Done.
-parsing GTF file: /tmp/nxf.KBRk8LzrnL/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.KBRk8LzrnL/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.KBRk8LzrnL/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.KBRk8LzrnL/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.KBRk8LzrnL/fi_workdir/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.KBRk8LzrnL/fi_workdir/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
22:34:57 : INFO : Done.
-parsing GTF file: /tmp/nxf.KBRk8LzrnL/fi_workdir/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.KBRk8LzrnL/fi_workdir/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[360000]   -done parsing /tmp/nxf.KBRk8LzrnL/fi_workdir/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'exons hit < 2' => 1,
          'small anchor length' => 4,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
          ' ** passed ** ' => 2548,
          'excessive soft clipping' => 2082,
          'per_id < 96' => 1005,
          'num genes matched < 2' => 10,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 3,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 36,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 24,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
          'low complexity anchor region' => 1
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.KBRk8LzrnL/fi_workdir/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[3000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

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[21000]   -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B

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[22000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

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[20000]   -fusion SPANNING read extraction for scaff: PCDHA5--PCDHAC1

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[19000]   -fusion SPANNING read extraction for scaff: PCDHA5--PCDHAC2

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[20000]   -fusion SPANNING read extraction for scaff: PMS2P6--CCDC146

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[29000]   -fusion SPANNING read extraction for scaff: YTHDC1--GABRA4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 1771
        };
EM: Starting log likelihood: -2553.550708
EM: Round [1] log likelihood: -2552.148846
EM: Round [2] log likelihood: -2552.125020
EM: Round [3] log likelihood: -2552.114312
EM: Round [4] log likelihood: -2552.104061
EM: Round [5] log likelihood: -2552.093949
EM: Round [6] log likelihood: -2552.083968
EM: Round [7] log likelihood: -2552.074114
EM: Round [8] log likelihood: -2552.064385
EM: Round [9] log likelihood: -2552.054779
EM: Round [10] log likelihood: -2552.045293
EM: Round [11] log likelihood: -2552.035925
EM: Round [12] log likelihood: -2552.026673
EM: Round [13] log likelihood: -2552.017535
EM: Round [14] log likelihood: -2552.008509
EM: Round [15] log likelihood: -2551.999594
EM: Round [16] log likelihood: -2551.990786
EM: Round [17] log likelihood: -2551.982084
EM: Round [18] log likelihood: -2551.973486
EM: Round [19] log likelihood: -2551.964992
EM: Round [20] log likelihood: -2551.956598
EM: Round [21] log likelihood: -2551.948303
EM: Round [22] log likelihood: -2551.940105
EM: Round [23] log likelihood: -2551.932004
EM: Round [24] log likelihood: -2551.923996
EM: Round [25] log likelihood: -2551.916082
EM: Round [26] log likelihood: -2551.908258
EM: Round [27] log likelihood: -2551.900525
EM: Round [28] log likelihood: -2551.892879
EM: Round [29] log likelihood: -2551.885321
EM: Round [30] log likelihood: -2551.877848
