Done.
-parsing GTF file: /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.uxAJ9Mobh9/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.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:25:45 : INFO : Done.
-parsing GTF file: /tmp/nxf.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[800000] -done parsing /tmp/nxf.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'excessive soft clipping' => 19454,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
'per_id < 96' => 6365,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 5,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 7496,
'seq-similar region overlap' => 673,
'low complexity anchor region' => 15,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 60,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 20,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 129,
' ** passed ** ' => 2219,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 14,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 424,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 322,
'num genes matched < 2' => 16,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 436
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[83000] -fusion SPANNING read extraction for scaff: ATP9A--KIF3B
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[223000] -fusion SPANNING read extraction for scaff: IGL-@-ext--AC097110.1
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[11000] -fusion SPANNING read extraction for scaff: MAP1LC3A--TTLL9
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[66000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[60000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[70000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[15000] -fusion SPANNING read extraction for scaff: RPRD1A--MOCOS
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[90000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[7000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[64000] -fusion SPANNING read extraction for scaff: TOX2--TSHZ2
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[42000] -fusion SPANNING read extraction for scaff: TOX2--AL109930.1
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[26000] -fusion SPANNING read extraction for scaff: TTC39C--CABLES1
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[16000] -fusion SPANNING read extraction for scaff: TTLL9--CABLES1
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[21000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 19859,
'seq similar region alignment' => 54545
};
EM: Starting log likelihood: -1899.187716
EM: Round [1] log likelihood: -1899.184567
EM: Round [2] log likelihood: -1899.181447
EM: Round [3] log likelihood: -1899.178357
EM: Round [4] log likelihood: -1899.175296
EM: Round [5] log likelihood: -1899.172264
EM: Round [6] log likelihood: -1899.169260
EM: Round [7] log likelihood: -1899.166284
EM: Round [8] log likelihood: -1899.163336
EM: Round [9] log likelihood: -1899.160415
EM: Round [10] log likelihood: -1899.157522
EM: Round [11] log likelihood: -1899.154655
EM: Round [12] log likelihood: -1899.151814
EM: Round [13] log likelihood: -1899.149000
EM: Round [14] log likelihood: -1899.146211
EM: Round [15] log likelihood: -1899.143447
EM: Round [16] log likelihood: -1899.140709
EM: Round [17] log likelihood: -1899.137996
EM: Round [18] log likelihood: -1899.135307
EM: Round [19] log likelihood: -1899.132642
EM: Round [20] log likelihood: -1899.130002
EM: Round [21] log likelihood: -1899.127385
EM: Round [22] log likelihood: -1899.124792
