Done.
-parsing GTF file: /tmp/nxf.81I38cEj2H/tih_rna_sample_00136_B23WHTKLT4_2.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.81I38cEj2H/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.81I38cEj2H/tih_rna_sample_00136_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.81I38cEj2H/tih_rna_sample_00136_B23WHTKLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.81I38cEj2H/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.81I38cEj2H/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00136_B23WHTKLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00136_B23WHTKLT4_2.star.sortedByCoord.out.bam
10:52:39 : INFO : Done.
-parsing GTF file: /tmp/nxf.81I38cEj2H/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_2.gtf
-parsing /tmp/nxf.81I38cEj2H/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_2.star.cSorted.dupsMarked.bam
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[3970000] -done parsing /tmp/nxf.81I38cEj2H/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'low complexity anchor region' => 12,
'per_id < 96' => 15537,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 500,
'small anchor length' => 14,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 106,
'seq-similar region overlap' => 146,
'exons hit < 2' => 8,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 578,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 18,
' ** passed ** ' => 13698,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 227,
'excessive soft clipping' => 23961,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8,
'num genes matched < 2' => 67
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.81I38cEj2H/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[179000] -fusion SPANNING read extraction for scaff: ACIN1--SLC7A8
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[10000] -fusion SPANNING read extraction for scaff: AL157834.2--PDLIM1
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[30000] -fusion SPANNING read extraction for scaff: ARHGEF10L--ACTL8
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[198000] -fusion SPANNING read extraction for scaff: BAZ2B--CRTC1
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[350000] -fusion SPANNING read extraction for scaff: BPNT2--KMT2C
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[27000] -fusion SPANNING read extraction for scaff: CALU--FAM71F1
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[45000] -fusion SPANNING read extraction for scaff: CTPS1--NFYC
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[36000] -fusion SPANNING read extraction for scaff: DDRGK1--SLC4A11
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[69000] -fusion SPANNING read extraction for scaff: FGD4--MAP3K13
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[68000] -fusion SPANNING read extraction for scaff: FGFR2--SORBS1
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[73000] -fusion SPANNING read extraction for scaff: IARS1--NOL8
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[34000] -fusion SPANNING read extraction for scaff: IFNGR2--EVA1C
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[27000] -fusion SPANNING read extraction for scaff: LCLAT1--WDR43
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[332000] -fusion SPANNING read extraction for scaff: MAPKAP1--ENG
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[166000] -fusion SPANNING read extraction for scaff: MDN1--BACH2
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[32000] -fusion SPANNING read extraction for scaff: MFSD6--PMS1
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[141000] -fusion SPANNING read extraction for scaff: NCOA6--TRPC4AP
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[63000] -fusion SPANNING read extraction for scaff: NMNAT3--AC046134.2
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[13000] -fusion SPANNING read extraction for scaff: NMNAT3--AC016933.1
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[95000] -fusion SPANNING read extraction for scaff: NPHP3--ACAD11
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[9000] -fusion SPANNING read extraction for scaff: OSBPL11--EGFEM1P
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[25000] -fusion SPANNING read extraction for scaff: PAWR--PPFIA2
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[8000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[7000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[8000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[31000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
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[49000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[10000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
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[10000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
