Done.
-parsing GTF file: /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.5gGev74vOT/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.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:01:44 : INFO : Done.
-parsing GTF file: /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[1320000] -done parsing /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4,
'small anchor length' => 118,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 1,
'per_id < 96' => 3765,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 12,
'excessive soft clipping' => 4343,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 5,
' ** passed ** ' => 15787,
'seq-similar region overlap' => 181,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 28,
'low complexity anchor region' => 33,
'num genes matched < 2' => 12,
'exons hit < 2' => 12,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 28,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 63
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[34000] -fusion SPANNING read extraction for scaff: INPP4A--DPP10
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8
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[19000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11
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[91000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[35000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[20000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[91000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[35000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[65000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[26000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[6000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[8000] -fusion SPANNING read extraction for scaff: TTC8--AL135746.1
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[15000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 2950,
'seq similar region alignment' => 53524
};
EM: Starting log likelihood: -4628.914988
EM: Round [1] log likelihood: -4627.706253
EM: Round [2] log likelihood: -4626.918580
EM: Round [3] log likelihood: -4626.268723
EM: Round [4] log likelihood: -4625.727668
EM: Round [5] log likelihood: -4625.273462
EM: Round [6] log likelihood: -4624.889039
EM: Round [7] log likelihood: -4624.561017
EM: Round [8] log likelihood: -4624.278837
EM: Round [9] log likelihood: -4624.034119
EM: Round [10] log likelihood: -4623.820177
EM: Round [11] log likelihood: -4623.631651
EM: Round [12] log likelihood: -4623.464226
EM: Round [13] log likelihood: -4623.314415
EM: Round [14] log likelihood: -4623.179387
EM: Round [15] log likelihood: -4623.056834
EM: Round [16] log likelihood: -4622.944869
EM: Round [17] log likelihood: -4622.841943
EM: Round [18] log likelihood: -4622.746777
EM: Round [19] log likelihood: -4622.658313
EM: Round [20] log likelihood: -4622.575669
EM: Round [21] log likelihood: -4622.498110
EM: Round [22] log likelihood: -4622.425021
EM: Round [23] log likelihood: -4622.355882
EM: Round [24] log likelihood: -4622.290253
EM: Round [25] log likelihood: -4622.227761
EM: Round [26] log likelihood: -4622.168087
EM: Round [27] log likelihood: -4622.110959
EM: Round [28] log likelihood: -4622.056140
EM: Round [29] log likelihood: -4622.003429
EM: Round [30] log likelihood: -4621.952648
EM: Round [31] log likelihood: -4621.903643
EM: Round [32] log likelihood: -4621.856279
EM: Round [33] log likelihood: -4621.810438
EM: Round [34] log likelihood: -4621.766016
EM: Round [35] log likelihood: -4621.722918
EM: Round [36] log likelihood: -4621.681062
EM: Round [37] log likelihood: -4621.640375
EM: Round [38] log likelihood: -4621.600790
EM: Round [39] log likelihood: -4621.562248
EM: Round [40] log likelihood: -4621.524694
EM: Round [41] log likelihood: -4621.488079
EM: Round [42] log likelihood: -4621.452360
EM: Round [43] log likelihood: -4621.417494
EM: Round [44] log likelihood: -4621.383444
