Done.
-parsing GTF file: /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.77MBojOn4X/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.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
22:21:45 : INFO : Done.
-parsing GTF file: /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[1290000] -done parsing /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'small anchor length' => 30,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 59,
'num genes matched < 2' => 7,
'per_id < 96' => 7151,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 6,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 48,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'excessive soft clipping' => 10698,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 20,
' ** passed ** ' => 8354,
'seq-similar region overlap' => 3,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 26,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 20
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[15000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
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[155000] -fusion SPANNING read extraction for scaff: EPC1--MYO3A
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[53000] -fusion SPANNING read extraction for scaff: FGGY--ZMYM4
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[204000] -fusion SPANNING read extraction for scaff: GMDS--GSE1
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[45000] -fusion SPANNING read extraction for scaff: NFIA--DAB1
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[49000] -fusion SPANNING read extraction for scaff: NFIA--OMA1
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[8000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[8000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[54000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[95000] -fusion SPANNING read extraction for scaff: SSBP3--PATJ
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[20000] -fusion SPANNING read extraction for scaff: STIL--LRRC42
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[43000] -fusion SPANNING read extraction for scaff: ZNF362--STIL
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 16202,
'lacks exon overlap' => 12719
};
EM: Starting log likelihood: -7174.658568
EM: Round [1] log likelihood: -7173.347976
EM: Round [2] log likelihood: -7173.027477
EM: Round [3] log likelihood: -7172.742674
EM: Round [4] log likelihood: -7172.486782
EM: Round [5] log likelihood: -7172.254836
EM: Round [6] log likelihood: -7172.043046
EM: Round [7] log likelihood: -7171.848456
EM: Round [8] log likelihood: -7171.668711
EM: Round [9] log likelihood: -7171.501910
EM: Round [10] log likelihood: -7171.346492
EM: Round [11] log likelihood: -7171.201161
EM: Round [12] log likelihood: -7171.064831
EM: Round [13] log likelihood: -7170.936579
EM: Round [14] log likelihood: -7170.815618
EM: Round [15] log likelihood: -7170.701268
EM: Round [16] log likelihood: -7170.592940
EM: Round [17] log likelihood: -7170.490121
EM: Round [18] log likelihood: -7170.392357
EM: Round [19] log likelihood: -7170.299251
EM: Round [20] log likelihood: -7170.210446
EM: Round [21] log likelihood: -7170.125629
EM: Round [22] log likelihood: -7170.044515
EM: Round [23] log likelihood: -7169.966851
EM: Round [24] log likelihood: -7169.892407
EM: Round [25] log likelihood: -7169.820975
EM: Round [26] log likelihood: -7169.752368
EM: Round [27] log likelihood: -7169.686412
EM: Round [28] log likelihood: -7169.622952
EM: Round [29] log likelihood: -7169.561843
EM: Round [30] log likelihood: -7169.502953
EM: Round [31] log likelihood: -7169.446162
EM: Round [32] log likelihood: -7169.391356
EM: Round [33] log likelihood: -7169.338433
EM: Round [34] log likelihood: -7169.287297
