Done.
-parsing GTF file: /tmp/nxf.vWFKtXFV5P/659_cYf-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.vWFKtXFV5P/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.vWFKtXFV5P/659_cYf-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.vWFKtXFV5P/659_cYf-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.vWFKtXFV5P/fi_workdir/659_cYf-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.vWFKtXFV5P/fi_workdir/659_cYf-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_cYf-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_cYf-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
10:54:57 : INFO : Done.
-parsing GTF file: /tmp/nxf.vWFKtXFV5P/fi_workdir/659_cYf-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.vWFKtXFV5P/fi_workdir/659_cYf-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[4490000] -done parsing /tmp/nxf.vWFKtXFV5P/fi_workdir/659_cYf-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num genes matched < 2' => 89,
'per_id < 96' => 27841,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 17,
'small anchor length' => 14,
'exons hit < 2' => 3,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 26,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 752,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 95,
'excessive soft clipping' => 41440,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 48,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 19,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 52,
' ** passed ** ' => 9048,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 10
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.vWFKtXFV5P/fi_workdir/659_cYf-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[55000] -fusion SPANNING read extraction for scaff: AC007216.5--PDPR
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[98000] -fusion SPANNING read extraction for scaff: AC096555.1--PCSK2
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[69000] -fusion SPANNING read extraction for scaff: AC138409.2--NAIP
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[62000] -fusion SPANNING read extraction for scaff: AC139256.1--PDPR
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[99000] -fusion SPANNING read extraction for scaff: ACKR2--PCSK2
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[904000] -fusion SPANNING read extraction for scaff: APBB2--GNAS
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[8000] -fusion SPANNING read extraction for scaff: C1QTNF3--AMACR
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[519000] -fusion SPANNING read extraction for scaff: EWSR1--FLI1
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[30000] -fusion SPANNING read extraction for scaff: FAM168A--PGA5
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[518000] -fusion SPANNING read extraction for scaff: FLI1--EWSR1
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[903000] -fusion SPANNING read extraction for scaff: GNAS--APBB2
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[38000] -fusion SPANNING read extraction for scaff: INSC--CALCB
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[58000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[55000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[69000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[85000] -fusion SPANNING read extraction for scaff: RPS6KA5--TTC7B
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[233000] -fusion SPANNING read extraction for scaff: SLCO5A1--ANK2
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[34000] -fusion SPANNING read extraction for scaff: TAS2R14--PRR4
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[25000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[14000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[15000] -fusion SPANNING read extraction for scaff: UBE2G1--TMCC1-AS1
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[187000] -fusion SPANNING read extraction for scaff: ZC3H4--AC073508.1
[1000]