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[21000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
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[22000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
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[21000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
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[22000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
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[21000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
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[31000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[48000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[22000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[22000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[20000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[119000] -fusion SPANNING read extraction for scaff: PIAS3--NBPF15
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[25000] -fusion SPANNING read extraction for scaff: PMS2P8--CCDC146
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[36000] -fusion SPANNING read extraction for scaff: PRKAR1B--MAD1L1
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[182000] -fusion SPANNING read extraction for scaff: PSMA7--LAMA5
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[304000] -fusion SPANNING read extraction for scaff: RERE--MTOR
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[3000] -fusion SPANNING read extraction for scaff: SGPP2--CT75
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[82000] -fusion SPANNING read extraction for scaff: SLC2A11--SMARCB1
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[42000] -fusion SPANNING read extraction for scaff: SMAD4--ME2
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[21000] -fusion SPANNING read extraction for scaff: SNORD62A--PLPP7
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[67000] -fusion SPANNING read extraction for scaff: SORBS1--FGFR2
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[27000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[28000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[46000] -fusion SPANNING read extraction for scaff: TRAPPC10--AGPAT3
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[89000] -fusion SPANNING read extraction for scaff: TULP4--SYNJ2
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[42000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[40000] -fusion SPANNING read extraction for scaff: ZBTB44--ADAMTS8
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 85125,
'seq similar region alignment' => 50021
};
EM: Starting log likelihood: -9759.300581
EM: Round [1] log likelihood: -9758.114276
EM: Round [2] log likelihood: -9758.078689
EM: Round [3] log likelihood: -9758.062006
EM: Round [4] log likelihood: -9758.045914
EM: Round [5] log likelihood: -9758.030229
EM: Round [6] log likelihood: -9758.014938
EM: Round [7] log likelihood: -9758.000029
EM: Round [8] log likelihood: -9757.985494
EM: Round [9] log likelihood: -9757.971321
EM: Round [10] log likelihood: -9757.957501
EM: Round [11] log likelihood: -9757.944025
EM: Round [12] log likelihood: -9757.930883
EM: Round [13] log likelihood: -9757.918066
EM: Round [14] log likelihood: -9757.905566
EM: Round [15] log likelihood: -9757.893374
EM: Round [16] log likelihood: -9757.881483
EM: Round [17] log likelihood: -9757.869884
EM: Round [18] log likelihood: -9757.858570
EM: Round [19] log likelihood: -9757.847534
EM: Round [20] log likelihood: -9757.836767
EM: Round [21] log likelihood: -9757.826263
EM: Round [22] log likelihood: -9757.816016
EM: Round [23] log likelihood: -9757.806018
EM: Round [24] log likelihood: -9757.796264
EM: Round [25] log likelihood: -9757.786746
EM: Round [26] log likelihood: -9757.777460
EM: Round [27] log likelihood: -9757.768398
EM: Round [28] log likelihood: -9757.759556
EM: Round [29] log likelihood: -9757.750927
EM: Round [30] log likelihood: -9757.742507
EM: Round [31] log likelihood: -9757.734290
EM: Round [32] log likelihood: -9757.726270
EM: Round [33] log likelihood: -9757.718444
EM: Round [34] log likelihood: -9757.710805
EM: Round [35] log likelihood: -9757.703350
EM: Round [36] log likelihood: -9757.696074
EM: Round [37] log likelihood: -9757.688972
EM: Round [38] log likelihood: -9757.682040
EM: Round [39] log likelihood: -9757.675274
EM: Round [40] log likelihood: -9757.668669
EM: Round [41] log likelihood: -9757.662222
EM: Round [42] log likelihood: -9757.655929
EM: Round [43] log likelihood: -9757.649785
EM: Round [44] log likelihood: -9757.643788
EM: Round [45] log likelihood: -9757.637933
EM: Round [46] log likelihood: -9757.632217
EM: Round [47] log likelihood: -9757.626637