EM: Round [45] log likelihood: -4621.350177
EM: Round [46] log likelihood: -4621.317659
EM: Round [47] log likelihood: -4621.285862
EM: Round [48] log likelihood: -4621.254758
EM: Round [49] log likelihood: -4621.224321
EM: Round [50] log likelihood: -4621.194528
EM: Round [51] log likelihood: -4621.165356
EM: Round [52] log likelihood: -4621.136783
EM: Round [53] log likelihood: -4621.108791
EM: Round [54] log likelihood: -4621.081359
EM: Round [55] log likelihood: -4621.054470
EM: Round [56] log likelihood: -4621.028107
EM: Round [57] log likelihood: -4621.002254
EM: Round [58] log likelihood: -4620.976896
EM: Round [59] log likelihood: -4620.952017
EM: Round [60] log likelihood: -4620.927604
EM: Round [61] log likelihood: -4620.903643
EM: Round [62] log likelihood: -4620.880121
EM: Round [63] log likelihood: -4620.857026
EM: Round [64] log likelihood: -4620.834346
EM: Round [65] log likelihood: -4620.812069
EM: Round [66] log likelihood: -4620.790184
EM: Round [67] log likelihood: -4620.768681
EM: Round [68] log likelihood: -4620.747550
EM: Round [69] log likelihood: -4620.726780
EM: Round [70] log likelihood: -4620.706361
EM: Round [71] log likelihood: -4620.686285
EM: Round [72] log likelihood: -4620.666543
EM: Round [73] log likelihood: -4620.647125
EM: Round [74] log likelihood: -4620.628024
EM: Round [75] log likelihood: -4620.609231
EM: Round [76] log likelihood: -4620.590739
EM: Round [77] log likelihood: -4620.572539
EM: Round [78] log likelihood: -4620.554625
EM: Round [79] log likelihood: -4620.536989
EM: Round [80] log likelihood: -4620.519625
EM: Round [81] log likelihood: -4620.502525
EM: Round [82] log likelihood: -4620.485683
EM: Round [83] log likelihood: -4620.469093
EM: Round [84] log likelihood: -4620.452749
EM: Round [85] log likelihood: -4620.436645
EM: Round [86] log likelihood: -4620.420774
EM: Round [87] log likelihood: -4620.405132
EM: Round [88] log likelihood: -4620.389713
EM: Round [89] log likelihood: -4620.374512
EM: Round [90] log likelihood: -4620.359523
EM: Round [91] log likelihood: -4620.344742
EM: Round [92] log likelihood: -4620.330164
EM: Round [93] log likelihood: -4620.315785
EM: Round [94] log likelihood: -4620.301599
EM: Round [95] log likelihood: -4620.287602
EM: Round [96] log likelihood: -4620.273791
EM: Round [97] log likelihood: -4620.260161
EM: Round [98] log likelihood: -4620.246708
EM: Round [99] log likelihood: -4620.233428
EM: Round [100] log likelihood: -4620.220317
EM: Round [101] log likelihood: -4620.207372
EM: Round [102] log likelihood: -4620.194589
EM: Round [103] log likelihood: -4620.181966
EM: Round [104] log likelihood: -4620.169497
EM: Round [105] log likelihood: -4620.157181
EM: Round [106] log likelihood: -4620.145014
EM: Round [107] log likelihood: -4620.132992
EM: Round [108] log likelihood: -4620.121114
EM: Round [109] log likelihood: -4620.109376
EM: Round [110] log likelihood: -4620.097775
EM: Round [111] log likelihood: -4620.086309
EM: Round [112] log likelihood: -4620.074975
EM: Round [113] log likelihood: -4620.063770
EM: Round [114] log likelihood: -4620.052692
EM: Round [115] log likelihood: -4620.041739
EM: Round [116] log likelihood: -4620.030907
EM: Round [117] log likelihood: -4620.020196
EM: Round [118] log likelihood: -4620.009602
EM: Round [119] log likelihood: -4619.999123
EM: Round [120] log likelihood: -4619.988758
EM: Round [121] log likelihood: -4619.978504
EM: Round [122] log likelihood: -4619.968360
EM: Round [123] log likelihood: -4619.958322
EM: Round [124] log likelihood: -4619.948390
EM: Round [125] log likelihood: -4619.938562
EM: Round [126] log likelihood: -4619.928835
EM: Round [127] log likelihood: -4619.919209
EM: Round [128] log likelihood: -4619.909681
EM: Round [129] log likelihood: -4619.900249
EM: Round [130] log likelihood: -4619.890913
EM: Round [131] log likelihood: -4619.881670
EM: Round [132] log likelihood: -4619.872519
EM: Round [133] log likelihood: -4619.863459