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[130000] -fusion SPANNING read extraction for scaff: ZNF875--PCSK2
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 13264,
'seq similar region alignment' => 14049
};
EM: Starting log likelihood: -12960.305842
EM: Round [1] log likelihood: -12956.198674
EM: Round [2] log likelihood: -12955.566879
EM: Round [3] log likelihood: -12955.313254
EM: Round [4] log likelihood: -12955.120289
EM: Round [5] log likelihood: -12954.954452
EM: Round [6] log likelihood: -12954.809265
EM: Round [7] log likelihood: -12954.681333
EM: Round [8] log likelihood: -12954.568079
EM: Round [9] log likelihood: -12954.467419
EM: Round [10] log likelihood: -12954.377635
EM: Round [11] log likelihood: -12954.297298
EM: Round [12] log likelihood: -12954.225206
EM: Round [13] log likelihood: -12954.160343
EM: Round [14] log likelihood: -12954.101840
EM: Round [15] log likelihood: -12954.048954
EM: Round [16] log likelihood: -12954.001041
EM: Round [17] log likelihood: -12953.957547
EM: Round [18] log likelihood: -12953.917984
EM: Round [19] log likelihood: -12953.881931
EM: Round [20] log likelihood: -12953.849016
EM: Round [21] log likelihood: -12953.818911
EM: Round [22] log likelihood: -12953.791329
EM: Round [23] log likelihood: -12953.766015
EM: Round [24] log likelihood: -12953.742741
EM: Round [25] log likelihood: -12953.721308
EM: Round [26] log likelihood: -12953.701537
EM: Round [27] log likelihood: -12953.683269
EM: Round [28] log likelihood: -12953.666360
EM: Round [29] log likelihood: -12953.650684
EM: Round [30] log likelihood: -12953.636126
EM: Round [31] log likelihood: -12953.622584
EM: Round [32] log likelihood: -12953.609967
EM: Round [33] log likelihood: -12953.598191
EM: Round [34] log likelihood: -12953.587182
EM: Round [35] log likelihood: -12953.576873
EM: Round [36] log likelihood: -12953.567204
EM: Round [37] log likelihood: -12953.558120
EM: Round [38] log likelihood: -12953.549572
EM: Round [39] log likelihood: -12953.541514
EM: Round [40] log likelihood: -12953.533907
EM: Round [41] log likelihood: -12953.526714
EM: Round [42] log likelihood: -12953.519902
EM: Round [43] log likelihood: -12953.513440
EM: Round [44] log likelihood: -12953.507302
EM: Round [45] log likelihood: -12953.501461
EM: Round [46] log likelihood: -12953.495896
EM: Round [47] log likelihood: -12953.490586
EM: Round [48] log likelihood: -12953.485512
EM: Round [49] log likelihood: -12953.480657
EM: Round [50] log likelihood: -12953.476005
EM: Round [51] log likelihood: -12953.471542
EM: Round [52] log likelihood: -12953.467254
EM: Round [53] log likelihood: -12953.463130
EM: Round [54] log likelihood: -12953.459158
EM: Round [55] log likelihood: -12953.455330
EM: Round [56] log likelihood: -12953.451634
EM: Round [57] log likelihood: -12953.448063
EM: Round [58] log likelihood: -12953.444608
EM: Round [59] log likelihood: -12953.441264
EM: Round [60] log likelihood: -12953.438022
EM: Round [61] log likelihood: -12953.434877
EM: Round [62] log likelihood: -12953.431824
EM: Round [63] log likelihood: -12953.428856
EM: Round [64] log likelihood: -12953.425969
EM: Round [65] log likelihood: -12953.423159
EM: Round [66] log likelihood: -12953.420422
EM: Round [67] log likelihood: -12953.417753
EM: Round [68] log likelihood: -12953.415149
EM: Round [69] log likelihood: -12953.412606
EM: Round [70] log likelihood: -12953.410122
EM: Round [71] log likelihood: -12953.407694
EM: Round [72] log likelihood: -12953.405319
EM: Round [73] log likelihood: -12953.402995
EM: Round [74] log likelihood: -12953.400718
EM: Round [75] log likelihood: -12953.398488
EM: Round [76] log likelihood: -12953.396301
EM: Round [77] log likelihood: -12953.394156
EM: Round [78] log likelihood: -12953.392052
EM: Round [79] log likelihood: -12953.389986
EM: Round [80] log likelihood: -12953.387957
EM: Round [81] log likelihood: -12953.385964
EM: Round [82] log likelihood: -12953.384004
EM: Round [83] log likelihood: -12953.382077
EM: Round [84] log likelihood: -12953.380182