EM: Round [35] log likelihood: -7169.237858
EM: Round [36] log likelihood: -7169.190034
EM: Round [37] log likelihood: -7169.143747
EM: Round [38] log likelihood: -7169.098927
EM: Round [39] log likelihood: -7169.055505
EM: Round [40] log likelihood: -7169.013419
EM: Round [41] log likelihood: -7168.972610
EM: Round [42] log likelihood: -7168.933023
EM: Round [43] log likelihood: -7168.894605
EM: Round [44] log likelihood: -7168.857309
EM: Round [45] log likelihood: -7168.821088
EM: Round [46] log likelihood: -7168.785899
EM: Round [47] log likelihood: -7168.751700
EM: Round [48] log likelihood: -7168.718454
EM: Round [49] log likelihood: -7168.686123
EM: Round [50] log likelihood: -7168.654674
EM: Round [51] log likelihood: -7168.624072
EM: Round [52] log likelihood: -7168.594288
EM: Round [53] log likelihood: -7168.565291
EM: Round [54] log likelihood: -7168.537053
EM: Round [55] log likelihood: -7168.509548
EM: Round [56] log likelihood: -7168.482750
EM: Round [57] log likelihood: -7168.456635
EM: Round [58] log likelihood: -7168.431180
EM: Round [59] log likelihood: -7168.406363
EM: Round [60] log likelihood: -7168.382163
EM: Round [61] log likelihood: -7168.358559
EM: Round [62] log likelihood: -7168.335533
EM: Round [63] log likelihood: -7168.313065
EM: Round [64] log likelihood: -7168.291140
EM: Round [65] log likelihood: -7168.269739
EM: Round [66] log likelihood: -7168.248846
EM: Round [67] log likelihood: -7168.228446
EM: Round [68] log likelihood: -7168.208525
EM: Round [69] log likelihood: -7168.189067
EM: Round [70] log likelihood: -7168.170060
EM: Round [71] log likelihood: -7168.151490
EM: Round [72] log likelihood: -7168.133344
EM: Round [73] log likelihood: -7168.115610
EM: Round [74] log likelihood: -7168.098276
EM: Round [75] log likelihood: -7168.081332
EM: Round [76] log likelihood: -7168.064767
EM: Round [77] log likelihood: -7168.048569
EM: Round [78] log likelihood: -7168.032729
EM: Round [79] log likelihood: -7168.017237
EM: Round [80] log likelihood: -7168.002083
EM: Round [81] log likelihood: -7167.987260
EM: Round [82] log likelihood: -7167.972757
EM: Round [83] log likelihood: -7167.958566
EM: Round [84] log likelihood: -7167.944680
EM: Round [85] log likelihood: -7167.931091
EM: Round [86] log likelihood: -7167.917790
EM: Round [87] log likelihood: -7167.904771
EM: Round [88] log likelihood: -7167.892025
EM: Round [89] log likelihood: -7167.879548
EM: Round [90] log likelihood: -7167.867331
EM: Round [91] log likelihood: -7167.855368
EM: Round [92] log likelihood: -7167.843653
EM: Round [93] log likelihood: -7167.832180
EM: Round [94] log likelihood: -7167.820943
EM: Round [95] log likelihood: -7167.809936
EM: Round [96] log likelihood: -7167.799154
EM: Round [97] log likelihood: -7167.788591
EM: Round [98] log likelihood: -7167.778242
EM: Round [99] log likelihood: -7167.768103
EM: Round [100] log likelihood: -7167.758168
EM: Round [101] log likelihood: -7167.748432
EM: Round [102] log likelihood: -7167.738891
EM: Round [103] log likelihood: -7167.729540
EM: Round [104] log likelihood: -7167.720375
EM: Round [105] log likelihood: -7167.711392
EM: Round [106] log likelihood: -7167.702586
EM: Round [107] log likelihood: -7167.693954
EM: Round [108] log likelihood: -7167.685492
EM: Round [109] log likelihood: -7167.677195
EM: Round [110] log likelihood: -7167.669060
EM: Round [111] log likelihood: -7167.661084
EM: Round [112] log likelihood: -7167.653264
EM: Round [113] log likelihood: -7167.645594
EM: Round [114] log likelihood: -7167.638073
EM: Round [115] log likelihood: -7167.630697
EM: Round [116] log likelihood: -7167.623464
EM: Round [117] log likelihood: -7167.616369
EM: Round [118] log likelihood: -7167.609409
EM: Round [119] log likelihood: -7167.602583
EM: Round [120] log likelihood: -7167.595887
EM: Round [121] log likelihood: -7167.589319