EM: Round [31] log likelihood: -2551.870460
EM: Round [32] log likelihood: -2551.863154
EM: Round [33] log likelihood: -2551.855930
EM: Round [34] log likelihood: -2551.848787
EM: Round [35] log likelihood: -2551.841722
EM: Round [36] log likelihood: -2551.834736
EM: Round [37] log likelihood: -2551.827826
EM: Round [38] log likelihood: -2551.820992
EM: Round [39] log likelihood: -2551.814232
EM: Round [40] log likelihood: -2551.807546
EM: Round [41] log likelihood: -2551.800932
EM: Round [42] log likelihood: -2551.794389
EM: Round [43] log likelihood: -2551.787917
EM: Round [44] log likelihood: -2551.781514
EM: Round [45] log likelihood: -2551.775179
EM: Round [46] log likelihood: -2551.768911
EM: Round [47] log likelihood: -2551.762710
EM: Round [48] log likelihood: -2551.756574
EM: Round [49] log likelihood: -2551.750502
EM: Round [50] log likelihood: -2551.744494
EM: Round [51] log likelihood: -2551.738548
EM: Round [52] log likelihood: -2551.732665
EM: Round [53] log likelihood: -2551.726842
EM: Round [54] log likelihood: -2551.721079
EM: Round [55] log likelihood: -2551.715376
EM: Round [56] log likelihood: -2551.709731
EM: Round [57] log likelihood: -2551.704144
EM: Round [58] log likelihood: -2551.698614
EM: Round [59] log likelihood: -2551.693140
EM: Round [60] log likelihood: -2551.687722
EM: Round [61] log likelihood: -2551.682358
EM: Round [62] log likelihood: -2551.677048
EM: Round [63] log likelihood: -2551.671792
EM: Round [64] log likelihood: -2551.666588
EM: Round [65] log likelihood: -2551.661436
EM: Round [66] log likelihood: -2551.656335
EM: Round [67] log likelihood: -2551.651285
EM: Round [68] log likelihood: -2551.646284
EM: Round [69] log likelihood: -2551.641333
EM: Round [70] log likelihood: -2551.636431
EM: Round [71] log likelihood: -2551.631577
EM: Round [72] log likelihood: -2551.626770
EM: Round [73] log likelihood: -2551.622010
EM: Round [74] log likelihood: -2551.617297
EM: Round [75] log likelihood: -2551.612629
EM: Round [76] log likelihood: -2551.608006
EM: Round [77] log likelihood: -2551.603428
EM: Round [78] log likelihood: -2551.598894
EM: Round [79] log likelihood: -2551.594404
EM: Round [80] log likelihood: -2551.589956
EM: Round [81] log likelihood: -2551.585551
EM: Round [82] log likelihood: -2551.581188
EM: Round [83] log likelihood: -2551.576867
EM: Round [84] log likelihood: -2551.572586
EM: Round [85] log likelihood: -2551.568346
EM: Round [86] log likelihood: -2551.564146
EM: Round [87] log likelihood: -2551.559986
EM: Round [88] log likelihood: -2551.555865
EM: Round [89] log likelihood: -2551.551782
EM: Round [90] log likelihood: -2551.547737
EM: Round [91] log likelihood: -2551.543730
EM: Round [92] log likelihood: -2551.539761
EM: Round [93] log likelihood: -2551.535828
EM: Round [94] log likelihood: -2551.531932
EM: Round [95] log likelihood: -2551.528072
EM: Round [96] log likelihood: -2551.524247
EM: Round [97] log likelihood: -2551.520458
EM: Round [98] log likelihood: -2551.516704
EM: Round [99] log likelihood: -2551.512984
EM: Round [100] log likelihood: -2551.509298
EM: Round [101] log likelihood: -2551.505645
EM: Round [102] log likelihood: -2551.502026
EM: Round [103] log likelihood: -2551.498440
EM: Round [104] log likelihood: -2551.494887
EM: Round [105] log likelihood: -2551.491365
EM: Round [106] log likelihood: -2551.487876
EM: Round [107] log likelihood: -2551.484418
EM: Round [108] log likelihood: -2551.480991
EM: Round [109] log likelihood: -2551.477595
EM: Round [110] log likelihood: -2551.474229
EM: Round [111] log likelihood: -2551.470894
EM: Round [112] log likelihood: -2551.467588
EM: Round [113] log likelihood: -2551.464312