EM: Round [134] log likelihood: -4619.854487
EM: Round [135] log likelihood: -4619.845603
EM: Round [136] log likelihood: -4619.836806
EM: Round [137] log likelihood: -4619.828093
EM: Round [138] log likelihood: -4619.819464
EM: Round [139] log likelihood: -4619.810917
EM: Round [140] log likelihood: -4619.802452
EM: Round [141] log likelihood: -4619.794066
EM: Round [142] log likelihood: -4619.785759
EM: Round [143] log likelihood: -4619.777529
EM: Round [144] log likelihood: -4619.769375
EM: Round [145] log likelihood: -4619.761297
EM: Round [146] log likelihood: -4619.753293
EM: Round [147] log likelihood: -4619.745361
EM: Round [148] log likelihood: -4619.737502
EM: Round [149] log likelihood: -4619.729714
EM: Round [150] log likelihood: -4619.721996
EM: Round [151] log likelihood: -4619.714346
EM: Round [152] log likelihood: -4619.706765
EM: Round [153] log likelihood: -4619.699251
EM: Round [154] log likelihood: -4619.691803
EM: Round [155] log likelihood: -4619.684421
EM: Round [156] log likelihood: -4619.677103
EM: Round [157] log likelihood: -4619.669849
EM: Round [158] log likelihood: -4619.662657
EM: Round [159] log likelihood: -4619.655527
EM: Round [160] log likelihood: -4619.648459
EM: Round [161] log likelihood: -4619.641450
EM: Round [162] log likelihood: -4619.634502
EM: Round [163] log likelihood: -4619.627612
EM: Round [164] log likelihood: -4619.620780
EM: Round [165] log likelihood: -4619.614006
EM: Round [166] log likelihood: -4619.607289
EM: Round [167] log likelihood: -4619.600627
EM: Round [168] log likelihood: -4619.594020
EM: Round [169] log likelihood: -4619.587469
EM: Round [170] log likelihood: -4619.580971
EM: Round [171] log likelihood: -4619.574526
EM: Round [172] log likelihood: -4619.568134
EM: Round [173] log likelihood: -4619.561794
EM: Round [174] log likelihood: -4619.555506
EM: Round [175] log likelihood: -4619.549268
EM: Round [176] log likelihood: -4619.543081
EM: Round [177] log likelihood: -4619.536943
EM: Round [178] log likelihood: -4619.530854
EM: Round [179] log likelihood: -4619.524814
EM: Round [180] log likelihood: -4619.518821
EM: Round [181] log likelihood: -4619.512876
EM: Round [182] log likelihood: -4619.506978
EM: Round [183] log likelihood: -4619.501127
EM: Round [184] log likelihood: -4619.495321
EM: Round [185] log likelihood: -4619.489561
EM: Round [186] log likelihood: -4619.483845
EM: Round [187] log likelihood: -4619.478174
EM: Round [188] log likelihood: -4619.472546
EM: Round [189] log likelihood: -4619.466962
EM: Round [190] log likelihood: -4619.461421
EM: Round [191] log likelihood: -4619.455922
EM: Round [192] log likelihood: -4619.450466
EM: Round [193] log likelihood: -4619.445051
EM: Round [194] log likelihood: -4619.439677
EM: Round [195] log likelihood: -4619.434344
EM: Round [196] log likelihood: -4619.429051
EM: Round [197] log likelihood: -4619.423798
EM: Round [198] log likelihood: -4619.418584
EM: Round [199] log likelihood: -4619.413409
EM: Round [200] log likelihood: -4619.408273
EM: Round [201] log likelihood: -4619.403176
EM: Round [202] log likelihood: -4619.398116
EM: Round [203] log likelihood: -4619.393094
EM: Round [204] log likelihood: -4619.388108
EM: Round [205] log likelihood: -4619.383160
EM: Round [206] log likelihood: -4619.378248
EM: Round [207] log likelihood: -4619.373371
EM: Round [208] log likelihood: -4619.368531
EM: Round [209] log likelihood: -4619.363726
EM: Round [210] log likelihood: -4619.358955
EM: Round [211] log likelihood: -4619.354220
EM: Round [212] log likelihood: -4619.349518
EM: Round [213] log likelihood: -4619.344851
EM: Round [214] log likelihood: -4619.340217
EM: Round [215] log likelihood: -4619.335616
EM: Round [216] log likelihood: -4619.331049
EM: Round [217] log likelihood: -4619.326514
EM: Round [218] log likelihood: -4619.322011
EM: Round [219] log likelihood: -4619.317541
EM: Round [220] log likelihood: -4619.313102
