Done.
-parsing GTF file: /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.sortedByCoord.out.bam
12:11:09 : INFO : Done.
-parsing GTF file: /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf
-parsing /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam

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[310000]   -done parsing /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'per_id < 96' => 1786,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 72,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 9,
          'seq-similar region overlap' => 65,
          'num genes matched < 2' => 20,
          'excessive soft clipping' => 2693,
          'small anchor length' => 36,
          ' ** passed ** ' => 3277
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[108000]   -fusion SPANNING read extraction for scaff: CCDC6--RET

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[7000]   -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B

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[8000]   -fusion SPANNING read extraction for scaff: DNAJC1--C10orf143

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[6000]   -fusion SPANNING read extraction for scaff: NEBL--CDK1

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[11000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[11000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[8000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[8000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 4916,
          'lacks exon overlap' => 1997
        };
EM: Starting log likelihood: -2892.601368
EM: Round [1] log likelihood: -2890.826180
EM: Round [2] log likelihood: -2890.817047
EM: Round [3] log likelihood: -2890.808458
EM: Round [4] log likelihood: -2890.800020
EM: Round [5] log likelihood: -2890.791728
EM: Round [6] log likelihood: -2890.783579
EM: Round [7] log likelihood: -2890.775569
EM: Round [8] log likelihood: -2890.767695
EM: Round [9] log likelihood: -2890.759953
EM: Round [10] log likelihood: -2890.752341
EM: Round [11] log likelihood: -2890.744854
EM: Round [12] log likelihood: -2890.737490
EM: Round [13] log likelihood: -2890.730247
EM: Round [14] log likelihood: -2890.723121
EM: Round [15] log likelihood: -2890.716109
EM: Round [16] log likelihood: -2890.709210
EM: Round [17] log likelihood: -2890.702420
EM: Round [18] log likelihood: -2890.695737
EM: Round [19] log likelihood: -2890.689158
EM: Round [20] log likelihood: -2890.682682
EM: Round [21] log likelihood: -2890.676306
EM: Round [22] log likelihood: -2890.670028
EM: Round [23] log likelihood: -2890.663845
EM: Round [24] log likelihood: -2890.657757
EM: Round [25] log likelihood: -2890.651760
EM: Round [26] log likelihood: -2890.645853
EM: Round [27] log likelihood: -2890.640034
EM: Round [28] log likelihood: -2890.634301
EM: Round [29] log likelihood: -2890.628652
EM: Round [30] log likelihood: -2890.623087
EM: Round [31] log likelihood: -2890.617602
EM: Round [32] log likelihood: -2890.612197
EM: Round [33] log likelihood: -2890.606869
EM: Round [34] log likelihood: -2890.601618
EM: Round [35] log likelihood: -2890.596442
EM: Round [36] log likelihood: -2890.591339
EM: Round [37] log likelihood: -2890.586309
EM: Round [38] log likelihood: -2890.581349
EM: Round [39] log likelihood: -2890.576458
EM: Round [40] log likelihood: -2890.571635
EM: Round [41] log likelihood: -2890.566879
EM: Round [42] log likelihood: -2890.562188
EM: Round [43] log likelihood: -2890.557562