EM: Round [85] log likelihood: -12953.378317
EM: Round [86] log likelihood: -12953.376481
EM: Round [87] log likelihood: -12953.374673
EM: Round [88] log likelihood: -12953.372893
EM: Round [89] log likelihood: -12953.371138
EM: Round [90] log likelihood: -12953.369409
EM: Round [91] log likelihood: -12953.367705
EM: Round [92] log likelihood: -12953.366024
EM: Round [93] log likelihood: -12953.364367
EM: Round [94] log likelihood: -12953.362731
EM: Round [95] log likelihood: -12953.361117
EM: Round [96] log likelihood: -12953.359524
EM: Round [97] log likelihood: -12953.357952
EM: Round [98] log likelihood: -12953.356399
EM: Round [99] log likelihood: -12953.354865
EM: Round [100] log likelihood: -12953.353350
EM: Round [101] log likelihood: -12953.351853
EM: Round [102] log likelihood: -12953.350373
EM: Round [103] log likelihood: -12953.348911
EM: Round [104] log likelihood: -12953.347466
EM: Round [105] log likelihood: -12953.346037
EM: Round [106] log likelihood: -12953.344624
EM: Round [107] log likelihood: -12953.343227
EM: Round [108] log likelihood: -12953.341844
EM: Round [109] log likelihood: -12953.340477
EM: Round [110] log likelihood: -12953.339124
EM: Round [111] log likelihood: -12953.337785
EM: Round [112] log likelihood: -12953.336460
EM: Round [113] log likelihood: -12953.335149
EM: Round [114] log likelihood: -12953.333851
EM: Round [115] log likelihood: -12953.332566
EM: Round [116] log likelihood: -12953.331293
EM: Round [117] log likelihood: -12953.330034
EM: Round [118] log likelihood: -12953.328786
EM: Round [119] log likelihood: -12953.327551
EM: Round [120] log likelihood: -12953.326327
EM: Round [121] log likelihood: -12953.325115
EM: Round [122] log likelihood: -12953.323914
EM: Round [123] log likelihood: -12953.322724
EM: Round [124] log likelihood: -12953.321545
EM: Round [125] log likelihood: -12953.320377
EM: Round [126] log likelihood: -12953.319220
EM: Round [127] log likelihood: -12953.318073
EM: Round [128] log likelihood: -12953.316936
EM: Round [129] log likelihood: -12953.315810
EM: Round [130] log likelihood: -12953.314693
EM: Round [131] log likelihood: -12953.313586
EM: Round [132] log likelihood: -12953.312489
EM: Round [133] log likelihood: -12953.311401
EM: Round [134] log likelihood: -12953.310322
EM: Round [135] log likelihood: -12953.309253
EM: Round [136] log likelihood: -12953.308192
EM: Round [137] log likelihood: -12953.307141
EM: Round [138] log likelihood: -12953.306098
EM: Round [139] log likelihood: -12953.305065
EM: Round [140] log likelihood: -12953.304039
EM: Round [141] log likelihood: -12953.303022
EM: Round [142] log likelihood: -12953.302014
EM: Round [143] log likelihood: -12953.301013
EM: Round [144] log likelihood: -12953.300021
EM: Round [145] log likelihood: -12953.299037
EM: Round [146] log likelihood: -12953.298061
EM: Round [147] log likelihood: -12953.297092
EM: Round [148] log likelihood: -12953.296132
EM: Round [149] log likelihood: -12953.295179
EM: Round [150] log likelihood: -12953.294233
EM: Round [151] log likelihood: -12953.293295
EM: Round [152] log likelihood: -12953.292365
EM: Round [153] log likelihood: -12953.291441
EM: Round [154] log likelihood: -12953.290525
EM: Round [155] log likelihood: -12953.289616
EM: Round [156] log likelihood: -12953.288714
EM: Round [157] log likelihood: -12953.287819
EM: Round [158] log likelihood: -12953.286931
EM: Round [159] log likelihood: -12953.286050
EM: Round [160] log likelihood: -12953.285175
EM: Round [161] log likelihood: -12953.284307
EM: Round [162] log likelihood: -12953.283446
EM: Round [163] log likelihood: -12953.282591
EM: Round [164] log likelihood: -12953.281743
EM: Round [165] log likelihood: -12953.280901
EM: Round [166] log likelihood: -12953.280066
EM: Round [167] log likelihood: -12953.279236
EM: Round [168] log likelihood: -12953.278413
EM: Round [169] log likelihood: -12953.277597
EM: Round [170] log likelihood: -12953.276786
EM: Round [171] log likelihood: -12953.275981
EM: Round [172] log likelihood: -12953.275183