EM: Round [122] log likelihood: -7167.582875
EM: Round [123] log likelihood: -7167.576553
EM: Round [124] log likelihood: -7167.570351
EM: Round [125] log likelihood: -7167.564265
EM: Round [126] log likelihood: -7167.558295
EM: Round [127] log likelihood: -7167.552436
EM: Round [128] log likelihood: -7167.546687
EM: Round [129] log likelihood: -7167.541046
EM: Round [130] log likelihood: -7167.535511
EM: Round [131] log likelihood: -7167.530078
EM: Round [132] log likelihood: -7167.524747
EM: Round [133] log likelihood: -7167.519515
EM: Round [134] log likelihood: -7167.514379
EM: Round [135] log likelihood: -7167.509339
EM: Round [136] log likelihood: -7167.504392
EM: Round [137] log likelihood: -7167.499537
EM: Round [138] log likelihood: -7167.494771
EM: Round [139] log likelihood: -7167.490092
EM: Round [140] log likelihood: -7167.485500
EM: Round [141] log likelihood: -7167.480992
EM: Round [142] log likelihood: -7167.476566
EM: Round [143] log likelihood: -7167.472222
EM: Round [144] log likelihood: -7167.467956
EM: Round [145] log likelihood: -7167.463769
EM: Round [146] log likelihood: -7167.459657
EM: Round [147] log likelihood: -7167.455621
EM: Round [148] log likelihood: -7167.451658
EM: Round [149] log likelihood: -7167.447766
EM: Round [150] log likelihood: -7167.443946
EM: Round [151] log likelihood: -7167.440194
EM: Round [152] log likelihood: -7167.436510
EM: Round [153] log likelihood: -7167.432893
EM: Round [154] log likelihood: -7167.429341
EM: Round [155] log likelihood: -7167.425853
EM: Round [156] log likelihood: -7167.422427
EM: Round [157] log likelihood: -7167.419063
EM: Round [158] log likelihood: -7167.415760
EM: Round [159] log likelihood: -7167.412515
EM: Round [160] log likelihood: -7167.409329
EM: Round [161] log likelihood: -7167.406200
EM: Round [162] log likelihood: -7167.403127
EM: Round [163] log likelihood: -7167.400108
EM: Round [164] log likelihood: -7167.397144
EM: Round [165] log likelihood: -7167.394232
EM: Round [166] log likelihood: -7167.391372
EM: Round [167] log likelihood: -7167.388563
EM: Round [168] log likelihood: -7167.385803
EM: Round [169] log likelihood: -7167.383093
EM: Round [170] log likelihood: -7167.380431
EM: Round [171] log likelihood: -7167.377816
EM: Round [172] log likelihood: -7167.375247
EM: Round [173] log likelihood: -7167.372724
EM: Round [174] log likelihood: -7167.370245
EM: Round [175] log likelihood: -7167.367811
EM: Round [176] log likelihood: -7167.365419
EM: Round [177] log likelihood: -7167.363069
EM: Round [178] log likelihood: -7167.360760
EM: Round [179] log likelihood: -7167.358493
EM: Round [180] log likelihood: -7167.356265
EM: Round [181] log likelihood: -7167.354076
EM: Round [182] log likelihood: -7167.351926
EM: Round [183] log likelihood: -7167.349813
EM: Round [184] log likelihood: -7167.347738
EM: Round [185] log likelihood: -7167.345699
EM: Round [186] log likelihood: -7167.343696
EM: Round [187] log likelihood: -7167.341727
EM: Round [188] log likelihood: -7167.339793
EM: Round [189] log likelihood: -7167.337893
EM: Round [190] log likelihood: -7167.336027
EM: Round [191] log likelihood: -7167.334192
EM: Round [192] log likelihood: -7167.332390
EM: Round [193] log likelihood: -7167.330619
EM: Round [194] log likelihood: -7167.328879
EM: Round [195] log likelihood: -7167.327170
EM: Round [196] log likelihood: -7167.325490
EM: Round [197] log likelihood: -7167.323839
EM: Round [198] log likelihood: -7167.322217
EM: Round [199] log likelihood: -7167.320623
EM: Round [200] log likelihood: -7167.319057
EM: Round [201] log likelihood: -7167.317518
EM: Round [202] log likelihood: -7167.316006
EM: Round [203] log likelihood: -7167.314520
EM: Round [204] log likelihood: -7167.313060
EM: Round [205] log likelihood: -7167.311625