EM: Round [44] log likelihood: -2890.552999
EM: Round [45] log likelihood: -2890.548498
EM: Round [46] log likelihood: -2890.544058
EM: Round [47] log likelihood: -2890.539677
EM: Round [48] log likelihood: -2890.535356
EM: Round [49] log likelihood: -2890.531091
EM: Round [50] log likelihood: -2890.526884
EM: Round [51] log likelihood: -2890.522732
EM: Round [52] log likelihood: -2890.518635
EM: Round [53] log likelihood: -2890.514592
EM: Round [54] log likelihood: -2890.510602
EM: Round [55] log likelihood: -2890.506664
EM: Round [56] log likelihood: -2890.502776
EM: Round [57] log likelihood: -2890.498939
EM: Round [58] log likelihood: -2890.495152
EM: Round [59] log likelihood: -2890.491413
EM: Round [60] log likelihood: -2890.487721
EM: Round [61] log likelihood: -2890.484077
EM: Round [62] log likelihood: -2890.480479
EM: Round [63] log likelihood: -2890.476927
EM: Round [64] log likelihood: -2890.473419
EM: Round [65] log likelihood: -2890.469955
EM: Round [66] log likelihood: -2890.466535
EM: Round [67] log likelihood: -2890.463157
EM: Round [68] log likelihood: -2890.459821
EM: Round [69] log likelihood: -2890.456526
EM: Round [70] log likelihood: -2890.453273
EM: Round [71] log likelihood: -2890.450059
EM: Round [72] log likelihood: -2890.446884
EM: Round [73] log likelihood: -2890.443749
EM: Round [74] log likelihood: -2890.440651
EM: Round [75] log likelihood: -2890.437592
EM: Round [76] log likelihood: -2890.434569
EM: Round [77] log likelihood: -2890.431583
EM: Round [78] log likelihood: -2890.428632
EM: Round [79] log likelihood: -2890.425718
EM: Round [80] log likelihood: -2890.422838
EM: Round [81] log likelihood: -2890.419992
EM: Round [82] log likelihood: -2890.417180
EM: Round [83] log likelihood: -2890.414402
EM: Round [84] log likelihood: -2890.411657
EM: Round [85] log likelihood: -2890.408944
EM: Round [86] log likelihood: -2890.406262
EM: Round [87] log likelihood: -2890.403613
EM: Round [88] log likelihood: -2890.400994
EM: Round [89] log likelihood: -2890.398406
EM: Round [90] log likelihood: -2890.395848
EM: Round [91] log likelihood: -2890.393320
EM: Round [92] log likelihood: -2890.390821
EM: Round [93] log likelihood: -2890.388352
EM: Round [94] log likelihood: -2890.385910
EM: Round [95] log likelihood: -2890.383497
EM: Round [96] log likelihood: -2890.381111
EM: Round [97] log likelihood: -2890.378753
EM: Round [98] log likelihood: -2890.376421
EM: Round [99] log likelihood: -2890.374117
EM: Round [100] log likelihood: -2890.371838
EM: Round [101] log likelihood: -2890.369585
EM: Round [102] log likelihood: -2890.367358
EM: Round [103] log likelihood: -2890.365156
EM: Round [104] log likelihood: -2890.362979
EM: Round [105] log likelihood: -2890.360826
EM: Round [106] log likelihood: -2890.358697
EM: Round [107] log likelihood: -2890.356592
EM: Round [108] log likelihood: -2890.354511
EM: Round [109] log likelihood: -2890.352453
EM: Round [110] log likelihood: -2890.350418
EM: Round [111] log likelihood: -2890.348405
EM: Round [112] log likelihood: -2890.346415
EM: Round [113] log likelihood: -2890.344447
EM: Round [114] log likelihood: -2890.342500
EM: Round [115] log likelihood: -2890.340575
EM: Round [116] log likelihood: -2890.338672
EM: Round [117] log likelihood: -2890.336789
EM: Round [118] log likelihood: -2890.334926
EM: Round [119] log likelihood: -2890.333084
EM: Round [120] log likelihood: -2890.331262
EM: Round [121] log likelihood: -2890.329460
EM: Round [122] log likelihood: -2890.327678
EM: Round [123] log likelihood: -2890.325915