EM: Round [114] log likelihood: -2551.461065
EM: Round [115] log likelihood: -2551.457847
EM: Round [116] log likelihood: -2551.454658
EM: Round [117] log likelihood: -2551.451496
EM: Round [118] log likelihood: -2551.448363
EM: Round [119] log likelihood: -2551.445258
EM: Round [120] log likelihood: -2551.442179
EM: Round [121] log likelihood: -2551.439128
EM: Round [122] log likelihood: -2551.436104
EM: Round [123] log likelihood: -2551.433106
EM: Round [124] log likelihood: -2551.430135
EM: Round [125] log likelihood: -2551.427189
EM: Round [126] log likelihood: -2551.424269
EM: Round [127] log likelihood: -2551.421375
EM: Round [128] log likelihood: -2551.418506
EM: Round [129] log likelihood: -2551.415662
EM: Round [130] log likelihood: -2551.412842
EM: Round [131] log likelihood: -2551.410047
EM: Round [132] log likelihood: -2551.407276
EM: Round [133] log likelihood: -2551.404529
EM: Round [134] log likelihood: -2551.401806
EM: Round [135] log likelihood: -2551.399106
EM: Round [136] log likelihood: -2551.396429
EM: Round [137] log likelihood: -2551.393775
EM: Round [138] log likelihood: -2551.391144
EM: Round [139] log likelihood: -2551.388536
EM: Round [140] log likelihood: -2551.385950
EM: Round [141] log likelihood: -2551.383385
EM: Round [142] log likelihood: -2551.380843
EM: Round [143] log likelihood: -2551.378323
EM: Round [144] log likelihood: -2551.375823
EM: Round [145] log likelihood: -2551.373346
EM: Round [146] log likelihood: -2551.370889
EM: Round [147] log likelihood: -2551.368452
EM: Round [148] log likelihood: -2551.366037
EM: Round [149] log likelihood: -2551.363642
EM: Round [150] log likelihood: -2551.361267
EM: Round [151] log likelihood: -2551.358912
EM: Round [152] log likelihood: -2551.356577
EM: Round [153] log likelihood: -2551.354261
EM: Round [154] log likelihood: -2551.351965
EM: Round [155] log likelihood: -2551.349688
EM: Round [156] log likelihood: -2551.347430
EM: Round [157] log likelihood: -2551.345191
EM: Round [158] log likelihood: -2551.342971
EM: Round [159] log likelihood: -2551.340769
EM: Round [160] log likelihood: -2551.338586
EM: Round [161] log likelihood: -2551.336420
EM: Round [162] log likelihood: -2551.334273
EM: Round [163] log likelihood: -2551.332144
EM: Round [164] log likelihood: -2551.330032
EM: Round [165] log likelihood: -2551.327938
EM: Round [166] log likelihood: -2551.325861
EM: Round [167] log likelihood: -2551.323801
EM: Round [168] log likelihood: -2551.321758
EM: Round [169] log likelihood: -2551.319732
EM: Round [170] log likelihood: -2551.317723
EM: Round [171] log likelihood: -2551.315730
EM: Round [172] log likelihood: -2551.313753
EM: Round [173] log likelihood: -2551.311793
EM: Round [174] log likelihood: -2551.309849
EM: Round [175] log likelihood: -2551.307921
EM: Round [176] log likelihood: -2551.306009
EM: Round [177] log likelihood: -2551.304112
EM: Round [178] log likelihood: -2551.302230
EM: Round [179] log likelihood: -2551.300364
EM: Round [180] log likelihood: -2551.298514
EM: Round [181] log likelihood: -2551.296678
EM: Round [182] log likelihood: -2551.294857
EM: Round [183] log likelihood: -2551.293051
EM: Round [184] log likelihood: -2551.291260
EM: Round [185] log likelihood: -2551.289483
EM: Round [186] log likelihood: -2551.287721
EM: Round [187] log likelihood: -2551.285973
EM: Round [188] log likelihood: -2551.284239
EM: Round [189] log likelihood: -2551.282519
EM: Round [190] log likelihood: -2551.280813
EM: Round [191] log likelihood: -2551.279120
EM: Round [192] log likelihood: -2551.277441
EM: Round [193] log likelihood: -2551.275776
EM: Round [194] log likelihood: -2551.274124