EM: Round [206] log likelihood: -7167.310215
EM: Round [207] log likelihood: -7167.308830
EM: Round [208] log likelihood: -7167.307468
EM: Round [209] log likelihood: -7167.306130
EM: Round [210] log likelihood: -7167.304815
EM: Round [211] log likelihood: -7167.303523
EM: Round [212] log likelihood: -7167.302253
EM: Round [213] log likelihood: -7167.301005
EM: Round [214] log likelihood: -7167.299778
EM: Round [215] log likelihood: -7167.298573
EM: Round [216] log likelihood: -7167.297389
EM: Round [217] log likelihood: -7167.296224
EM: Round [218] log likelihood: -7167.295080
EM: Round [219] log likelihood: -7167.293956
EM: Round [220] log likelihood: -7167.292851
EM: Round [221] log likelihood: -7167.291765
EM: Round [222] log likelihood: -7167.290698
EM: Round [223] log likelihood: -7167.289649
EM: Round [224] log likelihood: -7167.288618
EM: Round [225] log likelihood: -7167.287605
EM: Round [226] log likelihood: -7167.286609
EM: Round [227] log likelihood: -7167.285631
EM: Round [228] log likelihood: -7167.284669
EM: Round [229] log likelihood: -7167.283724
EM: Round [230] log likelihood: -7167.282794
EM: Round [231] log likelihood: -7167.281881
EM: Round [232] log likelihood: -7167.280984
EM: Round [233] log likelihood: -7167.280102
EM: Round [234] log likelihood: -7167.279235
EM: Round [235] log likelihood: -7167.278383
EM: Round [236] log likelihood: -7167.277545
EM: Round [237] log likelihood: -7167.276722
EM: Round [238] log likelihood: -7167.275913
EM: Round [239] log likelihood: -7167.275118
EM: Round [240] log likelihood: -7167.274336
EM: Round [241] log likelihood: -7167.273568
EM: Round [242] log likelihood: -7167.272813
EM: Round [243] log likelihood: -7167.272070
EM: Round [244] log likelihood: -7167.271341
EM: Round [245] log likelihood: -7167.270624
EM: Round [246] log likelihood: -7167.269919
EM: Round [247] log likelihood: -7167.269226
EM: Round [248] log likelihood: -7167.268545
EM: Round [249] log likelihood: -7167.267876
EM: Round [250] log likelihood: -7167.267218
EM: Round [251] log likelihood: -7167.266571
EM: Round [252] log likelihood: -7167.265936
EM: Round [253] log likelihood: -7167.265311
EM: Round [254] log likelihood: -7167.264697
EM: Round [255] log likelihood: -7167.264093
EM: Round [256] log likelihood: -7167.263500
EM: Round [257] log likelihood: -7167.262917
EM: Round [258] log likelihood: -7167.262343
EM: Round [259] log likelihood: -7167.261780
EM: Round [260] log likelihood: -7167.261226
EM: Round [261] log likelihood: -7167.260682
EM: Round [262] log likelihood: -7167.260146
EM: Round [263] log likelihood: -7167.259620
EM: Round [264] log likelihood: -7167.259103
EM: Round [265] log likelihood: -7167.258595
EM: Round [266] log likelihood: -7167.258095
EM: Round [267] log likelihood: -7167.257604
EM: Round [268] log likelihood: -7167.257121
EM: Round [269] log likelihood: -7167.256646
EM: Round [270] log likelihood: -7167.256180
EM: Round [271] log likelihood: -7167.255721
EM: Round [272] log likelihood: -7167.255270
EM: Round [273] log likelihood: -7167.254827
EM: Round [274] log likelihood: -7167.254392
EM: Round [275] log likelihood: -7167.253963
EM: Round [276] log likelihood: -7167.253543
EM: Round [277] log likelihood: -7167.253129
EM: Round [278] log likelihood: -7167.252722
EM: Round [279] log likelihood: -7167.252322
EM: Round [280] log likelihood: -7167.251929
EM: Round [281] log likelihood: -7167.251543
EM: Round [282] log likelihood: -7167.251163
EM: Round [283] log likelihood: -7167.250789
EM: Round [284] log likelihood: -7167.250422
EM: Round [285] log likelihood: -7167.250062
EM: Round [286] log likelihood: -7167.249707
EM: Round [287] log likelihood: -7167.249358
EM: Round [288] log likelihood: -7167.249016
EM: Round [289] log likelihood: -7167.248679
EM: Round [290] log likelihood: -7167.248347