EM: Round [23] log likelihood: -1899.122221
EM: Round [24] log likelihood: -1899.119674
EM: Round [25] log likelihood: -1899.117149
EM: Round [26] log likelihood: -1899.114647
EM: Round [27] log likelihood: -1899.112167
EM: Round [28] log likelihood: -1899.109708
EM: Round [29] log likelihood: -1899.107272
EM: Round [30] log likelihood: -1899.104856
EM: Round [31] log likelihood: -1899.102462
EM: Round [32] log likelihood: -1899.100089
EM: Round [33] log likelihood: -1899.097736
EM: Round [34] log likelihood: -1899.095404
EM: Round [35] log likelihood: -1899.093092
EM: Round [36] log likelihood: -1899.090800
EM: Round [37] log likelihood: -1899.088528
EM: Round [38] log likelihood: -1899.086276
EM: Round [39] log likelihood: -1899.084042
EM: Round [40] log likelihood: -1899.081828
EM: Round [41] log likelihood: -1899.079633
EM: Round [42] log likelihood: -1899.077457
EM: Round [43] log likelihood: -1899.075299
EM: Round [44] log likelihood: -1899.073160
EM: Round [45] log likelihood: -1899.071038
EM: Round [46] log likelihood: -1899.068935
EM: Round [47] log likelihood: -1899.066850
EM: Round [48] log likelihood: -1899.064782
EM: Round [49] log likelihood: -1899.062731
EM: Round [50] log likelihood: -1899.060698
EM: Round [51] log likelihood: -1899.058681
EM: Round [52] log likelihood: -1899.056682
EM: Round [53] log likelihood: -1899.054699
EM: Round [54] log likelihood: -1899.052733
EM: Round [55] log likelihood: -1899.050783
EM: Round [56] log likelihood: -1899.048849
EM: Round [57] log likelihood: -1899.046931
EM: Round [58] log likelihood: -1899.045030
EM: Round [59] log likelihood: -1899.043143
EM: Round [60] log likelihood: -1899.041273
EM: Round [61] log likelihood: -1899.039417
EM: Round [62] log likelihood: -1899.037577
EM: Round [63] log likelihood: -1899.035752
EM: Round [64] log likelihood: -1899.033942
EM: Round [65] log likelihood: -1899.032147
EM: Round [66] log likelihood: -1899.030366
EM: Round [67] log likelihood: -1899.028600
EM: Round [68] log likelihood: -1899.026848
EM: Round [69] log likelihood: -1899.025111
EM: Round [70] log likelihood: -1899.023387
EM: Round [71] log likelihood: -1899.021677
EM: Round [72] log likelihood: -1899.019981
EM: Round [73] log likelihood: -1899.018299
EM: Round [74] log likelihood: -1899.016630
EM: Round [75] log likelihood: -1899.014975
EM: Round [76] log likelihood: -1899.013333
EM: Round [77] log likelihood: -1899.011704
EM: Round [78] log likelihood: -1899.010088
EM: Round [79] log likelihood: -1899.008485
EM: Round [80] log likelihood: -1899.006894
EM: Round [81] log likelihood: -1899.005317
EM: Round [82] log likelihood: -1899.003751
EM: Round [83] log likelihood: -1899.002198
EM: Round [84] log likelihood: -1899.000658
EM: Round [85] log likelihood: -1898.999129
EM: Round [86] log likelihood: -1898.997613
EM: Round [87] log likelihood: -1898.996109
EM: Round [88] log likelihood: -1898.994616
EM: Round [89] log likelihood: -1898.993135
EM: Round [90] log likelihood: -1898.991666
EM: Round [91] log likelihood: -1898.990208
EM: Round [92] log likelihood: -1898.988762
EM: Round [93] log likelihood: -1898.987327
EM: Round [94] log likelihood: -1898.985903
EM: Round [95] log likelihood: -1898.984490
EM: Round [96] log likelihood: -1898.983088
EM: Round [97] log likelihood: -1898.981697
EM: Round [98] log likelihood: -1898.980316
EM: Round [99] log likelihood: -1898.978947
EM: Round [100] log likelihood: -1898.977588
EM: Round [101] log likelihood: -1898.976239
EM: Round [102] log likelihood: -1898.974901