EM: Round [195] log likelihood: -2551.272486
EM: Round [196] log likelihood: -2551.270860
EM: Round [197] log likelihood: -2551.269248
EM: Round [198] log likelihood: -2551.267649
EM: Round [199] log likelihood: -2551.266062
EM: Round [200] log likelihood: -2551.264488
EM: Round [201] log likelihood: -2551.262927
EM: Round [202] log likelihood: -2551.261378
EM: Round [203] log likelihood: -2551.259841
EM: Round [204] log likelihood: -2551.258317
EM: Round [205] log likelihood: -2551.256805
EM: Round [206] log likelihood: -2551.255305
EM: Round [207] log likelihood: -2551.253817
EM: Round [208] log likelihood: -2551.252340
EM: Round [209] log likelihood: -2551.250876
EM: Round [210] log likelihood: -2551.249423
EM: Round [211] log likelihood: -2551.247981
EM: Round [212] log likelihood: -2551.246551
EM: Round [213] log likelihood: -2551.245132
EM: Round [214] log likelihood: -2551.243725
EM: Round [215] log likelihood: -2551.242328
EM: Round [216] log likelihood: -2551.240943
EM: Round [217] log likelihood: -2551.239568
EM: Round [218] log likelihood: -2551.238205
EM: Round [219] log likelihood: -2551.236852
EM: Round [220] log likelihood: -2551.235510
EM: Round [221] log likelihood: -2551.234178
EM: Round [222] log likelihood: -2551.232857
EM: Round [223] log likelihood: -2551.231546
EM: Round [224] log likelihood: -2551.230246
EM: Round [225] log likelihood: -2551.228955
EM: Round [226] log likelihood: -2551.227675
EM: Round [227] log likelihood: -2551.226405
EM: Round [228] log likelihood: -2551.225145
EM: Round [229] log likelihood: -2551.223895
EM: Round [230] log likelihood: -2551.222654
EM: Round [231] log likelihood: -2551.221423
EM: Round [232] log likelihood: -2551.220202
EM: Round [233] log likelihood: -2551.218990
EM: Round [234] log likelihood: -2551.217788
EM: Round [235] log likelihood: -2551.216595
EM: Round [236] log likelihood: -2551.215411
EM: Round [237] log likelihood: -2551.214237
EM: Round [238] log likelihood: -2551.213072
EM: Round [239] log likelihood: -2551.211916
EM: Round [240] log likelihood: -2551.210768
EM: Round [241] log likelihood: -2551.209630
EM: Round [242] log likelihood: -2551.208501
EM: Round [243] log likelihood: -2551.207380
EM: Round [244] log likelihood: -2551.206268
EM: Round [245] log likelihood: -2551.205164
EM: Round [246] log likelihood: -2551.204070
EM: Round [247] log likelihood: -2551.202983
EM: Round [248] log likelihood: -2551.201905
EM: Round [249] log likelihood: -2551.200836
EM: Round [250] log likelihood: -2551.199774
EM: Round [251] log likelihood: -2551.198721
EM: Round [252] log likelihood: -2551.197676
EM: Round [253] log likelihood: -2551.196639
EM: Round [254] log likelihood: -2551.195610
EM: Round [255] log likelihood: -2551.194589
EM: Round [256] log likelihood: -2551.193576
EM: Round [257] log likelihood: -2551.192570
EM: Round [258] log likelihood: -2551.191572
EM: Round [259] log likelihood: -2551.190582
EM: Round [260] log likelihood: -2551.189600
EM: Round [261] log likelihood: -2551.188625
EM: Round [262] log likelihood: -2551.187658
EM: Round [263] log likelihood: -2551.186698
EM: Round [264] log likelihood: -2551.185745
EM: Round [265] log likelihood: -2551.184800
EM: Round [266] log likelihood: -2551.183862
EM: Round [267] log likelihood: -2551.182931
EM: Round [268] log likelihood: -2551.182007
EM: Round [269] log likelihood: -2551.181090
EM: Round [270] log likelihood: -2551.180180
EM: Round [271] log likelihood: -2551.179278
EM: Round [272] log likelihood: -2551.178382
EM: Round [273] log likelihood: -2551.177493
EM: Round [274] log likelihood: -2551.176610
EM: Round [275] log likelihood: -2551.175735
