Done.
-parsing GTF file: /tmp/nxf.rvUREQo5zB/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.rvUREQo5zB/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.rvUREQo5zB/A673_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.rvUREQo5zB/A673_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.rvUREQo5zB/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.rvUREQo5zB/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam A673_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index A673_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam
11:10:10 : INFO : Done.
-parsing GTF file: /tmp/nxf.rvUREQo5zB/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.gtf
-parsing /tmp/nxf.rvUREQo5zB/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam
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[5020000] -done parsing /tmp/nxf.rvUREQo5zB/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'exons hit < 2' => 3,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 364,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 90,
'excessive soft clipping' => 39781,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 115,
'low complexity anchor region' => 25,
'seq-similar region overlap' => 1155,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 59,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 78,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 232,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 88,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1299,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 18,
'num genes matched < 2' => 15,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 343,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 111,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 56,
'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 24,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 15,
'small anchor length' => 221,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 1965,
' ** passed ** ' => 35990,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 48,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 875,
'per_id < 96' => 30900,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 9
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.rvUREQo5zB/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[4000] -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2
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[429000] -fusion SPANNING read extraction for scaff: CPSF6--HOOK1
[1000]
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[3000] -fusion SPANNING read extraction for scaff: CYP7B1--LINC01414
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[25000] -fusion SPANNING read extraction for scaff: HIVEP3--AL158828.1
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[26000] -fusion SPANNING read extraction for scaff: HIVEP3--AL353613.1
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[1067000] -fusion SPANNING read extraction for scaff: NPM1--MT-RNR2
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[85000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[99000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[102000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[128000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[125000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[111000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[118000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[115000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[102000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
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[80000] -fusion SPANNING read extraction for scaff: PCDHA8--PCDHA10
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[35000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
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[71000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
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[29000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