EM: Round [103] log likelihood: -1898.973573
EM: Round [104] log likelihood: -1898.972256
EM: Round [105] log likelihood: -1898.970948
EM: Round [106] log likelihood: -1898.969651
EM: Round [107] log likelihood: -1898.968363
EM: Round [108] log likelihood: -1898.967085
EM: Round [109] log likelihood: -1898.965817
EM: Round [110] log likelihood: -1898.964559
EM: Round [111] log likelihood: -1898.963310
EM: Round [112] log likelihood: -1898.962071
EM: Round [113] log likelihood: -1898.960841
EM: Round [114] log likelihood: -1898.959621
EM: Round [115] log likelihood: -1898.958410
EM: Round [116] log likelihood: -1898.957207
EM: Round [117] log likelihood: -1898.956014
EM: Round [118] log likelihood: -1898.954830
EM: Round [119] log likelihood: -1898.953655
EM: Round [120] log likelihood: -1898.952489
EM: Round [121] log likelihood: -1898.951332
EM: Round [122] log likelihood: -1898.950183
EM: Round [123] log likelihood: -1898.949043
EM: Round [124] log likelihood: -1898.947911
EM: Round [125] log likelihood: -1898.946788
EM: Round [126] log likelihood: -1898.945673
EM: Round [127] log likelihood: -1898.944567
EM: Round [128] log likelihood: -1898.943469
EM: Round [129] log likelihood: -1898.942379
EM: Round [130] log likelihood: -1898.941297
EM: Round [131] log likelihood: -1898.940224
EM: Round [132] log likelihood: -1898.939158
EM: Round [133] log likelihood: -1898.938100
EM: Round [134] log likelihood: -1898.937050
EM: Round [135] log likelihood: -1898.936008
EM: Round [136] log likelihood: -1898.934973
EM: Round [137] log likelihood: -1898.933946
EM: Round [138] log likelihood: -1898.932927
EM: Round [139] log likelihood: -1898.931915
EM: Round [140] log likelihood: -1898.930911
EM: Round [141] log likelihood: -1898.929914
EM: Round [142] log likelihood: -1898.928924
EM: Round [143] log likelihood: -1898.927942
EM: Round [144] log likelihood: -1898.926967
EM: Round [145] log likelihood: -1898.925999
EM: Round [146] log likelihood: -1898.925038
EM: Round [147] log likelihood: -1898.924084
EM: Round [148] log likelihood: -1898.923137
EM: Round [149] log likelihood: -1898.922197
EM: Round [150] log likelihood: -1898.921264
EM: Round [151] log likelihood: -1898.920338
EM: Round [152] log likelihood: -1898.919419
EM: Round [153] log likelihood: -1898.918506
EM: Round [154] log likelihood: -1898.917600
EM: Round [155] log likelihood: -1898.916700
EM: Round [156] log likelihood: -1898.915807
EM: Round [157] log likelihood: -1898.914920
EM: Round [158] log likelihood: -1898.914040
EM: Round [159] log likelihood: -1898.913166
EM: Round [160] log likelihood: -1898.912299
EM: Round [161] log likelihood: -1898.911438
EM: Round [162] log likelihood: -1898.910583
EM: Round [163] log likelihood: -1898.909734
EM: Round [164] log likelihood: -1898.908891
EM: Round [165] log likelihood: -1898.908055
EM: Round [166] log likelihood: -1898.907224
EM: Round [167] log likelihood: -1898.906399
EM: Round [168] log likelihood: -1898.905581
EM: Round [169] log likelihood: -1898.904768
EM: Round [170] log likelihood: -1898.903961
EM: Round [171] log likelihood: -1898.903160
EM: Round [172] log likelihood: -1898.902364
EM: Round [173] log likelihood: -1898.901574
EM: Round [174] log likelihood: -1898.900790
EM: Round [175] log likelihood: -1898.900012
EM: Round [176] log likelihood: -1898.899239
EM: Round [177] log likelihood: -1898.898471
EM: Round [178] log likelihood: -1898.897709
EM: Round [179] log likelihood: -1898.896953
EM: Round [180] log likelihood: -1898.896202
EM: Round [181] log likelihood: -1898.895456