EM: Round [276] log likelihood: -2551.174866
EM: Round [277] log likelihood: -2551.174004
EM: Round [278] log likelihood: -2551.173148
EM: Round [279] log likelihood: -2551.172299
EM: Round [280] log likelihood: -2551.171456
EM: Round [281] log likelihood: -2551.170620
EM: Round [282] log likelihood: -2551.169790
EM: Round [283] log likelihood: -2551.168966
EM: Round [284] log likelihood: -2551.168149
EM: Round [285] log likelihood: -2551.167338
EM: Round [286] log likelihood: -2551.166533
EM: Round [287] log likelihood: -2551.165734
EM: Round [288] log likelihood: -2551.164941
EM: Round [289] log likelihood: -2551.164154
EM: Round [290] log likelihood: -2551.163373
EM: Round [291] log likelihood: -2551.162598
EM: Round [292] log likelihood: -2551.161829
EM: Round [293] log likelihood: -2551.161066
EM: Round [294] log likelihood: -2551.160309
EM: Round [295] log likelihood: -2551.159557
EM: Round [296] log likelihood: -2551.158811
EM: Round [297] log likelihood: -2551.158070
EM: Round [298] log likelihood: -2551.157335
EM: Round [299] log likelihood: -2551.156606
EM: Round [300] log likelihood: -2551.155882
EM: Round [301] log likelihood: -2551.155164
EM: Round [302] log likelihood: -2551.154451
EM: Round [303] log likelihood: -2551.153743
EM: Round [304] log likelihood: -2551.153041
EM: Round [305] log likelihood: -2551.152344
EM: Round [306] log likelihood: -2551.151652
EM: Round [307] log likelihood: -2551.150966
EM: Round [308] log likelihood: -2551.150284
EM: Round [309] log likelihood: -2551.149608
EM: Round [310] log likelihood: -2551.148937
EM: Round [311] log likelihood: -2551.148271
EM: Round [312] log likelihood: -2551.147610
EM: Round [313] log likelihood: -2551.146954
EM: Round [314] log likelihood: -2551.146302
EM: Round [315] log likelihood: -2551.145656
EM: Round [316] log likelihood: -2551.145014
EM: Round [317] log likelihood: -2551.144378
EM: Round [318] log likelihood: -2551.143746
EM: Round [319] log likelihood: -2551.143119
EM: Round [320] log likelihood: -2551.142496
EM: Round [321] log likelihood: -2551.141878
EM: Round [322] log likelihood: -2551.141265
EM: Round [323] log likelihood: -2551.140657
EM: Round [324] log likelihood: -2551.140053
EM: Round [325] log likelihood: -2551.139453
EM: Round [326] log likelihood: -2551.138858
EM: Round [327] log likelihood: -2551.138267
EM: Round [328] log likelihood: -2551.137681
EM: Round [329] log likelihood: -2551.137099
EM: Round [330] log likelihood: -2551.136522
EM: Round [331] log likelihood: -2551.135949
EM: Round [332] log likelihood: -2551.135380
EM: Round [333] log likelihood: -2551.134815
EM: Round [334] log likelihood: -2551.134255
EM: Round [335] log likelihood: -2551.133698
EM: Round [336] log likelihood: -2551.133146
EM: Round [337] log likelihood: -2551.132598
EM: Round [338] log likelihood: -2551.132054
EM: Round [339] log likelihood: -2551.131515
EM: Round [340] log likelihood: -2551.130979
EM: Round [341] log likelihood: -2551.130447
EM: Round [342] log likelihood: -2551.129919
EM: Round [343] log likelihood: -2551.129395
EM: Round [344] log likelihood: -2551.128875
EM: Round [345] log likelihood: -2551.128359
EM: Round [346] log likelihood: -2551.127846
EM: Round [347] log likelihood: -2551.127338
EM: Round [348] log likelihood: -2551.126833
EM: Round [349] log likelihood: -2551.126332
EM: Round [350] log likelihood: -2551.125834
EM: Round [351] log likelihood: -2551.125341
EM: Round [352] log likelihood: -2551.124851
EM: Round [353] log likelihood: -2551.124364
EM: Round [354] log likelihood: -2551.123882
EM: Round [355] log likelihood: -2551.123403
EM: Round [356] log likelihood: -2551.122927