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[95000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
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[34000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[70000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[26000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[28000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[94000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[240000] -fusion SPANNING read extraction for scaff: RCN3--FCGRT
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[32000] -fusion SPANNING read extraction for scaff: SMURF2P1--SP2
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[121000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408
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[59000] -fusion SPANNING read extraction for scaff: SPG7--PLSCR5
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[59000] -fusion SPANNING read extraction for scaff: SPG7--AC092957.1
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[17000] -fusion SPANNING read extraction for scaff: SUCLA2--AL158828.1
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[17000] -fusion SPANNING read extraction for scaff: SUCLA2--AL353613.1
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[8000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[45000] -fusion SPANNING read extraction for scaff: TMEM132B--TDG
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 223015,
'lacks exon overlap' => 69579
};
EM: Starting log likelihood: -17924.426466
EM: Round [1] log likelihood: -17907.033243
EM: Round [2] log likelihood: -17903.366952
EM: Round [3] log likelihood: -17900.703450
EM: Round [4] log likelihood: -17898.454464
EM: Round [5] log likelihood: -17896.497062
EM: Round [6] log likelihood: -17894.777272
EM: Round [7] log likelihood: -17893.258310
EM: Round [8] log likelihood: -17891.911235
EM: Round [9] log likelihood: -17890.712300
EM: Round [10] log likelihood: -17889.641707
EM: Round [11] log likelihood: -17888.682796
EM: Round [12] log likelihood: -17887.821449
EM: Round [13] log likelihood: -17887.045633
EM: Round [14] log likelihood: -17886.345036
EM: Round [15] log likelihood: -17885.710783
EM: Round [16] log likelihood: -17885.135206
EM: Round [17] log likelihood: -17884.611651
EM: Round [18] log likelihood: -17884.134328
EM: Round [19] log likelihood: -17883.698183
EM: Round [20] log likelihood: -17883.298793
EM: Round [21] log likelihood: -17882.932275
EM: Round [22] log likelihood: -17882.595215
EM: Round [23] log likelihood: -17882.284603
EM: Round [24] log likelihood: -17881.997781
EM: Round [25] log likelihood: -17881.732395
EM: Round [26] log likelihood: -17881.486360
EM: Round [27] log likelihood: -17881.257822
EM: Round [28] log likelihood: -17881.045132
EM: Round [29] log likelihood: -17880.846822
EM: Round [30] log likelihood: -17880.661580
EM: Round [31] log likelihood: -17880.488234
EM: Round [32] log likelihood: -17880.325734
EM: Round [33] log likelihood: -17880.173140
EM: Round [34] log likelihood: -17880.029606
EM: Round [35] log likelihood: -17879.894373
EM: Round [36] log likelihood: -17879.766756
EM: Round [37] log likelihood: -17879.646139
EM: Round [38] log likelihood: -17879.531964
EM: Round [39] log likelihood: -17879.423728
EM: Round [40] log likelihood: -17879.320973
EM: Round [41] log likelihood: -17879.223288
EM: Round [42] log likelihood: -17879.130294
EM: Round [43] log likelihood: -17879.041652
EM: Round [44] log likelihood: -17878.957050
EM: Round [45] log likelihood: -17878.876205
EM: Round [46] log likelihood: -17878.798856
EM: Round [47] log likelihood: -17878.724769
EM: Round [48] log likelihood: -17878.653725
EM: Round [49] log likelihood: -17878.585528
EM: Round [50] log likelihood: -17878.519993
EM: Round [51] log likelihood: -17878.456954
EM: Round [52] log likelihood: -17878.396257
EM: Round [53] log likelihood: -17878.337760
EM: Round [54] log likelihood: -17878.281332
EM: Round [55] log likelihood: -17878.226851
EM: Round [56] log likelihood: -17878.174208