EM: Round [173] log likelihood: -12953.274390
EM: Round [174] log likelihood: -12953.273603
EM: Round [175] log likelihood: -12953.272822
EM: Round [176] log likelihood: -12953.272047
EM: Round [177] log likelihood: -12953.271277
EM: Round [178] log likelihood: -12953.270513
EM: Round [179] log likelihood: -12953.269755
EM: Round [180] log likelihood: -12953.269002
EM: Round [181] log likelihood: -12953.268255
EM: Round [182] log likelihood: -12953.267513
EM: Round [183] log likelihood: -12953.266776
EM: Round [184] log likelihood: -12953.266045
EM: Round [185] log likelihood: -12953.265320
EM: Round [186] log likelihood: -12953.264599
EM: Round [187] log likelihood: -12953.263884
EM: Round [188] log likelihood: -12953.263174
EM: Round [189] log likelihood: -12953.262469
EM: Round [190] log likelihood: -12953.261769
EM: Round [191] log likelihood: -12953.261074
EM: Round [192] log likelihood: -12953.260384
EM: Round [193] log likelihood: -12953.259700
EM: Round [194] log likelihood: -12953.259020
EM: Round [195] log likelihood: -12953.258345
EM: Round [196] log likelihood: -12953.257674
EM: Round [197] log likelihood: -12953.257009
EM: Round [198] log likelihood: -12953.256348
EM: Round [199] log likelihood: -12953.255692
EM: Round [200] log likelihood: -12953.255041
EM: Round [201] log likelihood: -12953.254394
EM: Round [202] log likelihood: -12953.253752
EM: Round [203] log likelihood: -12953.253115
EM: Round [204] log likelihood: -12953.252482
EM: Round [205] log likelihood: -12953.251854
EM: Round [206] log likelihood: -12953.251230
EM: Round [207] log likelihood: -12953.250610
EM: Round [208] log likelihood: -12953.249995
EM: Round [209] log likelihood: -12953.249384
EM: Round [210] log likelihood: -12953.248778
EM: Round [211] log likelihood: -12953.248175
EM: Round [212] log likelihood: -12953.247577
EM: Round [213] log likelihood: -12953.246984
EM: Round [214] log likelihood: -12953.246394
EM: Round [215] log likelihood: -12953.245809
EM: Round [216] log likelihood: -12953.245227
EM: Round [217] log likelihood: -12953.244650
EM: Round [218] log likelihood: -12953.244077
EM: Round [219] log likelihood: -12953.243508
EM: Round [220] log likelihood: -12953.242942
EM: Round [221] log likelihood: -12953.242381
EM: Round [222] log likelihood: -12953.241824
EM: Round [223] log likelihood: -12953.241270
EM: Round [224] log likelihood: -12953.240721
EM: Round [225] log likelihood: -12953.240175
EM: Round [226] log likelihood: -12953.239633
EM: Round [227] log likelihood: -12953.239095
EM: Round [228] log likelihood: -12953.238561
EM: Round [229] log likelihood: -12953.238030
EM: Round [230] log likelihood: -12953.237503
EM: Round [231] log likelihood: -12953.236980
EM: Round [232] log likelihood: -12953.236460
EM: Round [233] log likelihood: -12953.235944
EM: Round [234] log likelihood: -12953.235431
EM: Round [235] log likelihood: -12953.234922
EM: Round [236] log likelihood: -12953.234417
EM: Round [237] log likelihood: -12953.233915
EM: Round [238] log likelihood: -12953.233417
EM: Round [239] log likelihood: -12953.232922
EM: Round [240] log likelihood: -12953.232430
EM: Round [241] log likelihood: -12953.231942
EM: Round [242] log likelihood: -12953.231457
EM: Round [243] log likelihood: -12953.230976
EM: Round [244] log likelihood: -12953.230498
EM: Round [245] log likelihood: -12953.230023
EM: Round [246] log likelihood: -12953.229551
EM: Round [247] log likelihood: -12953.229083
EM: Round [248] log likelihood: -12953.228618
EM: Round [249] log likelihood: -12953.228156
EM: Round [250] log likelihood: -12953.227697
EM: Round [251] log likelihood: -12953.227242
EM: Round [252] log likelihood: -12953.226789
EM: Round [253] log likelihood: -12953.226340
EM: Round [254] log likelihood: -12953.225894
EM: Round [255] log likelihood: -12953.225451
EM: Round [256] log likelihood: -12953.225010
EM: Round [257] log likelihood: -12953.224573
EM: Round [258] log likelihood: -12953.224139
EM: Round [259] log likelihood: -12953.223708