EM: Round [221] log likelihood: -4619.308694
EM: Round [222] log likelihood: -4619.304318
EM: Round [223] log likelihood: -4619.299973
EM: Round [224] log likelihood: -4619.295658
EM: Round [225] log likelihood: -4619.291374
EM: Round [226] log likelihood: -4619.287119
EM: Round [227] log likelihood: -4619.282894
EM: Round [228] log likelihood: -4619.278699
EM: Round [229] log likelihood: -4619.274533
EM: Round [230] log likelihood: -4619.270396
EM: Round [231] log likelihood: -4619.266287
EM: Round [232] log likelihood: -4619.262207
EM: Round [233] log likelihood: -4619.258155
EM: Round [234] log likelihood: -4619.254131
EM: Round [235] log likelihood: -4619.250135
EM: Round [236] log likelihood: -4619.246166
EM: Round [237] log likelihood: -4619.242224
EM: Round [238] log likelihood: -4619.238310
EM: Round [239] log likelihood: -4619.234421
EM: Round [240] log likelihood: -4619.230560
EM: Round [241] log likelihood: -4619.226724
EM: Round [242] log likelihood: -4619.222915
EM: Round [243] log likelihood: -4619.219131
EM: Round [244] log likelihood: -4619.215373
EM: Round [245] log likelihood: -4619.211640
EM: Round [246] log likelihood: -4619.207932
EM: Round [247] log likelihood: -4619.204249
EM: Round [248] log likelihood: -4619.200591
EM: Round [249] log likelihood: -4619.196958
EM: Round [250] log likelihood: -4619.193348
EM: Round [251] log likelihood: -4619.189763
EM: Round [252] log likelihood: -4619.186201
EM: Round [253] log likelihood: -4619.182663
EM: Round [254] log likelihood: -4619.179149
EM: Round [255] log likelihood: -4619.175658
EM: Round [256] log likelihood: -4619.172190
EM: Round [257] log likelihood: -4619.168744
EM: Round [258] log likelihood: -4619.165322
EM: Round [259] log likelihood: -4619.161922
EM: Round [260] log likelihood: -4619.158544
EM: Round [261] log likelihood: -4619.155188
EM: Round [262] log likelihood: -4619.151854
EM: Round [263] log likelihood: -4619.148542
EM: Round [264] log likelihood: -4619.145252
EM: Round [265] log likelihood: -4619.141983
EM: Round [266] log likelihood: -4619.138735
EM: Round [267] log likelihood: -4619.135508
EM: Round [268] log likelihood: -4619.132302
EM: Round [269] log likelihood: -4619.129117
EM: Round [270] log likelihood: -4619.125953
EM: Round [271] log likelihood: -4619.122808
EM: Round [272] log likelihood: -4619.119684
EM: Round [273] log likelihood: -4619.116581
EM: Round [274] log likelihood: -4619.113496
EM: Round [275] log likelihood: -4619.110432
EM: Round [276] log likelihood: -4619.107387
EM: Round [277] log likelihood: -4619.104362
EM: Round [278] log likelihood: -4619.101356
EM: Round [279] log likelihood: -4619.098369
EM: Round [280] log likelihood: -4619.095401
EM: Round [281] log likelihood: -4619.092452
EM: Round [282] log likelihood: -4619.089522
EM: Round [283] log likelihood: -4619.086610
EM: Round [284] log likelihood: -4619.083717
EM: Round [285] log likelihood: -4619.080841
EM: Round [286] log likelihood: -4619.077984
EM: Round [287] log likelihood: -4619.075145
EM: Round [288] log likelihood: -4619.072324
EM: Round [289] log likelihood: -4619.069520
EM: Round [290] log likelihood: -4619.066734
EM: Round [291] log likelihood: -4619.063965
EM: Round [292] log likelihood: -4619.061214
EM: Round [293] log likelihood: -4619.058480
EM: Round [294] log likelihood: -4619.055763
EM: Round [295] log likelihood: -4619.053062
EM: Round [296] log likelihood: -4619.050379
EM: Round [297] log likelihood: -4619.047712
EM: Round [298] log likelihood: -4619.045062
EM: Round [299] log likelihood: -4619.042428
EM: Round [300] log likelihood: -4619.039810
EM: Round [301] log likelihood: -4619.037208
EM: Round [302] log likelihood: -4619.034623
EM: Round [303] log likelihood: -4619.032053
EM: Round [304] log likelihood: -4619.029499
EM: Round [305] log likelihood: -4619.026961
EM: Round [306] log likelihood: -4619.024439
EM: Round [307] log likelihood: -4619.021931
EM: Round [308] log likelihood: -4619.019440