EM: Round [182] log likelihood: -1898.894715
EM: Round [183] log likelihood: -1898.893980
EM: Round [184] log likelihood: -1898.893250
EM: Round [185] log likelihood: -1898.892525
EM: Round [186] log likelihood: -1898.891805
EM: Round [187] log likelihood: -1898.891091
EM: Round [188] log likelihood: -1898.890381
EM: Round [189] log likelihood: -1898.889676
EM: Round [190] log likelihood: -1898.888977
EM: Round [191] log likelihood: -1898.888282
EM: Round [192] log likelihood: -1898.887592
EM: Round [193] log likelihood: -1898.886908
EM: Round [194] log likelihood: -1898.886228
EM: Round [195] log likelihood: -1898.885552
EM: Round [196] log likelihood: -1898.884882
EM: Round [197] log likelihood: -1898.884216
EM: Round [198] log likelihood: -1898.883555
EM: Round [199] log likelihood: -1898.882898
EM: Round [200] log likelihood: -1898.882247
EM: Round [201] log likelihood: -1898.881599
EM: Round [202] log likelihood: -1898.880956
EM: Round [203] log likelihood: -1898.880318
EM: Round [204] log likelihood: -1898.879684
EM: Round [205] log likelihood: -1898.879055
EM: Round [206] log likelihood: -1898.878430
EM: Round [207] log likelihood: -1898.877810
EM: Round [208] log likelihood: -1898.877193
EM: Round [209] log likelihood: -1898.876581
EM: Round [210] log likelihood: -1898.875974
EM: Round [211] log likelihood: -1898.875370
EM: Round [212] log likelihood: -1898.874771
EM: Round [213] log likelihood: -1898.874176
EM: Round [214] log likelihood: -1898.873585
EM: Round [215] log likelihood: -1898.872998
EM: Round [216] log likelihood: -1898.872415
EM: Round [217] log likelihood: -1898.871837
EM: Round [218] log likelihood: -1898.871262
EM: Round [219] log likelihood: -1898.870691
EM: Round [220] log likelihood: -1898.870125
EM: Round [221] log likelihood: -1898.869562
EM: Round [222] log likelihood: -1898.869003
EM: Round [223] log likelihood: -1898.868448
EM: Round [224] log likelihood: -1898.867897
EM: Round [225] log likelihood: -1898.867349
EM: Round [226] log likelihood: -1898.866806
EM: Round [227] log likelihood: -1898.866266
EM: Round [228] log likelihood: -1898.865730
EM: Round [229] log likelihood: -1898.865197
EM: Round [230] log likelihood: -1898.864669
EM: Round [231] log likelihood: -1898.864144
EM: Round [232] log likelihood: -1898.863622
EM: Round [233] log likelihood: -1898.863104
EM: Round [234] log likelihood: -1898.862590
EM: Round [235] log likelihood: -1898.862079
EM: Round [236] log likelihood: -1898.861572
EM: Round [237] log likelihood: -1898.861068
EM: Round [238] log likelihood: -1898.860568
EM: Round [239] log likelihood: -1898.860071
EM: Round [240] log likelihood: -1898.859577
EM: Round [241] log likelihood: -1898.859087
EM: Round [242] log likelihood: -1898.858601
EM: Round [243] log likelihood: -1898.858117
EM: Round [244] log likelihood: -1898.857637
EM: Round [245] log likelihood: -1898.857160
EM: Round [246] log likelihood: -1898.856687
EM: Round [247] log likelihood: -1898.856216
EM: Round [248] log likelihood: -1898.855749
EM: Round [249] log likelihood: -1898.855285
EM: Round [250] log likelihood: -1898.854825
EM: Round [251] log likelihood: -1898.854367
EM: Round [252] log likelihood: -1898.853913
EM: Round [253] log likelihood: -1898.853461
EM: Round [254] log likelihood: -1898.853013
EM: Round [255] log likelihood: -1898.852568
EM: Round [256] log likelihood: -1898.852125
EM: Round [257] log likelihood: -1898.851686
EM: Round [258] log likelihood: -1898.851250
EM: Round [259] log likelihood: -1898.850817
EM: Round [260] log likelihood: -1898.850386