EM: Round [124] log likelihood: -2890.324171
EM: Round [125] log likelihood: -2890.322446
EM: Round [126] log likelihood: -2890.320740
EM: Round [127] log likelihood: -2890.319052
EM: Round [128] log likelihood: -2890.317382
EM: Round [129] log likelihood: -2890.315730
EM: Round [130] log likelihood: -2890.314096
EM: Round [131] log likelihood: -2890.312479
EM: Round [132] log likelihood: -2890.310880
EM: Round [133] log likelihood: -2890.309297
EM: Round [134] log likelihood: -2890.307732
EM: Round [135] log likelihood: -2890.306183
EM: Round [136] log likelihood: -2890.304651
EM: Round [137] log likelihood: -2890.303135
EM: Round [138] log likelihood: -2890.301635
EM: Round [139] log likelihood: -2890.300151
EM: Round [140] log likelihood: -2890.298682
EM: Round [141] log likelihood: -2890.297229
EM: Round [142] log likelihood: -2890.295792
EM: Round [143] log likelihood: -2890.294369
EM: Round [144] log likelihood: -2890.292962
EM: Round [145] log likelihood: -2890.291569
EM: Round [146] log likelihood: -2890.290191
EM: Round [147] log likelihood: -2890.288827
EM: Round [148] log likelihood: -2890.287477
EM: Round [149] log likelihood: -2890.286142
EM: Round [150] log likelihood: -2890.284820
EM: Round [151] log likelihood: -2890.283513
EM: Round [152] log likelihood: -2890.282218
EM: Round [153] log likelihood: -2890.280938
EM: Round [154] log likelihood: -2890.279670
EM: Round [155] log likelihood: -2890.278416
EM: Round [156] log likelihood: -2890.277174
EM: Round [157] log likelihood: -2890.275946
EM: Round [158] log likelihood: -2890.274730
EM: Round [159] log likelihood: -2890.273526
EM: Round [160] log likelihood: -2890.272335
EM: Round [161] log likelihood: -2890.271157
EM: Round [162] log likelihood: -2890.269990
EM: Round [163] log likelihood: -2890.268835
EM: Round [164] log likelihood: -2890.267692
EM: Round [165] log likelihood: -2890.266561
EM: Round [166] log likelihood: -2890.265442
EM: Round [167] log likelihood: -2890.264333
EM: Round [168] log likelihood: -2890.263237
EM: Round [169] log likelihood: -2890.262151
EM: Round [170] log likelihood: -2890.261076
EM: Round [171] log likelihood: -2890.260012
EM: Round [172] log likelihood: -2890.258959
EM: Round [173] log likelihood: -2890.257917
EM: Round [174] log likelihood: -2890.256885
EM: Round [175] log likelihood: -2890.255864
EM: Round [176] log likelihood: -2890.254853
EM: Round [177] log likelihood: -2890.253852
EM: Round [178] log likelihood: -2890.252862
EM: Round [179] log likelihood: -2890.251881
EM: Round [180] log likelihood: -2890.250910
EM: Round [181] log likelihood: -2890.249949
EM: Round [182] log likelihood: -2890.248998
EM: Round [183] log likelihood: -2890.248056
EM: Round [184] log likelihood: -2890.247124
EM: Round [185] log likelihood: -2890.246201
EM: Round [186] log likelihood: -2890.245287
EM: Round [187] log likelihood: -2890.244382
EM: Round [188] log likelihood: -2890.243487
EM: Round [189] log likelihood: -2890.242600
EM: Round [190] log likelihood: -2890.241722
EM: Round [191] log likelihood: -2890.240853
EM: Round [192] log likelihood: -2890.239993
EM: Round [193] log likelihood: -2890.239141
EM: Round [194] log likelihood: -2890.238298
EM: Round [195] log likelihood: -2890.237463
EM: Round [196] log likelihood: -2890.236636
EM: Round [197] log likelihood: -2890.235817
EM: Round [198] log likelihood: -2890.235007
EM: Round [199] log likelihood: -2890.234205
EM: Round [200] log likelihood: -2890.233410
EM: Round [201] log likelihood: -2890.232624