EM: Round [357] log likelihood: -2551.122455
EM: Round [358] log likelihood: -2551.121986
EM: Round [359] log likelihood: -2551.121521
EM: Round [360] log likelihood: -2551.121059
EM: Round [361] log likelihood: -2551.120601
EM: Round [362] log likelihood: -2551.120146
EM: Round [363] log likelihood: -2551.119695
EM: Round [364] log likelihood: -2551.119247
EM: Round [365] log likelihood: -2551.118802
EM: Round [366] log likelihood: -2551.118360
EM: Round [367] log likelihood: -2551.117922
EM: Round [368] log likelihood: -2551.117487
EM: Round [369] log likelihood: -2551.117055
EM: Round [370] log likelihood: -2551.116626
EM: Round [371] log likelihood: -2551.116201
EM: Round [372] log likelihood: -2551.115778
EM: Round [373] log likelihood: -2551.115359
EM: Round [374] log likelihood: -2551.114943
EM: Round [375] log likelihood: -2551.114530
EM: Round [376] log likelihood: -2551.114120
EM: Round [377] log likelihood: -2551.113713
EM: Round [378] log likelihood: -2551.113309
EM: Round [379] log likelihood: -2551.112908
EM: Round [380] log likelihood: -2551.112510
EM: Round [381] log likelihood: -2551.112115
EM: Round [382] log likelihood: -2551.111722
EM: Round [383] log likelihood: -2551.111333
EM: Round [384] log likelihood: -2551.110947
EM: Round [385] log likelihood: -2551.110563
EM: Round [386] log likelihood: -2551.110182
EM: Round [387] log likelihood: -2551.109804
EM: Round [388] log likelihood: -2551.109429
EM: Round [389] log likelihood: -2551.109057
EM: Round [390] log likelihood: -2551.108687
EM: Round [391] log likelihood: -2551.108320
EM: Round [392] log likelihood: -2551.107956
EM: Round [393] log likelihood: -2551.107594
EM: Round [394] log likelihood: -2551.107235
EM: Round [395] log likelihood: -2551.106879
EM: Round [396] log likelihood: -2551.106525
EM: Round [397] log likelihood: -2551.106174
EM: Round [398] log likelihood: -2551.105825
EM: Round [399] log likelihood: -2551.105479
EM: Round [400] log likelihood: -2551.105136
EM: Round [401] log likelihood: -2551.104795
EM: Round [402] log likelihood: -2551.104456
EM: Round [403] log likelihood: -2551.104120
EM: Round [404] log likelihood: -2551.103787
EM: Round [405] log likelihood: -2551.103456
EM: Round [406] log likelihood: -2551.103127
EM: Round [407] log likelihood: -2551.102801
EM: Round [408] log likelihood: -2551.102477
EM: Round [409] log likelihood: -2551.102156
EM: Round [410] log likelihood: -2551.101837
EM: Round [411] log likelihood: -2551.101520
EM: Round [412] log likelihood: -2551.101206
EM: Round [413] log likelihood: -2551.100893
EM: Round [414] log likelihood: -2551.100584
EM: Round [415] log likelihood: -2551.100276
EM: Round [416] log likelihood: -2551.099971
EM: Round [417] log likelihood: -2551.099668
EM: Round [418] log likelihood: -2551.099367
EM: Round [419] log likelihood: -2551.099068
EM: Round [420] log likelihood: -2551.098772
EM: Round [421] log likelihood: -2551.098477
EM: Round [422] log likelihood: -2551.098185
EM: Round [423] log likelihood: -2551.097895
EM: Round [424] log likelihood: -2551.097607
EM: Round [425] log likelihood: -2551.097321
EM: Round [426] log likelihood: -2551.097038
EM: Round [427] log likelihood: -2551.096756
EM: Round [428] log likelihood: -2551.096476
EM: Round [429] log likelihood: -2551.096199
EM: Round [430] log likelihood: -2551.095923
EM: Round [431] log likelihood: -2551.095650
EM: Round [432] log likelihood: -2551.095378
EM: Round [433] log likelihood: -2551.095109
EM: Round [434] log likelihood: -2551.094841
EM: Round [435] log likelihood: -2551.094576
EM: Round [436] log likelihood: -2551.094312
EM: Round [437] log likelihood: -2551.094050
EM: Round [438] log likelihood: -2551.093790