EM: Round [309] log likelihood: -4619.016963
EM: Round [310] log likelihood: -4619.014502
EM: Round [311] log likelihood: -4619.012055
EM: Round [312] log likelihood: -4619.009623
EM: Round [313] log likelihood: -4619.007207
EM: Round [314] log likelihood: -4619.004804
EM: Round [315] log likelihood: -4619.002417
EM: Round [316] log likelihood: -4619.000044
EM: Round [317] log likelihood: -4618.997685
EM: Round [318] log likelihood: -4618.995340
EM: Round [319] log likelihood: -4618.993010
EM: Round [320] log likelihood: -4618.990693
EM: Round [321] log likelihood: -4618.988391
EM: Round [322] log likelihood: -4618.986102
EM: Round [323] log likelihood: -4618.983827
EM: Round [324] log likelihood: -4618.981566
EM: Round [325] log likelihood: -4618.979319
EM: Round [326] log likelihood: -4618.977084
EM: Round [327] log likelihood: -4618.974864
EM: Round [328] log likelihood: -4618.972656
EM: Round [329] log likelihood: -4618.970462
EM: Round [330] log likelihood: -4618.968280
EM: Round [331] log likelihood: -4618.966112
EM: Round [332] log likelihood: -4618.963956
EM: Round [333] log likelihood: -4618.961814
EM: Round [334] log likelihood: -4618.959684
EM: Round [335] log likelihood: -4618.957566
EM: Round [336] log likelihood: -4618.955462
EM: Round [337] log likelihood: -4618.953369
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EM: Round [798] log likelihood: -4618.603357
EM: Round [799] log likelihood: -4618.603173
EM: Round [800] log likelihood: -4618.602989
EM: Round [801] log likelihood: -4618.602806
EM: Round [802] log likelihood: -4618.602624
EM: Round [803] log likelihood: -4618.602443
EM: Round [804] log likelihood: -4618.602263
EM: Round [805] log likelihood: -4618.602084
EM: Round [806] log likelihood: -4618.601906
EM: Round [807] log likelihood: -4618.601728
EM: Round [808] log likelihood: -4618.601552
EM: Round [809] log likelihood: -4618.601376
EM: Round [810] log likelihood: -4618.601201
EM: Round [811] log likelihood: -4618.601027
EM: Round [812] log likelihood: -4618.600854
EM: Round [813] log likelihood: -4618.600682
EM: Round [814] log likelihood: -4618.600510
EM: Round [815] log likelihood: -4618.600340
EM: Round [816] log likelihood: -4618.600170
EM: Round [817] log likelihood: -4618.600001
EM: Round [818] log likelihood: -4618.599833
EM: Round [819] log likelihood: -4618.599666
EM: Round [820] log likelihood: -4618.599500
EM: Round [821] log likelihood: -4618.599334
EM: Round [822] log likelihood: -4618.599169
EM: Round [823] log likelihood: -4618.599005
EM: Round [824] log likelihood: -4618.598842
EM: Round [825] log likelihood: -4618.598680
EM: Round [826] log likelihood: -4618.598518
EM: Round [827] log likelihood: -4618.598358
EM: Round [828] log likelihood: -4618.598198
EM: Round [829] log likelihood: -4618.598039
EM: Round [830] log likelihood: -4618.597880
EM: Round [831] log likelihood: -4618.597723
EM: Round [832] log likelihood: -4618.597566
EM: Round [833] log likelihood: -4618.597410
EM: Round [834] log likelihood: -4618.597255
EM: Round [835] log likelihood: -4618.597100
EM: Round [836] log likelihood: -4618.596947
EM: Round [837] log likelihood: -4618.596794
EM: Round [838] log likelihood: -4618.596641
EM: Round [839] log likelihood: -4618.596490
EM: Round [840] log likelihood: -4618.596339
EM: Round [841] log likelihood: -4618.596189
EM: Round [842] log likelihood: -4618.596040
EM: Round [843] log likelihood: -4618.595892
EM: Round [844] log likelihood: -4618.595744
EM: Round [845] log likelihood: -4618.595597
EM: Round [846] log likelihood: -4618.595450
EM: Round [847] log likelihood: -4618.595305
EM: Round [848] log likelihood: -4618.595160
EM: Round [849] log likelihood: -4618.595016
EM: Round [850] log likelihood: -4618.594872
EM: Round [851] log likelihood: -4618.594730
EM: Round [852] log likelihood: -4618.594588
EM: Round [853] log likelihood: -4618.594446
EM: Round [854] log likelihood: -4618.594306
EM: Round [855] log likelihood: -4618.594166