EM: Round [202] log likelihood: -2890.231845
EM: Round [203] log likelihood: -2890.231074
EM: Round [204] log likelihood: -2890.230310
EM: Round [205] log likelihood: -2890.229554
EM: Round [206] log likelihood: -2890.228806
EM: Round [207] log likelihood: -2890.228065
EM: Round [208] log likelihood: -2890.227331
EM: Round [209] log likelihood: -2890.226604
EM: Round [210] log likelihood: -2890.225885
EM: Round [211] log likelihood: -2890.225172
EM: Round [212] log likelihood: -2890.224467
EM: Round [213] log likelihood: -2890.223768
EM: Round [214] log likelihood: -2890.223076
EM: Round [215] log likelihood: -2890.222391
EM: Round [216] log likelihood: -2890.221713
EM: Round [217] log likelihood: -2890.221041
EM: Round [218] log likelihood: -2890.220376
EM: Round [219] log likelihood: -2890.219718
EM: Round [220] log likelihood: -2890.219066
EM: Round [221] log likelihood: -2890.218420
EM: Round [222] log likelihood: -2890.217780
EM: Round [223] log likelihood: -2890.217147
EM: Round [224] log likelihood: -2890.216520
EM: Round [225] log likelihood: -2890.215899
EM: Round [226] log likelihood: -2890.215284
EM: Round [227] log likelihood: -2890.214675
EM: Round [228] log likelihood: -2890.214072
EM: Round [229] log likelihood: -2890.213474
EM: Round [230] log likelihood: -2890.212883
EM: Round [231] log likelihood: -2890.212297
EM: Round [232] log likelihood: -2890.211717
EM: Round [233] log likelihood: -2890.211143
EM: Round [234] log likelihood: -2890.210574
EM: Round [235] log likelihood: -2890.210010
EM: Round [236] log likelihood: -2890.209452
EM: Round [237] log likelihood: -2890.208900
EM: Round [238] log likelihood: -2890.208353
EM: Round [239] log likelihood: -2890.207811
EM: Round [240] log likelihood: -2890.207274
EM: Round [241] log likelihood: -2890.206742
EM: Round [242] log likelihood: -2890.206216
EM: Round [243] log likelihood: -2890.205694
EM: Round [244] log likelihood: -2890.205178
EM: Round [245] log likelihood: -2890.204667
EM: Round [246] log likelihood: -2890.204160
EM: Round [247] log likelihood: -2890.203658
EM: Round [248] log likelihood: -2890.203162
EM: Round [249] log likelihood: -2890.202669
EM: Round [250] log likelihood: -2890.202182
EM: Round [251] log likelihood: -2890.201699
EM: Round [252] log likelihood: -2890.201221
EM: Round [253] log likelihood: -2890.200748
EM: Round [254] log likelihood: -2890.200279
EM: Round [255] log likelihood: -2890.199815
EM: Round [256] log likelihood: -2890.199355
EM: Round [257] log likelihood: -2890.198899
EM: Round [258] log likelihood: -2890.198448
EM: Round [259] log likelihood: -2890.198001
EM: Round [260] log likelihood: -2890.197558
EM: Round [261] log likelihood: -2890.197120
EM: Round [262] log likelihood: -2890.196685
EM: Round [263] log likelihood: -2890.196255
EM: Round [264] log likelihood: -2890.195829
EM: Round [265] log likelihood: -2890.195407
EM: Round [266] log likelihood: -2890.194989
EM: Round [267] log likelihood: -2890.194575
EM: Round [268] log likelihood: -2890.194165
EM: Round [269] log likelihood: -2890.193759
EM: Round [270] log likelihood: -2890.193357
EM: Round [271] log likelihood: -2890.192958
EM: Round [272] log likelihood: -2890.192563
EM: Round [273] log likelihood: -2890.192173
EM: Round [274] log likelihood: -2890.191785
EM: Round [275] log likelihood: -2890.191402
EM: Round [276] log likelihood: -2890.191022
EM: Round [277] log likelihood: -2890.190645
EM: Round [278] log likelihood: -2890.190273
EM: Round [279] log likelihood: -2890.189903