EM: Round [260] log likelihood: -12953.223280
EM: Round [261] log likelihood: -12953.222854
EM: Round [262] log likelihood: -12953.222432
EM: Round [263] log likelihood: -12953.222013
EM: Round [264] log likelihood: -12953.221596
EM: Round [265] log likelihood: -12953.221182
EM: Round [266] log likelihood: -12953.220771
EM: Round [267] log likelihood: -12953.220363
EM: Round [268] log likelihood: -12953.219958
EM: Round [269] log likelihood: -12953.219555
EM: Round [270] log likelihood: -12953.219155
EM: Round [271] log likelihood: -12953.218758
EM: Round [272] log likelihood: -12953.218364
EM: Round [273] log likelihood: -12953.217972
EM: Round [274] log likelihood: -12953.217583
EM: Round [275] log likelihood: -12953.217196
EM: Round [276] log likelihood: -12953.216813
EM: Round [277] log likelihood: -12953.216431
EM: Round [278] log likelihood: -12953.216053
EM: Round [279] log likelihood: -12953.215677
EM: Round [280] log likelihood: -12953.215303
EM: Round [281] log likelihood: -12953.214932
EM: Round [282] log likelihood: -12953.214564
EM: Round [283] log likelihood: -12953.214198
EM: Round [284] log likelihood: -12953.213834
EM: Round [285] log likelihood: -12953.213473
EM: Round [286] log likelihood: -12953.213115
EM: Round [287] log likelihood: -12953.212759
EM: Round [288] log likelihood: -12953.212405
EM: Round [289] log likelihood: -12953.212054
EM: Round [290] log likelihood: -12953.211705
EM: Round [291] log likelihood: -12953.211358
EM: Round [292] log likelihood: -12953.211014
EM: Round [293] log likelihood: -12953.210672
EM: Round [294] log likelihood: -12953.210332
EM: Round [295] log likelihood: -12953.209995
EM: Round [296] log likelihood: -12953.209660
EM: Round [297] log likelihood: -12953.209327
EM: Round [298] log likelihood: -12953.208997
EM: Round [299] log likelihood: -12953.208668
EM: Round [300] log likelihood: -12953.208342
EM: Round [301] log likelihood: -12953.208018
EM: Round [302] log likelihood: -12953.207696
EM: Round [303] log likelihood: -12953.207377
EM: Round [304] log likelihood: -12953.207059
EM: Round [305] log likelihood: -12953.206744
EM: Round [306] log likelihood: -12953.206431
EM: Round [307] log likelihood: -12953.206120
EM: Round [308] log likelihood: -12953.205811
EM: Round [309] log likelihood: -12953.205504
EM: Round [310] log likelihood: -12953.205199
EM: Round [311] log likelihood: -12953.204896
EM: Round [312] log likelihood: -12953.204596
EM: Round [313] log likelihood: -12953.204297
EM: Round [314] log likelihood: -12953.204000
EM: Round [315] log likelihood: -12953.203705
EM: Round [316] log likelihood: -12953.203413
EM: Round [317] log likelihood: -12953.203122
EM: Round [318] log likelihood: -12953.202833
EM: Round [319] log likelihood: -12953.202546
EM: Round [320] log likelihood: -12953.202261
EM: Round [321] log likelihood: -12953.201978
EM: Round [322] log likelihood: -12953.201697
EM: Round [323] log likelihood: -12953.201417
EM: Round [324] log likelihood: -12953.201140
EM: Round [325] log likelihood: -12953.200864
EM: Round [326] log likelihood: -12953.200590
EM: Round [327] log likelihood: -12953.200318
EM: Round [328] log likelihood: -12953.200048
EM: Round [329] log likelihood: -12953.199780
EM: Round [330] log likelihood: -12953.199514
EM: Round [331] log likelihood: -12953.199249
EM: Round [332] log likelihood: -12953.198986
EM: Round [333] log likelihood: -12953.198725
EM: Round [334] log likelihood: -12953.198465
EM: Round [335] log likelihood: -12953.198207
EM: Round [336] log likelihood: -12953.197951
EM: Round [337] log likelihood: -12953.197697
EM: Round [338] log likelihood: -12953.197444
EM: Round [339] log likelihood: -12953.197193
EM: Round [340] log likelihood: -12953.196944
EM: Round [341] log likelihood: -12953.196697
EM: Round [342] log likelihood: -12953.196451
EM: Round [343] log likelihood: -12953.196206
EM: Round [344] log likelihood: -12953.195963
EM: Round [345] log likelihood: -12953.195722
EM: Round [346] log likelihood: -12953.195483
EM: Round [347] log likelihood: -12953.195245