EM: Round [57] log likelihood: -17878.123297
EM: Round [58] log likelihood: -17878.074023
EM: Round [59] log likelihood: -17878.026298
EM: Round [60] log likelihood: -17877.980038
EM: Round [61] log likelihood: -17877.935168
EM: Round [62] log likelihood: -17877.891615
EM: Round [63] log likelihood: -17877.849314
EM: Round [64] log likelihood: -17877.808202
EM: Round [65] log likelihood: -17877.768221
EM: Round [66] log likelihood: -17877.729318
EM: Round [67] log likelihood: -17877.691442
EM: Round [68] log likelihood: -17877.654546
EM: Round [69] log likelihood: -17877.618585
EM: Round [70] log likelihood: -17877.583518
EM: Round [71] log likelihood: -17877.549306
EM: Round [72] log likelihood: -17877.515912
EM: Round [73] log likelihood: -17877.483303
EM: Round [74] log likelihood: -17877.451445
EM: Round [75] log likelihood: -17877.420308
EM: Round [76] log likelihood: -17877.389863
EM: Round [77] log likelihood: -17877.360085
EM: Round [78] log likelihood: -17877.330946
EM: Round [79] log likelihood: -17877.302423
EM: Round [80] log likelihood: -17877.274493
EM: Round [81] log likelihood: -17877.247135
EM: Round [82] log likelihood: -17877.220328
EM: Round [83] log likelihood: -17877.194052
EM: Round [84] log likelihood: -17877.168291
EM: Round [85] log likelihood: -17877.143026
EM: Round [86] log likelihood: -17877.118240
EM: Round [87] log likelihood: -17877.093919
EM: Round [88] log likelihood: -17877.070047
EM: Round [89] log likelihood: -17877.046610
EM: Round [90] log likelihood: -17877.023595
EM: Round [91] log likelihood: -17877.000989
EM: Round [92] log likelihood: -17876.978780
EM: Round [93] log likelihood: -17876.956956
EM: Round [94] log likelihood: -17876.935506
EM: Round [95] log likelihood: -17876.914419
EM: Round [96] log likelihood: -17876.893686
EM: Round [97] log likelihood: -17876.873296
EM: Round [98] log likelihood: -17876.853241
EM: Round [99] log likelihood: -17876.833511
EM: Round [100] log likelihood: -17876.814099
EM: Round [101] log likelihood: -17876.794995
EM: Round [102] log likelihood: -17876.776193
EM: Round [103] log likelihood: -17876.757684
EM: Round [104] log likelihood: -17876.739461
EM: Round [105] log likelihood: -17876.721519
EM: Round [106] log likelihood: -17876.703849
EM: Round [107] log likelihood: -17876.686446
EM: Round [108] log likelihood: -17876.669303
EM: Round [109] log likelihood: -17876.652415
EM: Round [110] log likelihood: -17876.635775
EM: Round [111] log likelihood: -17876.619379
EM: Round [112] log likelihood: -17876.603221
EM: Round [113] log likelihood: -17876.587296
EM: Round [114] log likelihood: -17876.571599
EM: Round [115] log likelihood: -17876.556126
EM: Round [116] log likelihood: -17876.540870
EM: Round [117] log likelihood: -17876.525829
EM: Round [118] log likelihood: -17876.510998
EM: Round [119] log likelihood: -17876.496373
EM: Round [120] log likelihood: -17876.481949
EM: Round [121] log likelihood: -17876.467723
EM: Round [122] log likelihood: -17876.453691
EM: Round [123] log likelihood: -17876.439849
EM: Round [124] log likelihood: -17876.426194
EM: Round [125] log likelihood: -17876.412722
EM: Round [126] log likelihood: -17876.399430
EM: Round [127] log likelihood: -17876.386315
EM: Round [128] log likelihood: -17876.373373
EM: Round [129] log likelihood: -17876.360601
EM: Round [130] log likelihood: -17876.347997
EM: Round [131] log likelihood: -17876.335557
EM: Round [132] log likelihood: -17876.323278
EM: Round [133] log likelihood: -17876.311158
EM: Round [134] log likelihood: -17876.299194
EM: Round [135] log likelihood: -17876.287384
EM: Round [136] log likelihood: -17876.275724
EM: Round [137] log likelihood: -17876.264213
EM: Round [138] log likelihood: -17876.252848
EM: Round [139] log likelihood: -17876.241626
EM: Round [140] log likelihood: -17876.230545
EM: Round [141] log likelihood: -17876.219603
EM: Round [142] log likelihood: -17876.208798
EM: Round [143] log likelihood: -17876.198127
EM: Round [144] log likelihood: -17876.187588
EM: Round [145] log likelihood: -17876.177180
EM: Round [146] log likelihood: -17876.166901