EM: Round [280] log likelihood: -2890.189538
EM: Round [281] log likelihood: -2890.189175
EM: Round [282] log likelihood: -2890.188817
EM: Round [283] log likelihood: -2890.188461
EM: Round [284] log likelihood: -2890.188109
EM: Round [285] log likelihood: -2890.187760
EM: Round [286] log likelihood: -2890.187415
EM: Round [287] log likelihood: -2890.187073
EM: Round [288] log likelihood: -2890.186734
EM: Round [289] log likelihood: -2890.186398
EM: Round [290] log likelihood: -2890.186065
EM: Round [291] log likelihood: -2890.185736
EM: Round [292] log likelihood: -2890.185409
EM: Round [293] log likelihood: -2890.185086
EM: Round [294] log likelihood: -2890.184766
EM: Round [295] log likelihood: -2890.184449
EM: Round [296] log likelihood: -2890.184134
EM: Round [297] log likelihood: -2890.183823
EM: Round [298] log likelihood: -2890.183515
EM: Round [299] log likelihood: -2890.183209
EM: Round [300] log likelihood: -2890.182907
EM: Round [301] log likelihood: -2890.182607
EM: Round [302] log likelihood: -2890.182310
EM: Round [303] log likelihood: -2890.182016
EM: Round [304] log likelihood: -2890.181725
EM: Round [305] log likelihood: -2890.181436
EM: Round [306] log likelihood: -2890.181150
EM: Round [307] log likelihood: -2890.180867
EM: Round [308] log likelihood: -2890.180586
EM: Round [309] log likelihood: -2890.180308
EM: Round [310] log likelihood: -2890.180033
EM: Round [311] log likelihood: -2890.179760
EM: Round [312] log likelihood: -2890.179490
EM: Round [313] log likelihood: -2890.179222
EM: Round [314] log likelihood: -2890.178957
EM: Round [315] log likelihood: -2890.178695
EM: Round [316] log likelihood: -2890.178434
EM: Round [317] log likelihood: -2890.178177
EM: Round [318] log likelihood: -2890.177921
EM: Round [319] log likelihood: -2890.177668
EM: Round [320] log likelihood: -2890.177418
EM: Round [321] log likelihood: -2890.177169
EM: Round [322] log likelihood: -2890.176923
EM: Round [323] log likelihood: -2890.176680
EM: Round [324] log likelihood: -2890.176438
EM: Round [325] log likelihood: -2890.176199
EM: Round [326] log likelihood: -2890.175962
EM: Round [327] log likelihood: -2890.175728
EM: Round [328] log likelihood: -2890.175495
EM: Round [329] log likelihood: -2890.175265
EM: Round [330] log likelihood: -2890.175037
EM: Round [331] log likelihood: -2890.174811
EM: Round [332] log likelihood: -2890.174587
EM: Round [333] log likelihood: -2890.174365
EM: Round [334] log likelihood: -2890.174145
EM: Round [335] log likelihood: -2890.173927
EM: Round [336] log likelihood: -2890.173712
EM: Round [337] log likelihood: -2890.173498
EM: Round [338] log likelihood: -2890.173286
EM: Round [339] log likelihood: -2890.173077
EM: Round [340] log likelihood: -2890.172869
EM: Round [341] log likelihood: -2890.172663
EM: Round [342] log likelihood: -2890.172459
EM: Round [343] log likelihood: -2890.172257
EM: Round [344] log likelihood: -2890.172057
EM: Round [345] log likelihood: -2890.171859
EM: Round [346] log likelihood: -2890.171662
EM: Round [347] log likelihood: -2890.171468
EM: Round [348] log likelihood: -2890.171275
EM: Round [349] log likelihood: -2890.171084
EM: Round [350] log likelihood: -2890.170895
EM: Round [351] log likelihood: -2890.170707
EM: Round [352] log likelihood: -2890.170521
EM: Round [353] log likelihood: -2890.170337
EM: Round [354] log likelihood: -2890.170155
EM: Round [355] log likelihood: -2890.169974
EM: Round [356] log likelihood: -2890.169796
EM: Round [357] log likelihood: -2890.169618