EM: Round [48] log likelihood: -9757.621190
EM: Round [49] log likelihood: -9757.615871
EM: Round [50] log likelihood: -9757.610679
EM: Round [51] log likelihood: -9757.605609
EM: Round [52] log likelihood: -9757.600660
EM: Round [53] log likelihood: -9757.595827
EM: Round [54] log likelihood: -9757.591108
EM: Round [55] log likelihood: -9757.586501
EM: Round [56] log likelihood: -9757.582002
EM: Round [57] log likelihood: -9757.577610
EM: Round [58] log likelihood: -9757.573321
EM: Round [59] log likelihood: -9757.569133
EM: Round [60] log likelihood: -9757.565043
EM: Round [61] log likelihood: -9757.561050
EM: Round [62] log likelihood: -9757.557150
EM: Round [63] log likelihood: -9757.553342
EM: Round [64] log likelihood: -9757.549624
EM: Round [65] log likelihood: -9757.545993
EM: Round [66] log likelihood: -9757.542446
EM: Round [67] log likelihood: -9757.538983
EM: Round [68] log likelihood: -9757.535602
EM: Round [69] log likelihood: -9757.532299
EM: Round [70] log likelihood: -9757.529074
EM: Round [71] log likelihood: -9757.525924
EM: Round [72] log likelihood: -9757.522847
EM: Round [73] log likelihood: -9757.519843
EM: Round [74] log likelihood: -9757.516909
EM: Round [75] log likelihood: -9757.514043
EM: Round [76] log likelihood: -9757.511245
EM: Round [77] log likelihood: -9757.508511
EM: Round [78] log likelihood: -9757.505841
EM: Round [79] log likelihood: -9757.503234
EM: Round [80] log likelihood: -9757.500687
EM: Round [81] log likelihood: -9757.498200
EM: Round [82] log likelihood: -9757.495771
EM: Round [83] log likelihood: -9757.493398
EM: Round [84] log likelihood: -9757.491081
EM: Round [85] log likelihood: -9757.488817
EM: Round [86] log likelihood: -9757.486606
EM: Round [87] log likelihood: -9757.484447
EM: Round [88] log likelihood: -9757.482337
EM: Round [89] log likelihood: -9757.480277
EM: Round [90] log likelihood: -9757.478264
EM: Round [91] log likelihood: -9757.476299
EM: Round [92] log likelihood: -9757.474379
EM: Round [93] log likelihood: -9757.472503
EM: Round [94] log likelihood: -9757.470671
EM: Round [95] log likelihood: -9757.468882
EM: Round [96] log likelihood: -9757.467134
EM: Round [97] log likelihood: -9757.465427
EM: Round [98] log likelihood: -9757.463759
EM: Round [99] log likelihood: -9757.462130
EM: Round [100] log likelihood: -9757.460538
EM: Round [101] log likelihood: -9757.458984
EM: Round [102] log likelihood: -9757.457465
EM: Round [103] log likelihood: -9757.455982
EM: Round [104] log likelihood: -9757.454533
EM: Round [105] log likelihood: -9757.453118
EM: Round [106] log likelihood: -9757.451735
EM: Round [107] log likelihood: -9757.450384
EM: Round [108] log likelihood: -9757.449065
EM: Round [109] log likelihood: -9757.447776
EM: Round [110] log likelihood: -9757.446517
EM: Round [111] log likelihood: -9757.445287
EM: Round [112] log likelihood: -9757.444085
EM: Round [113] log likelihood: -9757.442912
EM: Round [114] log likelihood: -9757.441765
EM: Round [115] log likelihood: -9757.440645
EM: Round [116] log likelihood: -9757.439551
EM: Round [117] log likelihood: -9757.438482
EM: Round [118] log likelihood: -9757.437437
EM: Round [119] log likelihood: -9757.436417
EM: Round [120] log likelihood: -9757.435421
EM: Round [121] log likelihood: -9757.434447
EM: Round [122] log likelihood: -9757.433496
EM: Round [123] log likelihood: -9757.432567
EM: Round [124] log likelihood: -9757.431659
EM: Round [125] log likelihood: -9757.430772
EM: Round [126] log likelihood: -9757.429906
EM: Round [127] log likelihood: -9757.429060
EM: Round [128] log likelihood: -9757.428233
EM: Round [129] log likelihood: -9757.427425
EM: Round [130] log likelihood: -9757.426636
EM: Round [131] log likelihood: -9757.425865
EM: Round [132] log likelihood: -9757.425112
EM: Round [133] log likelihood: -9757.424376
EM: Round [134] log likelihood: -9757.423657
EM: Round [135] log likelihood: -9757.422955
EM: Round [136] log likelihood: -9757.422269
EM: Round [137] log likelihood: -9757.421599
EM: Round [138] log likelihood: -9757.420944
EM: Round [139] log likelihood: -9757.420304
EM: Round [140] log likelihood: -9757.419679
EM: Round [141] log likelihood: -9757.419069
EM: Round [142] log likelihood: -9757.418472
EM: Round [143] log likelihood: -9757.417890
EM: Round [144] log likelihood: -9757.417320
EM: Round [145] log likelihood: -9757.416764
EM: Round [146] log likelihood: -9757.416221
EM: Round [147] log likelihood: -9757.415690
EM: Round [148] log likelihood: -9757.415171
EM: Round [149] log likelihood: -9757.414664
EM: Round [150] log likelihood: -9757.414169
EM: Round [151] log likelihood: -9757.413685
EM: Round [152] log likelihood: -9757.413213
EM: Round [153] log likelihood: -9757.412751
EM: Round [154] log likelihood: -9757.412300
EM: Round [155] log likelihood: -9757.411859
EM: Round [156] log likelihood: -9757.411429
