: Round [112] log likelihood: -2334.257390
EM: Round [113] log likelihood: -2334.256557
EM: Round [114] log likelihood: -2334.255739
EM: Round [115] log likelihood: -2334.254936
EM: Round [116] log likelihood: -2334.254148
EM: Round [117] log likelihood: -2334.253374
EM: Round [118] log likelihood: -2334.252615
EM: Round [119] log likelihood: -2334.251869
EM: Round [120] log likelihood: -2334.251138
EM: Round [121] log likelihood: -2334.250419
EM: Round [122] log likelihood: -2334.249714
EM: Round [123] log likelihood: -2334.249021
EM: Round [124] log likelihood: -2334.248341
EM: Round [125] log likelihood: -2334.247674
EM: Round [126] log likelihood: -2334.247018
EM: Round [127] log likelihood: -2334.246375
EM: Round [128] log likelihood: -2334.245743
EM: Round [129] log likelihood: -2334.245122
EM: Round [130] log likelihood: -2334.244513
EM: Round [131] log likelihood: -2334.243915
EM: Round [132] log likelihood: -2334.243328
EM: Round [133] log likelihood: -2334.242751
EM: Round [134] log likelihood: -2334.242185
EM: Round [135] log likelihood: -2334.241629
EM: Round [136] log likelihood: -2334.241082
EM: Round [137] log likelihood: -2334.240546
EM: Round [138] log likelihood: -2334.240020
EM: Round [139] log likelihood: -2334.239503
EM: Round [140] log likelihood: -2334.238995
EM: Round [141] log likelihood: -2334.238496
EM: Round [142] log likelihood: -2334.238006
EM: Round [143] log likelihood: -2334.237525
EM: Round [144] log likelihood: -2334.237053
EM: Round [145] log likelihood: -2334.236589
EM: Round [146] log likelihood: -2334.236134
EM: Round [147] log likelihood: -2334.235686
EM: Round [148] log likelihood: -2334.235247
EM: Round [149] log likelihood: -2334.234815
EM: Round [150] log likelihood: -2334.234391
EM: Round [151] log likelihood: -2334.233975
EM: Round [152] log likelihood: -2334.233566
EM: Round [153] log likelihood: -2334.233165
EM: Round [154] log likelihood: -2334.232770
EM: Round [155] log likelihood: -2334.232383
EM: Round [156] log likelihood: -2334.232003
EM: Round [157] log likelihood: -2334.231629
EM: Round [158] log likelihood: -2334.231262
EM: Round [159] log likelihood: -2334.230901
EM: Round [160] log likelihood: -2334.230547
EM: Round [161] log likelihood: -2334.230200
EM: Round [162] log likelihood: -2334.229858
EM: Round [163] log likelihood: -2334.229522
EM: Round [164] log likelihood: -2334.229193
EM: Round [165] log likelihood: -2334.228869
EM: Round [166] log likelihood: -2334.228551
EM: Round [167] log likelihood: -2334.228239
EM: Round [168] log likelihood: -2334.227932
EM: Round [169] log likelihood: -2334.227631
EM: Round [170] log likelihood: -2334.227335
EM: Round [171] log likelihood: -2334.227044
EM: Round [172] log likelihood: -2334.226758
EM: Round [173] log likelihood: -2334.226477
EM: Round [174] log likelihood: -2334.226202
EM: Round [175] log likelihood: -2334.225931
EM: Round [176] log likelihood: -2334.225665
EM: Round [177] log likelihood: -2334.225404
EM: Round [178] log likelihood: -2334.225147
EM: Round [179] log likelihood: -2334.224895
EM: Round [180] log likelihood: -2334.224647
EM: Round [181] log likelihood: -2334.224404
EM: Round [182] log likelihood: -2334.224165
EM: Round [183] log likelihood: -2334.223930
EM: Round [184] log likelihood: -2334.223699
EM: Round [185] log likelihood: -2334.223473
EM: Round [186] log likelihood: -2334.223250
EM: Round [187] log likelihood: -2334.223031
EM: Round [188] log likelihood: -2334.222816
EM: Round [189] log likelihood: -2334.222605
EM: Round [190] log likelihood: -2334.222398
EM: Round [191] log likelihood: -2334.222194