EM: Round [358] log likelihood: -2890.169443
EM: Round [359] log likelihood: -2890.169269
EM: Round [360] log likelihood: -2890.169096
EM: Round [361] log likelihood: -2890.168925
EM: Round [362] log likelihood: -2890.168756
EM: Round [363] log likelihood: -2890.168589
EM: Round [364] log likelihood: -2890.168423
EM: Round [365] log likelihood: -2890.168258
EM: Round [366] log likelihood: -2890.168095
EM: Round [367] log likelihood: -2890.167933
EM: Round [368] log likelihood: -2890.167773
EM: Round [369] log likelihood: -2890.167615
EM: Round [370] log likelihood: -2890.167458
EM: Round [371] log likelihood: -2890.167302
EM: Round [372] log likelihood: -2890.167148
EM: Round [373] log likelihood: -2890.166995
EM: Round [374] log likelihood: -2890.166844
EM: Round [375] log likelihood: -2890.166694
EM: Round [376] log likelihood: -2890.166546
EM: Round [377] log likelihood: -2890.166398
EM: Round [378] log likelihood: -2890.166253
EM: Round [379] log likelihood: -2890.166108
EM: Round [380] log likelihood: -2890.165965
EM: Round [381] log likelihood: -2890.165823
EM: Round [382] log likelihood: -2890.165683
EM: Round [383] log likelihood: -2890.165544
EM: Round [384] log likelihood: -2890.165406
EM: Round [385] log likelihood: -2890.165269
EM: Round [386] log likelihood: -2890.165134
EM: Round [387] log likelihood: -2890.165000
EM: Round [388] log likelihood: -2890.164867
EM: Round [389] log likelihood: -2890.164735
EM: Round [390] log likelihood: -2890.164605
EM: Round [391] log likelihood: -2890.164475
EM: Round [392] log likelihood: -2890.164347
EM: Round [393] log likelihood: -2890.164220
EM: Round [394] log likelihood: -2890.164095
EM: Round [395] log likelihood: -2890.163970
EM: Round [396] log likelihood: -2890.163847
EM: Round [397] log likelihood: -2890.163725
EM: Round [398] log likelihood: -2890.163604
EM: Round [399] log likelihood: -2890.163484
EM: Round [400] log likelihood: -2890.163365
EM: Round [401] log likelihood: -2890.163247
EM: Round [402] log likelihood: -2890.163130
EM: Round [403] log likelihood: -2890.163015
EM: Round [404] log likelihood: -2890.162900
EM: Round [405] log likelihood: -2890.162786
EM: Round [406] log likelihood: -2890.162674
EM: Round [407] log likelihood: -2890.162563
EM: Round [408] log likelihood: -2890.162452
EM: Round [409] log likelihood: -2890.162343
EM: Round [410] log likelihood: -2890.162234
EM: Round [411] log likelihood: -2890.162127
EM: Round [412] log likelihood: -2890.162021
EM: Round [413] log likelihood: -2890.161915
EM: Round [414] log likelihood: -2890.161811
EM: Round [415] log likelihood: -2890.161707
EM: Round [416] log likelihood: -2890.161605
EM: Round [417] log likelihood: -2890.161503
EM: Round [418] log likelihood: -2890.161403
EM: Round [419] log likelihood: -2890.161303
EM: Stopping iterations at round 419 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam into /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.frag_coords > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2645.228701
EM: Round [1] log likelihood: -2645.073177
EM: Round [2] log likelihood: -2645.072982
EM: Round [3] log likelihood: -2645.072982
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz: 295366080
Warning - not locating file: /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000236438.7]
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 [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 [ENSG00000242193.11]
ls: cannot access 'IGV_inputs': No such file or directory