EM: Round [856] log likelihood: -4618.594026
EM: Round [857] log likelihood: -4618.593888
EM: Round [858] log likelihood: -4618.593750
EM: Round [859] log likelihood: -4618.593613
EM: Round [860] log likelihood: -4618.593476
EM: Round [861] log likelihood: -4618.593340
EM: Round [862] log likelihood: -4618.593205
EM: Round [863] log likelihood: -4618.593071
EM: Round [864] log likelihood: -4618.592937
EM: Round [865] log likelihood: -4618.592803
EM: Round [866] log likelihood: -4618.592671
EM: Round [867] log likelihood: -4618.592539
EM: Round [868] log likelihood: -4618.592408
EM: Round [869] log likelihood: -4618.592277
EM: Round [870] log likelihood: -4618.592147
EM: Round [871] log likelihood: -4618.592018
EM: Round [872] log likelihood: -4618.591889
EM: Round [873] log likelihood: -4618.591761
EM: Round [874] log likelihood: -4618.591634
EM: Round [875] log likelihood: -4618.591507
EM: Round [876] log likelihood: -4618.591381
EM: Round [877] log likelihood: -4618.591255
EM: Round [878] log likelihood: -4618.591130
EM: Round [879] log likelihood: -4618.591006
EM: Round [880] log likelihood: -4618.590882
EM: Round [881] log likelihood: -4618.590759
EM: Round [882] log likelihood: -4618.590636
EM: Round [883] log likelihood: -4618.590515
EM: Round [884] log likelihood: -4618.590393
EM: Round [885] log likelihood: -4618.590272
EM: Round [886] log likelihood: -4618.590152
EM: Round [887] log likelihood: -4618.590033
EM: Round [888] log likelihood: -4618.589914
EM: Round [889] log likelihood: -4618.589796
EM: Round [890] log likelihood: -4618.589678
EM: Round [891] log likelihood: -4618.589561
EM: Round [892] log likelihood: -4618.589444
EM: Round [893] log likelihood: -4618.589328
EM: Round [894] log likelihood: -4618.589212
EM: Round [895] log likelihood: -4618.589097
EM: Round [896] log likelihood: -4618.588983
EM: Round [897] log likelihood: -4618.588869
EM: Round [898] log likelihood: -4618.588756
EM: Round [899] log likelihood: -4618.588643
EM: Round [900] log likelihood: -4618.588531
EM: Round [901] log likelihood: -4618.588420
EM: Round [902] log likelihood: -4618.588309
EM: Round [903] log likelihood: -4618.588198
EM: Round [904] log likelihood: -4618.588088
EM: Round [905] log likelihood: -4618.587979
EM: Round [906] log likelihood: -4618.587870
EM: Round [907] log likelihood: -4618.587762
EM: Round [908] log likelihood: -4618.587654
EM: Round [909] log likelihood: -4618.587547
EM: Round [910] log likelihood: -4618.587440
EM: Round [911] log likelihood: -4618.587334
EM: Round [912] log likelihood: -4618.587228
EM: Round [913] log likelihood: -4618.587123
EM: Round [914] log likelihood: -4618.587018
EM: Round [915] log likelihood: -4618.586914
EM: Round [916] log likelihood: -4618.586810
EM: Round [917] log likelihood: -4618.586707
EM: Round [918] log likelihood: -4618.586605
EM: Round [919] log likelihood: -4618.586502
EM: Round [920] log likelihood: -4618.586401
EM: Round [921] log likelihood: -4618.586300
EM: Round [922] log likelihood: -4618.586199
EM: Round [923] log likelihood: -4618.586099
EM: Round [924] log likelihood: -4618.585999
EM: Stopping iterations at round 924 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-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.5gGev74vOT/fi_workdir/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2866.976802
EM: Round [1] log likelihood: -2866.841495
EM: Round [2] log likelihood: -2866.841126
EM: Round [3] log likelihood: -2866.841124
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296712379
Warning - not locating file: /tmp/nxf.5gGev74vOT/aih-tih-sc-7f9674-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
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 [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 [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
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 [ENSG00000259028.1]
ls: cannot access 'IGV_inputs': No such file or directory