EM: Round [291] log likelihood: -7167.248022
EM: Round [292] log likelihood: -7167.247702
EM: Round [293] log likelihood: -7167.247387
EM: Round [294] log likelihood: -7167.247078
EM: Round [295] log likelihood: -7167.246774
EM: Round [296] log likelihood: -7167.246475
EM: Round [297] log likelihood: -7167.246181
EM: Round [298] log likelihood: -7167.245892
EM: Round [299] log likelihood: -7167.245608
EM: Round [300] log likelihood: -7167.245329
EM: Round [301] log likelihood: -7167.245055
EM: Round [302] log likelihood: -7167.244785
EM: Round [303] log likelihood: -7167.244520
EM: Round [304] log likelihood: -7167.244259
EM: Round [305] log likelihood: -7167.244003
EM: Round [306] log likelihood: -7167.243751
EM: Round [307] log likelihood: -7167.243503
EM: Round [308] log likelihood: -7167.243259
EM: Round [309] log likelihood: -7167.243020
EM: Round [310] log likelihood: -7167.242785
EM: Round [311] log likelihood: -7167.242553
EM: Round [312] log likelihood: -7167.242326
EM: Round [313] log likelihood: -7167.242102
EM: Round [314] log likelihood: -7167.241883
EM: Round [315] log likelihood: -7167.241667
EM: Round [316] log likelihood: -7167.241454
EM: Round [317] log likelihood: -7167.241245
EM: Round [318] log likelihood: -7167.241040
EM: Round [319] log likelihood: -7167.240838
EM: Round [320] log likelihood: -7167.240640
EM: Round [321] log likelihood: -7167.240445
EM: Round [322] log likelihood: -7167.240253
EM: Round [323] log likelihood: -7167.240065
EM: Round [324] log likelihood: -7167.239879
EM: Round [325] log likelihood: -7167.239697
EM: Round [326] log likelihood: -7167.239518
EM: Round [327] log likelihood: -7167.239342
EM: Round [328] log likelihood: -7167.239169
EM: Round [329] log likelihood: -7167.238999
EM: Round [330] log likelihood: -7167.238831
EM: Round [331] log likelihood: -7167.238667
EM: Round [332] log likelihood: -7167.238505
EM: Round [333] log likelihood: -7167.238346
EM: Round [334] log likelihood: -7167.238190
EM: Round [335] log likelihood: -7167.238036
EM: Round [336] log likelihood: -7167.237885
EM: Round [337] log likelihood: -7167.237737
EM: Round [338] log likelihood: -7167.237591
EM: Round [339] log likelihood: -7167.237448
EM: Round [340] log likelihood: -7167.237307
EM: Round [341] log likelihood: -7167.237168
EM: Round [342] log likelihood: -7167.237032
EM: Round [343] log likelihood: -7167.236897
EM: Round [344] log likelihood: -7167.236766
EM: Round [345] log likelihood: -7167.236636
EM: Round [346] log likelihood: -7167.236509
EM: Round [347] log likelihood: -7167.236384
EM: Round [348] log likelihood: -7167.236261
EM: Round [349] log likelihood: -7167.236140
EM: Round [350] log likelihood: -7167.236021
EM: Round [351] log likelihood: -7167.235904
EM: Round [352] log likelihood: -7167.235789
EM: Round [353] log likelihood: -7167.235676
EM: Round [354] log likelihood: -7167.235565
EM: Round [355] log likelihood: -7167.235455
EM: Round [356] log likelihood: -7167.235348
EM: Round [357] log likelihood: -7167.235242
EM: Round [358] log likelihood: -7167.235139
EM: Round [359] log likelihood: -7167.235036
EM: Round [360] log likelihood: -7167.234936
EM: Round [361] log likelihood: -7167.234837
EM: Stopping iterations at round 361 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_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.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_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.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -6816.915798
EM: Round [1] log likelihood: -6816.426848
EM: Round [2] log likelihood: -6816.426782
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296887005
Warning - not locating file: /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
ls: cannot access 'IGV_inputs': No such file or directory