EM: Round [439] log likelihood: -2551.093532
EM: Round [440] log likelihood: -2551.093276
EM: Round [441] log likelihood: -2551.093022
EM: Round [442] log likelihood: -2551.092770
EM: Round [443] log likelihood: -2551.092519
EM: Round [444] log likelihood: -2551.092271
EM: Round [445] log likelihood: -2551.092024
EM: Round [446] log likelihood: -2551.091779
EM: Round [447] log likelihood: -2551.091535
EM: Round [448] log likelihood: -2551.091294
EM: Round [449] log likelihood: -2551.091054
EM: Round [450] log likelihood: -2551.090816
EM: Round [451] log likelihood: -2551.090580
EM: Round [452] log likelihood: -2551.090345
EM: Round [453] log likelihood: -2551.090112
EM: Round [454] log likelihood: -2551.089881
EM: Round [455] log likelihood: -2551.089652
EM: Round [456] log likelihood: -2551.089424
EM: Round [457] log likelihood: -2551.089198
EM: Round [458] log likelihood: -2551.088973
EM: Round [459] log likelihood: -2551.088751
EM: Round [460] log likelihood: -2551.088529
EM: Round [461] log likelihood: -2551.088310
EM: Round [462] log likelihood: -2551.088092
EM: Round [463] log likelihood: -2551.087875
EM: Round [464] log likelihood: -2551.087660
EM: Round [465] log likelihood: -2551.087447
EM: Round [466] log likelihood: -2551.087235
EM: Round [467] log likelihood: -2551.087025
EM: Round [468] log likelihood: -2551.086816
EM: Round [469] log likelihood: -2551.086609
EM: Round [470] log likelihood: -2551.086403
EM: Round [471] log likelihood: -2551.086199
EM: Round [472] log likelihood: -2551.085996
EM: Round [473] log likelihood: -2551.085795
EM: Round [474] log likelihood: -2551.085595
EM: Round [475] log likelihood: -2551.085397
EM: Round [476] log likelihood: -2551.085200
EM: Round [477] log likelihood: -2551.085005
EM: Round [478] log likelihood: -2551.084811
EM: Round [479] log likelihood: -2551.084618
EM: Round [480] log likelihood: -2551.084427
EM: Round [481] log likelihood: -2551.084237
EM: Round [482] log likelihood: -2551.084049
EM: Round [483] log likelihood: -2551.083861
EM: Round [484] log likelihood: -2551.083676
EM: Round [485] log likelihood: -2551.083491
EM: Round [486] log likelihood: -2551.083308
EM: Round [487] log likelihood: -2551.083126
EM: Round [488] log likelihood: -2551.082946
EM: Round [489] log likelihood: -2551.082767
EM: Round [490] log likelihood: -2551.082589
EM: Round [491] log likelihood: -2551.082413
EM: Round [492] log likelihood: -2551.082237
EM: Round [493] log likelihood: -2551.082063
EM: Round [494] log likelihood: -2551.081891
EM: Round [495] log likelihood: -2551.081719
EM: Round [496] log likelihood: -2551.081549
EM: Round [497] log likelihood: -2551.081380
EM: Round [498] log likelihood: -2551.081212
EM: Round [499] log likelihood: -2551.081046
EM: Round [500] log likelihood: -2551.080880
EM: Round [501] log likelihood: -2551.080716
EM: Round [502] log likelihood: -2551.080553
EM: Round [503] log likelihood: -2551.080391
EM: Round [504] log likelihood: -2551.080231
EM: Round [505] log likelihood: -2551.080071
EM: Round [506] log likelihood: -2551.079913
EM: Round [507] log likelihood: -2551.079756
EM: Round [508] log likelihood: -2551.079600
EM: Round [509] log likelihood: -2551.079445
EM: Round [510] log likelihood: -2551.079291
EM: Round [511] log likelihood: -2551.079139
EM: Round [512] log likelihood: -2551.078987
EM: Round [513] log likelihood: -2551.078837
EM: Round [514] log likelihood: -2551.078687
EM: Round [515] log likelihood: -2551.078539
EM: Round [516] log likelihood: -2551.078392
EM: Round [517] log likelihood: -2551.078246
EM: Round [518] log likelihood: -2551.078101
EM: Round [519] log likelihood: -2551.077957