EM: Round [348] log likelihood: -12953.195009
EM: Round [349] log likelihood: -12953.194774
EM: Round [350] log likelihood: -12953.194541
EM: Round [351] log likelihood: -12953.194309
EM: Round [352] log likelihood: -12953.194079
EM: Round [353] log likelihood: -12953.193850
EM: Round [354] log likelihood: -12953.193623
EM: Round [355] log likelihood: -12953.193398
EM: Round [356] log likelihood: -12953.193174
EM: Round [357] log likelihood: -12953.192951
EM: Round [358] log likelihood: -12953.192730
EM: Round [359] log likelihood: -12953.192510
EM: Round [360] log likelihood: -12953.192292
EM: Round [361] log likelihood: -12953.192076
EM: Round [362] log likelihood: -12953.191860
EM: Round [363] log likelihood: -12953.191646
EM: Round [364] log likelihood: -12953.191434
EM: Round [365] log likelihood: -12953.191223
EM: Round [366] log likelihood: -12953.191013
EM: Round [367] log likelihood: -12953.190805
EM: Round [368] log likelihood: -12953.190598
EM: Round [369] log likelihood: -12953.190393
EM: Round [370] log likelihood: -12953.190188
EM: Round [371] log likelihood: -12953.189986
EM: Round [372] log likelihood: -12953.189784
EM: Round [373] log likelihood: -12953.189584
EM: Round [374] log likelihood: -12953.189385
EM: Round [375] log likelihood: -12953.189188
EM: Round [376] log likelihood: -12953.188992
EM: Round [377] log likelihood: -12953.188797
EM: Round [378] log likelihood: -12953.188603
EM: Round [379] log likelihood: -12953.188411
EM: Round [380] log likelihood: -12953.188220
EM: Round [381] log likelihood: -12953.188030
EM: Round [382] log likelihood: -12953.187841
EM: Round [383] log likelihood: -12953.187654
EM: Round [384] log likelihood: -12953.187468
EM: Round [385] log likelihood: -12953.187283
EM: Round [386] log likelihood: -12953.187100
EM: Round [387] log likelihood: -12953.186917
EM: Round [388] log likelihood: -12953.186736
EM: Round [389] log likelihood: -12953.186556
EM: Round [390] log likelihood: -12953.186377
EM: Round [391] log likelihood: -12953.186199
EM: Round [392] log likelihood: -12953.186023
EM: Round [393] log likelihood: -12953.185848
EM: Round [394] log likelihood: -12953.185673
EM: Round [395] log likelihood: -12953.185500
EM: Round [396] log likelihood: -12953.185329
EM: Round [397] log likelihood: -12953.185158
EM: Round [398] log likelihood: -12953.184988
EM: Round [399] log likelihood: -12953.184820
EM: Round [400] log likelihood: -12953.184652
EM: Round [401] log likelihood: -12953.184486
EM: Round [402] log likelihood: -12953.184321
EM: Round [403] log likelihood: -12953.184157
EM: Round [404] log likelihood: -12953.183994
EM: Round [405] log likelihood: -12953.183832
EM: Round [406] log likelihood: -12953.183671
EM: Round [407] log likelihood: -12953.183511
EM: Round [408] log likelihood: -12953.183352
EM: Round [409] log likelihood: -12953.183194
EM: Round [410] log likelihood: -12953.183038
EM: Round [411] log likelihood: -12953.182882
EM: Round [412] log likelihood: -12953.182727
EM: Round [413] log likelihood: -12953.182574
EM: Round [414] log likelihood: -12953.182421
EM: Round [415] log likelihood: -12953.182269
EM: Round [416] log likelihood: -12953.182119
EM: Round [417] log likelihood: -12953.181969
EM: Round [418] log likelihood: -12953.181820
EM: Round [419] log likelihood: -12953.181673
EM: Round [420] log likelihood: -12953.181526
EM: Round [421] log likelihood: -12953.181380
EM: Round [422] log likelihood: -12953.181235
EM: Round [423] log likelihood: -12953.181091
EM: Round [424] log likelihood: -12953.180949
EM: Round [425] log likelihood: -12953.180807
EM: Round [426] log likelihood: -12953.180665
EM: Round [427] log likelihood: -12953.180525
EM: Round [428] log likelihood: -12953.180386
EM: Round [429] log likelihood: -12953.180248
EM: Round [430] log likelihood: -12953.180110
EM: Round [431] log likelihood: -12953.179974
EM: Round [432] log likelihood: -12953.179838
EM: Round [433] log likelihood: -12953.179704
EM: Round [434] log likelihood: -12953.179570