EM: Round [261] log likelihood: -1898.849959
EM: Round [262] log likelihood: -1898.849535
EM: Round [263] log likelihood: -1898.849113
EM: Round [264] log likelihood: -1898.848694
EM: Round [265] log likelihood: -1898.848278
EM: Round [266] log likelihood: -1898.847865
EM: Round [267] log likelihood: -1898.847455
EM: Round [268] log likelihood: -1898.847048
EM: Round [269] log likelihood: -1898.846643
EM: Round [270] log likelihood: -1898.846241
EM: Round [271] log likelihood: -1898.845842
EM: Round [272] log likelihood: -1898.845445
EM: Round [273] log likelihood: -1898.845051
EM: Round [274] log likelihood: -1898.844660
EM: Round [275] log likelihood: -1898.844271
EM: Round [276] log likelihood: -1898.843885
EM: Round [277] log likelihood: -1898.843502
EM: Round [278] log likelihood: -1898.843121
EM: Round [279] log likelihood: -1898.842743
EM: Round [280] log likelihood: -1898.842368
EM: Round [281] log likelihood: -1898.841994
EM: Round [282] log likelihood: -1898.841624
EM: Round [283] log likelihood: -1898.841256
EM: Round [284] log likelihood: -1898.840890
EM: Round [285] log likelihood: -1898.840527
EM: Round [286] log likelihood: -1898.840166
EM: Round [287] log likelihood: -1898.839808
EM: Round [288] log likelihood: -1898.839452
EM: Round [289] log likelihood: -1898.839099
EM: Round [290] log likelihood: -1898.838747
EM: Round [291] log likelihood: -1898.838399
EM: Round [292] log likelihood: -1898.838052
EM: Round [293] log likelihood: -1898.837708
EM: Round [294] log likelihood: -1898.837366
EM: Round [295] log likelihood: -1898.837027
EM: Round [296] log likelihood: -1898.836690
EM: Round [297] log likelihood: -1898.836355
EM: Round [298] log likelihood: -1898.836022
EM: Round [299] log likelihood: -1898.835692
EM: Round [300] log likelihood: -1898.835363
EM: Round [301] log likelihood: -1898.835037
EM: Round [302] log likelihood: -1898.834713
EM: Round [303] log likelihood: -1898.834392
EM: Round [304] log likelihood: -1898.834072
EM: Round [305] log likelihood: -1898.833755
EM: Round [306] log likelihood: -1898.833439
EM: Round [307] log likelihood: -1898.833126
EM: Round [308] log likelihood: -1898.832815
EM: Round [309] log likelihood: -1898.832506
EM: Round [310] log likelihood: -1898.832199
EM: Round [311] log likelihood: -1898.831894
EM: Round [312] log likelihood: -1898.831591
EM: Round [313] log likelihood: -1898.831290
EM: Round [314] log likelihood: -1898.830992
EM: Round [315] log likelihood: -1898.830695
EM: Round [316] log likelihood: -1898.830400
EM: Round [317] log likelihood: -1898.830107
EM: Round [318] log likelihood: -1898.829816
EM: Round [319] log likelihood: -1898.829527
EM: Round [320] log likelihood: -1898.829240
EM: Round [321] log likelihood: -1898.828955
EM: Round [322] log likelihood: -1898.828671
EM: Round [323] log likelihood: -1898.828390
EM: Round [324] log likelihood: -1898.828110
EM: Round [325] log likelihood: -1898.827833
EM: Round [326] log likelihood: -1898.827557
EM: Round [327] log likelihood: -1898.827283
EM: Round [328] log likelihood: -1898.827011
EM: Round [329] log likelihood: -1898.826740
EM: Round [330] log likelihood: -1898.826472
EM: Round [331] log likelihood: -1898.826205
EM: Round [332] log likelihood: -1898.825940
EM: Round [333] log likelihood: -1898.825676
EM: Round [334] log likelihood: -1898.825415
EM: Round [335] log likelihood: -1898.825155
EM: Round [336] log likelihood: -1898.824897
EM: Round [337] log likelihood: -1898.824641
EM: Round [338] log likelihood: -1898.824386
EM: Round [339] log likelihood: -1898.824133