EM: Round [147] log likelihood: -17876.156747
EM: Round [148] log likelihood: -17876.146718
EM: Round [149] log likelihood: -17876.136811
EM: Round [150] log likelihood: -17876.127025
EM: Round [151] log likelihood: -17876.117358
EM: Round [152] log likelihood: -17876.107807
EM: Round [153] log likelihood: -17876.098372
EM: Round [154] log likelihood: -17876.089050
EM: Round [155] log likelihood: -17876.079841
EM: Round [156] log likelihood: -17876.070741
EM: Round [157] log likelihood: -17876.061750
EM: Round [158] log likelihood: -17876.052867
EM: Round [159] log likelihood: -17876.044088
EM: Round [160] log likelihood: -17876.035414
EM: Round [161] log likelihood: -17876.026842
EM: Round [162] log likelihood: -17876.018371
EM: Round [163] log likelihood: -17876.010000
EM: Round [164] log likelihood: -17876.001727
EM: Round [165] log likelihood: -17875.993551
EM: Round [166] log likelihood: -17875.985471
EM: Round [167] log likelihood: -17875.977484
EM: Round [168] log likelihood: -17875.969590
EM: Round [169] log likelihood: -17875.961788
EM: Round [170] log likelihood: -17875.954077
EM: Round [171] log likelihood: -17875.946454
EM: Round [172] log likelihood: -17875.938919
EM: Round [173] log likelihood: -17875.931471
EM: Round [174] log likelihood: -17875.924108
EM: Round [175] log likelihood: -17875.916830
EM: Round [176] log likelihood: -17875.909635
EM: Round [177] log likelihood: -17875.902522
EM: Round [178] log likelihood: -17875.895490
EM: Round [179] log likelihood: -17875.888538
EM: Round [180] log likelihood: -17875.881665
EM: Round [181] log likelihood: -17875.874870
EM: Round [182] log likelihood: -17875.868151
EM: Round [183] log likelihood: -17875.861509
EM: Round [184] log likelihood: -17875.854941
EM: Round [185] log likelihood: -17875.848447
EM: Round [186] log likelihood: -17875.842026
EM: Round [187] log likelihood: -17875.835677
EM: Round [188] log likelihood: -17875.829399
EM: Round [189] log likelihood: -17875.823191
EM: Round [190] log likelihood: -17875.817052
EM: Round [191] log likelihood: -17875.810982
EM: Round [192] log likelihood: -17875.804979
EM: Round [193] log likelihood: -17875.799042
EM: Round [194] log likelihood: -17875.793172
EM: Round [195] log likelihood: -17875.787366
EM: Round [196] log likelihood: -17875.781625
EM: Round [197] log likelihood: -17875.775946
EM: Round [198] log likelihood: -17875.770331
EM: Round [199] log likelihood: -17875.764777
EM: Round [200] log likelihood: -17875.759284
EM: Round [201] log likelihood: -17875.753851
EM: Round [202] log likelihood: -17875.748478
EM: Round [203] log likelihood: -17875.743163
EM: Round [204] log likelihood: -17875.737907
EM: Round [205] log likelihood: -17875.732708
EM: Round [206] log likelihood: -17875.727565
EM: Round [207] log likelihood: -17875.722478
EM: Round [208] log likelihood: -17875.717447
EM: Round [209] log likelihood: -17875.712470
EM: Round [210] log likelihood: -17875.707547
EM: Round [211] log likelihood: -17875.702677
EM: Round [212] log likelihood: -17875.697860
EM: Round [213] log likelihood: -17875.693095
EM: Round [214] log likelihood: -17875.688381
EM: Round [215] log likelihood: -17875.683718
EM: Round [216] log likelihood: -17875.679105
EM: Round [217] log likelihood: -17875.674541
EM: Round [218] log likelihood: -17875.670026
EM: Round [219] log likelihood: -17875.665560
EM: Round [220] log likelihood: -17875.661142
EM: Round [221] log likelihood: -17875.656770
EM: Round [222] log likelihood: -17875.652446
EM: Round [223] log likelihood: -17875.648167
EM: Round [224] log likelihood: -17875.643934
EM: Round [225] log likelihood: -17875.639746
EM: Round [226] log likelihood: -17875.635602
EM: Round [227] log likelihood: -17875.631503
EM: Round [228] log likelihood: -17875.627447
EM: Round [229] log likelihood: -17875.623434
EM: Round [230] log likelihood: -17875.619463
EM: Round [231] log likelihood: -17875.615534
EM: Round [232] log likelihood: -17875.611647
EM: Round [233] log likelihood: -17875.607801
EM: Round [234] log likelihood: -17875.603995
EM: Round [235] log likelihood: -17875.600229