EM: Round [157] log likelihood: -9757.411008
EM: Round [158] log likelihood: -9757.410597
EM: Round [159] log likelihood: -9757.410196
EM: Round [160] log likelihood: -9757.409804
EM: Round [161] log likelihood: -9757.409420
EM: Round [162] log likelihood: -9757.409046
EM: Round [163] log likelihood: -9757.408680
EM: Round [164] log likelihood: -9757.408323
EM: Round [165] log likelihood: -9757.407974
EM: Round [166] log likelihood: -9757.407632
EM: Round [167] log likelihood: -9757.407299
EM: Round [168] log likelihood: -9757.406973
EM: Round [169] log likelihood: -9757.406655
EM: Round [170] log likelihood: -9757.406345
EM: Round [171] log likelihood: -9757.406041
EM: Round [172] log likelihood: -9757.405744
EM: Round [173] log likelihood: -9757.405454
EM: Round [174] log likelihood: -9757.405171
EM: Round [175] log likelihood: -9757.404894
EM: Round [176] log likelihood: -9757.404624
EM: Round [177] log likelihood: -9757.404360
EM: Round [178] log likelihood: -9757.404102
EM: Round [179] log likelihood: -9757.403850
EM: Round [180] log likelihood: -9757.403603
EM: Round [181] log likelihood: -9757.403363
EM: Round [182] log likelihood: -9757.403128
EM: Round [183] log likelihood: -9757.402898
EM: Round [184] log likelihood: -9757.402673
EM: Round [185] log likelihood: -9757.402454
EM: Round [186] log likelihood: -9757.402240
EM: Round [187] log likelihood: -9757.402031
EM: Round [188] log likelihood: -9757.401826
EM: Round [189] log likelihood: -9757.401626
EM: Round [190] log likelihood: -9757.401431
EM: Round [191] log likelihood: -9757.401240
EM: Round [192] log likelihood: -9757.401054
EM: Round [193] log likelihood: -9757.400872
EM: Round [194] log likelihood: -9757.400694
EM: Round [195] log likelihood: -9757.400520
EM: Round [196] log likelihood: -9757.400350
EM: Round [197] log likelihood: -9757.400184
EM: Round [198] log likelihood: -9757.400022
EM: Round [199] log likelihood: -9757.399864
EM: Round [200] log likelihood: -9757.399709
EM: Round [201] log likelihood: -9757.399558
EM: Round [202] log likelihood: -9757.399410
EM: Round [203] log likelihood: -9757.399266
EM: Round [204] log likelihood: -9757.399125
EM: Round [205] log likelihood: -9757.398987
EM: Round [206] log likelihood: -9757.398853
EM: Round [207] log likelihood: -9757.398721
EM: Round [208] log likelihood: -9757.398593
EM: Round [209] log likelihood: -9757.398467
EM: Round [210] log likelihood: -9757.398344
EM: Round [211] log likelihood: -9757.398225
EM: Round [212] log likelihood: -9757.398108
EM: Round [213] log likelihood: -9757.397993
EM: Round [214] log likelihood: -9757.397881
EM: Round [215] log likelihood: -9757.397772
EM: Round [216] log likelihood: -9757.397665
EM: Round [217] log likelihood: -9757.397561
EM: Round [218] log likelihood: -9757.397459
EM: Round [219] log likelihood: -9757.397360
EM: Stopping iterations at round 219 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.81I38cEj2H/tih_rna_sample_00136_B23WHTKLT4_2.consolidated.bam into /tmp/nxf.81I38cEj2H/tih_rna_sample_00136_B23WHTKLT4_2.consolidated.bam.read_coords
CMD: touch /tmp/nxf.81I38cEj2H/tih_rna_sample_00136_B23WHTKLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.81I38cEj2H/tih_rna_sample_00136_B23WHTKLT4_2.consolidated.bam.read_coords > /tmp/nxf.81I38cEj2H/tih_rna_sample_00136_B23WHTKLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.81I38cEj2H/tih_rna_sample_00136_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.81I38cEj2H/tih_rna_sample_00136_B23WHTKLT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.81I38cEj2H/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_2.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.81I38cEj2H/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_2.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.81I38cEj2H/fi_workdir/tih_rna_sample_00136_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.81I38cEj2H/tih_rna_sample_00136_B23WHTKLT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.81I38cEj2H/tih_rna_sample_00136_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -9235.706690
EM: Round [1] log likelihood: -9235.598910
EM: Round [2] log likelihood: -9235.598501
EM: Round [3] log likelihood: -9235.598499
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.81I38cEj2H/tih_rna_sample_00136_B23WHTKLT4_2_1.fastp.fastq.gz: 265963273
Warning - not locating file: /tmp/nxf.81I38cEj2H/tih_rna_sample_00136_B23WHTKLT4_2.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]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000237732.9]
WARNING, no entry stored in dbm for [ENSG00000237732.9]
WARNING, no entry stored in dbm for [ENSG00000237732.9]
WARNING, no entry stored in dbm for [ENSG00000206120.11]
WARNING, no entry stored in dbm for [ENSG00000234026.1]
ls: cannot access 'IGV_inputs': No such file or directory