EM: Round [340] log likelihood: -1898.823882
EM: Round [341] log likelihood: -1898.823632
EM: Round [342] log likelihood: -1898.823384
EM: Round [343] log likelihood: -1898.823138
EM: Round [344] log likelihood: -1898.822893
EM: Round [345] log likelihood: -1898.822650
EM: Round [346] log likelihood: -1898.822408
EM: Round [347] log likelihood: -1898.822168
EM: Round [348] log likelihood: -1898.821930
EM: Round [349] log likelihood: -1898.821693
EM: Round [350] log likelihood: -1898.821458
EM: Round [351] log likelihood: -1898.821225
EM: Round [352] log likelihood: -1898.820992
EM: Round [353] log likelihood: -1898.820762
EM: Round [354] log likelihood: -1898.820533
EM: Round [355] log likelihood: -1898.820305
EM: Round [356] log likelihood: -1898.820079
EM: Round [357] log likelihood: -1898.819855
EM: Round [358] log likelihood: -1898.819632
EM: Round [359] log likelihood: -1898.819410
EM: Round [360] log likelihood: -1898.819190
EM: Round [361] log likelihood: -1898.818971
EM: Round [362] log likelihood: -1898.818754
EM: Round [363] log likelihood: -1898.818538
EM: Round [364] log likelihood: -1898.818324
EM: Round [365] log likelihood: -1898.818111
EM: Round [366] log likelihood: -1898.817899
EM: Round [367] log likelihood: -1898.817689
EM: Round [368] log likelihood: -1898.817480
EM: Round [369] log likelihood: -1898.817273
EM: Round [370] log likelihood: -1898.817067
EM: Round [371] log likelihood: -1898.816862
EM: Round [372] log likelihood: -1898.816659
EM: Round [373] log likelihood: -1898.816457
EM: Round [374] log likelihood: -1898.816256
EM: Round [375] log likelihood: -1898.816057
EM: Round [376] log likelihood: -1898.815859
EM: Round [377] log likelihood: -1898.815662
EM: Round [378] log likelihood: -1898.815466
EM: Round [379] log likelihood: -1898.815272
EM: Round [380] log likelihood: -1898.815079
EM: Round [381] log likelihood: -1898.814888
EM: Round [382] log likelihood: -1898.814697
EM: Round [383] log likelihood: -1898.814508
EM: Round [384] log likelihood: -1898.814320
EM: Round [385] log likelihood: -1898.814134
EM: Round [386] log likelihood: -1898.813948
EM: Round [387] log likelihood: -1898.813764
EM: Round [388] log likelihood: -1898.813581
EM: Round [389] log likelihood: -1898.813399
EM: Round [390] log likelihood: -1898.813218
EM: Round [391] log likelihood: -1898.813039
EM: Round [392] log likelihood: -1898.812861
EM: Round [393] log likelihood: -1898.812683
EM: Round [394] log likelihood: -1898.812508
EM: Round [395] log likelihood: -1898.812333
EM: Round [396] log likelihood: -1898.812159
EM: Round [397] log likelihood: -1898.811987
EM: Round [398] log likelihood: -1898.811815
EM: Round [399] log likelihood: -1898.811645
EM: Round [400] log likelihood: -1898.811476
EM: Round [401] log likelihood: -1898.811308
EM: Round [402] log likelihood: -1898.811141
EM: Round [403] log likelihood: -1898.810975
EM: Round [404] log likelihood: -1898.810810
EM: Round [405] log likelihood: -1898.810646
EM: Round [406] log likelihood: -1898.810484
EM: Round [407] log likelihood: -1898.810322
EM: Round [408] log likelihood: -1898.810162
EM: Round [409] log likelihood: -1898.810002
EM: Round [410] log likelihood: -1898.809844
EM: Round [411] log likelihood: -1898.809686
EM: Round [412] log likelihood: -1898.809530
EM: Round [413] log likelihood: -1898.809375
EM: Round [414] log likelihood: -1898.809220
EM: Round [415] log likelihood: -1898.809067
EM: Round [416] log likelihood: -1898.808915
EM: Round [417] log likelihood: -1898.808763
EM: Round [418] log likelihood: -1898.808613