EM: Round [520] log likelihood: -2551.077814
EM: Round [521] log likelihood: -2551.077672
EM: Round [522] log likelihood: -2551.077531
EM: Round [523] log likelihood: -2551.077391
EM: Round [524] log likelihood: -2551.077252
EM: Round [525] log likelihood: -2551.077114
EM: Round [526] log likelihood: -2551.076977
EM: Round [527] log likelihood: -2551.076841
EM: Round [528] log likelihood: -2551.076706
EM: Round [529] log likelihood: -2551.076572
EM: Round [530] log likelihood: -2551.076439
EM: Round [531] log likelihood: -2551.076307
EM: Round [532] log likelihood: -2551.076176
EM: Round [533] log likelihood: -2551.076046
EM: Round [534] log likelihood: -2551.075917
EM: Round [535] log likelihood: -2551.075788
EM: Round [536] log likelihood: -2551.075661
EM: Round [537] log likelihood: -2551.075535
EM: Round [538] log likelihood: -2551.075409
EM: Round [539] log likelihood: -2551.075284
EM: Round [540] log likelihood: -2551.075161
EM: Round [541] log likelihood: -2551.075038
EM: Round [542] log likelihood: -2551.074916
EM: Round [543] log likelihood: -2551.074795
EM: Round [544] log likelihood: -2551.074675
EM: Round [545] log likelihood: -2551.074556
EM: Round [546] log likelihood: -2551.074437
EM: Round [547] log likelihood: -2551.074319
EM: Round [548] log likelihood: -2551.074203
EM: Round [549] log likelihood: -2551.074087
EM: Round [550] log likelihood: -2551.073972
EM: Round [551] log likelihood: -2551.073858
EM: Round [552] log likelihood: -2551.073744
EM: Round [553] log likelihood: -2551.073632
EM: Round [554] log likelihood: -2551.073520
EM: Round [555] log likelihood: -2551.073409
EM: Round [556] log likelihood: -2551.073299
EM: Round [557] log likelihood: -2551.073189
EM: Round [558] log likelihood: -2551.073081
EM: Round [559] log likelihood: -2551.072973
EM: Round [560] log likelihood: -2551.072866
EM: Round [561] log likelihood: -2551.072759
EM: Round [562] log likelihood: -2551.072654
EM: Round [563] log likelihood: -2551.072549
EM: Round [564] log likelihood: -2551.072445
EM: Round [565] log likelihood: -2551.072342
EM: Round [566] log likelihood: -2551.072240
EM: Round [567] log likelihood: -2551.072138
EM: Round [568] log likelihood: -2551.072037
EM: Round [569] log likelihood: -2551.071936
EM: Round [570] log likelihood: -2551.071837
EM: Stopping iterations at round 570 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.KBRk8LzrnL/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.KBRk8LzrnL/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.KBRk8LzrnL/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.KBRk8LzrnL/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.KBRk8LzrnL/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.KBRk8LzrnL/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.KBRk8LzrnL/aih-tih-sc-a9fe91-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.KBRk8LzrnL/fi_workdir/aih-tih-sc-a9fe91-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.KBRk8LzrnL/fi_workdir/aih-tih-sc-a9fe91-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.KBRk8LzrnL/fi_workdir/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.KBRk8LzrnL/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.KBRk8LzrnL/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2274.404256
EM: Round [1] log likelihood: -2274.155836
EM: Round [2] log likelihood: -2274.155770
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.KBRk8LzrnL/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296622551
Warning - not locating file: /tmp/nxf.KBRk8LzrnL/aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
ls: cannot access 'IGV_inputs': No such file or directory