EM: Round [192] log likelihood: -2334.221994
EM: Round [193] log likelihood: -2334.221797
EM: Round [194] log likelihood: -2334.221604
EM: Round [195] log likelihood: -2334.221414
EM: Round [196] log likelihood: -2334.221228
EM: Round [197] log likelihood: -2334.221044
EM: Round [198] log likelihood: -2334.220864
EM: Round [199] log likelihood: -2334.220688
EM: Round [200] log likelihood: -2334.220514
EM: Round [201] log likelihood: -2334.220343
EM: Round [202] log likelihood: -2334.220175
EM: Round [203] log likelihood: -2334.220011
EM: Round [204] log likelihood: -2334.219849
EM: Round [205] log likelihood: -2334.219690
EM: Round [206] log likelihood: -2334.219533
EM: Round [207] log likelihood: -2334.219380
EM: Round [208] log likelihood: -2334.219229
EM: Round [209] log likelihood: -2334.219081
EM: Round [210] log likelihood: -2334.218935
EM: Round [211] log likelihood: -2334.218792
EM: Round [212] log likelihood: -2334.218651
EM: Round [213] log likelihood: -2334.218513
EM: Round [214] log likelihood: -2334.218377
EM: Round [215] log likelihood: -2334.218244
EM: Round [216] log likelihood: -2334.218113
EM: Round [217] log likelihood: -2334.217984
EM: Round [218] log likelihood: -2334.217858
EM: Round [219] log likelihood: -2334.217733
EM: Round [220] log likelihood: -2334.217611
EM: Round [221] log likelihood: -2334.217491
EM: Round [222] log likelihood: -2334.217373
EM: Round [223] log likelihood: -2334.217257
EM: Round [224] log likelihood: -2334.217143
EM: Round [225] log likelihood: -2334.217031
EM: Round [226] log likelihood: -2334.216921
EM: Round [227] log likelihood: -2334.216813
EM: Round [228] log likelihood: -2334.216707
EM: Round [229] log likelihood: -2334.216603
EM: Round [230] log likelihood: -2334.216500
EM: Round [231] log likelihood: -2334.216399
EM: Round [232] log likelihood: -2334.216300
EM: Stopping iterations at round 232 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.cSkHntQf4x/aih-tih-sc-804b22-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.cSkHntQf4x/aih-tih-sc-804b22-R1_A23WJ53LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.cSkHntQf4x/aih-tih-sc-804b22-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.cSkHntQf4x/aih-tih-sc-804b22-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.cSkHntQf4x/aih-tih-sc-804b22-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.cSkHntQf4x/aih-tih-sc-804b22-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.cSkHntQf4x/aih-tih-sc-804b22-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.cSkHntQf4x/fi_workdir/aih-tih-sc-804b22-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.cSkHntQf4x/fi_workdir/aih-tih-sc-804b22-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.cSkHntQf4x/fi_workdir/aih-tih-sc-804b22-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.cSkHntQf4x/aih-tih-sc-804b22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.cSkHntQf4x/aih-tih-sc-804b22-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2048.988971
EM: Round [1] log likelihood: -2048.901793
EM: Round [2] log likelihood: -2048.901777
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.cSkHntQf4x/aih-tih-sc-804b22-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 273828684
Warning - not locating file: /tmp/nxf.cSkHntQf4x/aih-tih-sc-804b22-R1_A23WJ53LT4_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]
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]
WARNING, no entry stored in dbm for [ENSG00000277631.5]
WARNING, no entry stored in dbm for [ENSG00000277631.5]
ls: cannot access 'IGV_inputs': No such file or directory