EM: Round [419] log likelihood: -1898.808464
EM: Round [420] log likelihood: -1898.808315
EM: Round [421] log likelihood: -1898.808168
EM: Round [422] log likelihood: -1898.808021
EM: Round [423] log likelihood: -1898.807876
EM: Round [424] log likelihood: -1898.807731
EM: Round [425] log likelihood: -1898.807588
EM: Round [426] log likelihood: -1898.807445
EM: Round [427] log likelihood: -1898.807303
EM: Round [428] log likelihood: -1898.807162
EM: Round [429] log likelihood: -1898.807022
EM: Round [430] log likelihood: -1898.806883
EM: Round [431] log likelihood: -1898.806745
EM: Round [432] log likelihood: -1898.806608
EM: Round [433] log likelihood: -1898.806472
EM: Round [434] log likelihood: -1898.806336
EM: Round [435] log likelihood: -1898.806202
EM: Round [436] log likelihood: -1898.806068
EM: Round [437] log likelihood: -1898.805935
EM: Round [438] log likelihood: -1898.805803
EM: Round [439] log likelihood: -1898.805672
EM: Round [440] log likelihood: -1898.805542
EM: Round [441] log likelihood: -1898.805413
EM: Round [442] log likelihood: -1898.805284
EM: Round [443] log likelihood: -1898.805156
EM: Round [444] log likelihood: -1898.805029
EM: Round [445] log likelihood: -1898.804903
EM: Round [446] log likelihood: -1898.804778
EM: Round [447] log likelihood: -1898.804654
EM: Round [448] log likelihood: -1898.804530
EM: Round [449] log likelihood: -1898.804407
EM: Round [450] log likelihood: -1898.804285
EM: Round [451] log likelihood: -1898.804164
EM: Round [452] log likelihood: -1898.804044
EM: Round [453] log likelihood: -1898.803924
EM: Round [454] log likelihood: -1898.803805
EM: Round [455] log likelihood: -1898.803687
EM: Round [456] log likelihood: -1898.803570
EM: Round [457] log likelihood: -1898.803453
EM: Round [458] log likelihood: -1898.803337
EM: Round [459] log likelihood: -1898.803222
EM: Round [460] log likelihood: -1898.803108
EM: Round [461] log likelihood: -1898.802994
EM: Round [462] log likelihood: -1898.802881
EM: Round [463] log likelihood: -1898.802769
EM: Round [464] log likelihood: -1898.802658
EM: Round [465] log likelihood: -1898.802547
EM: Round [466] log likelihood: -1898.802437
EM: Round [467] log likelihood: -1898.802328
EM: Round [468] log likelihood: -1898.802219
EM: Round [469] log likelihood: -1898.802112
EM: Round [470] log likelihood: -1898.802004
EM: Round [471] log likelihood: -1898.801898
EM: Round [472] log likelihood: -1898.801792
EM: Round [473] log likelihood: -1898.801687
EM: Round [474] log likelihood: -1898.801583
EM: Round [475] log likelihood: -1898.801479
EM: Round [476] log likelihood: -1898.801376
EM: Round [477] log likelihood: -1898.801274
EM: Round [478] log likelihood: -1898.801172
EM: Round [479] log likelihood: -1898.801071
EM: Round [480] log likelihood: -1898.800971
EM: Round [481] log likelihood: -1898.800871
EM: Stopping iterations at round 481 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-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.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-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.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-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.uxAJ9Mobh9/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1863.820188
EM: Round [1] log likelihood: -1863.820188
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296445688
Warning - not locating file: /tmp/nxf.uxAJ9Mobh9/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
ls: cannot access 'IGV_inputs': No such file or directory