EM: Round [435] log likelihood: -12953.179437
EM: Round [436] log likelihood: -12953.179305
EM: Round [437] log likelihood: -12953.179173
EM: Round [438] log likelihood: -12953.179043
EM: Round [439] log likelihood: -12953.178914
EM: Round [440] log likelihood: -12953.178785
EM: Round [441] log likelihood: -12953.178657
EM: Round [442] log likelihood: -12953.178530
EM: Round [443] log likelihood: -12953.178404
EM: Round [444] log likelihood: -12953.178279
EM: Round [445] log likelihood: -12953.178154
EM: Round [446] log likelihood: -12953.178030
EM: Round [447] log likelihood: -12953.177907
EM: Round [448] log likelihood: -12953.177785
EM: Round [449] log likelihood: -12953.177664
EM: Round [450] log likelihood: -12953.177544
EM: Round [451] log likelihood: -12953.177424
EM: Round [452] log likelihood: -12953.177305
EM: Round [453] log likelihood: -12953.177187
EM: Round [454] log likelihood: -12953.177069
EM: Round [455] log likelihood: -12953.176953
EM: Round [456] log likelihood: -12953.176837
EM: Round [457] log likelihood: -12953.176722
EM: Round [458] log likelihood: -12953.176607
EM: Round [459] log likelihood: -12953.176494
EM: Round [460] log likelihood: -12953.176381
EM: Round [461] log likelihood: -12953.176269
EM: Round [462] log likelihood: -12953.176157
EM: Round [463] log likelihood: -12953.176047
EM: Round [464] log likelihood: -12953.175937
EM: Round [465] log likelihood: -12953.175827
EM: Round [466] log likelihood: -12953.175719
EM: Round [467] log likelihood: -12953.175611
EM: Round [468] log likelihood: -12953.175504
EM: Round [469] log likelihood: -12953.175398
EM: Round [470] log likelihood: -12953.175292
EM: Round [471] log likelihood: -12953.175187
EM: Round [472] log likelihood: -12953.175083
EM: Round [473] log likelihood: -12953.174979
EM: Round [474] log likelihood: -12953.174876
EM: Round [475] log likelihood: -12953.174774
EM: Round [476] log likelihood: -12953.174672
EM: Round [477] log likelihood: -12953.174571
EM: Round [478] log likelihood: -12953.174471
EM: Round [479] log likelihood: -12953.174371
EM: Stopping iterations at round 479 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.vWFKtXFV5P/659_cYf-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.vWFKtXFV5P/659_cYf-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.vWFKtXFV5P/659_cYf-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.vWFKtXFV5P/659_cYf-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.vWFKtXFV5P/659_cYf-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.vWFKtXFV5P/659_cYf-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.vWFKtXFV5P/659_cYf-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.vWFKtXFV5P/fi_workdir/659_cYf-T1-TRNA-1_B23MHV2LT4_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.vWFKtXFV5P/fi_workdir/659_cYf-T1-TRNA-1_B23MHV2LT4_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.vWFKtXFV5P/fi_workdir/659_cYf-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.vWFKtXFV5P/659_cYf-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.vWFKtXFV5P/659_cYf-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -10088.562516
EM: Round [1] log likelihood: -10088.457140
EM: Round [2] log likelihood: -10088.457130
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.vWFKtXFV5P/659_cYf-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 294565227
Warning - not locating file: /tmp/nxf.vWFKtXFV5P/659_cYf-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000224244.1]
WARNING, no entry stored in dbm for [ENSG00000224244.1]
WARNING, no entry stored in dbm for [ENSG00000224244.1]
WARNING, no entry stored in dbm for [ENSG00000277458.1]
WARNING, no entry stored in dbm for [ENSG00000215158.9]
WARNING, no entry stored in dbm for [ENSG00000215158.9]
WARNING, no entry stored in dbm for [ENSG00000286152.1]
WARNING, no entry stored in dbm for [ENSG00000271270.7]
WARNING, no entry stored in dbm for [ENSG00000257127.6]
WARNING, no entry stored in dbm for [ENSG00000257127.6]
ls: cannot access 'IGV_inputs': No such file or directory