EM: Round [236] log likelihood: -17875.596503
EM: Round [237] log likelihood: -17875.592816
EM: Round [238] log likelihood: -17875.589167
EM: Round [239] log likelihood: -17875.585557
EM: Round [240] log likelihood: -17875.581985
EM: Round [241] log likelihood: -17875.578450
EM: Round [242] log likelihood: -17875.574952
EM: Round [243] log likelihood: -17875.571491
EM: Round [244] log likelihood: -17875.568065
EM: Round [245] log likelihood: -17875.564676
EM: Round [246] log likelihood: -17875.561321
EM: Round [247] log likelihood: -17875.558002
EM: Round [248] log likelihood: -17875.554717
EM: Round [249] log likelihood: -17875.551466
EM: Round [250] log likelihood: -17875.548249
EM: Round [251] log likelihood: -17875.545065
EM: Round [252] log likelihood: -17875.541915
EM: Round [253] log likelihood: -17875.538797
EM: Round [254] log likelihood: -17875.535711
EM: Round [255] log likelihood: -17875.532657
EM: Round [256] log likelihood: -17875.529634
EM: Round [257] log likelihood: -17875.526643
EM: Round [258] log likelihood: -17875.523682
EM: Round [259] log likelihood: -17875.520752
EM: Round [260] log likelihood: -17875.517853
EM: Round [261] log likelihood: -17875.514983
EM: Round [262] log likelihood: -17875.512142
EM: Round [263] log likelihood: -17875.509331
EM: Round [264] log likelihood: -17875.506548
EM: Round [265] log likelihood: -17875.503795
EM: Round [266] log likelihood: -17875.501069
EM: Round [267] log likelihood: -17875.498371
EM: Round [268] log likelihood: -17875.495701
EM: Round [269] log likelihood: -17875.493058
EM: Round [270] log likelihood: -17875.490442
EM: Round [271] log likelihood: -17875.487853
EM: Round [272] log likelihood: -17875.485290
EM: Round [273] log likelihood: -17875.482753
EM: Round [274] log likelihood: -17875.480243
EM: Round [275] log likelihood: -17875.477757
EM: Round [276] log likelihood: -17875.475297
EM: Round [277] log likelihood: -17875.472862
EM: Round [278] log likelihood: -17875.470452
EM: Round [279] log likelihood: -17875.468066
EM: Round [280] log likelihood: -17875.465705
EM: Round [281] log likelihood: -17875.463367
EM: Round [282] log likelihood: -17875.461053
EM: Round [283] log likelihood: -17875.458763
EM: Round [284] log likelihood: -17875.456496
EM: Round [285] log likelihood: -17875.454251
EM: Round [286] log likelihood: -17875.452030
EM: Round [287] log likelihood: -17875.449831
EM: Round [288] log likelihood: -17875.447654
EM: Round [289] log likelihood: -17875.445499
EM: Round [290] log likelihood: -17875.443365
EM: Round [291] log likelihood: -17875.441253
EM: Round [292] log likelihood: -17875.439163
EM: Round [293] log likelihood: -17875.437094
EM: Round [294] log likelihood: -17875.435045
EM: Round [295] log likelihood: -17875.433017
EM: Round [296] log likelihood: -17875.431009
EM: Round [297] log likelihood: -17875.429022
EM: Round [298] log likelihood: -17875.427054
EM: Round [299] log likelihood: -17875.425107
EM: Round [300] log likelihood: -17875.423178
EM: Round [301] log likelihood: -17875.421269
EM: Round [302] log likelihood: -17875.419380
EM: Round [303] log likelihood: -17875.417509
EM: Round [304] log likelihood: -17875.415657
EM: Round [305] log likelihood: -17875.413823
EM: Round [306] log likelihood: -17875.412008
EM: Round [307] log likelihood: -17875.410211
EM: Round [308] log likelihood: -17875.408432
EM: Round [309] log likelihood: -17875.406670
EM: Round [310] log likelihood: -17875.404926
EM: Round [311] log likelihood: -17875.403200
EM: Round [312] log likelihood: -17875.401491
EM: Round [313] log likelihood: -17875.399799
EM: Round [314] log likelihood: -17875.398123
EM: Round [315] log likelihood: -17875.396465
EM: Round [316] log likelihood: -17875.394822
EM: Round [317] log likelihood: -17875.393197
EM: Round [318] log likelihood: -17875.391587
EM: Round [319] log likelihood: -17875.389993
EM: Round [320] log likelihood: -17875.388416
EM: Round [321] log likelihood: -17875.386854
EM: Round [322] log likelihood: -17875.385307
EM: Round [323] log likelihood: -17875.383776
EM: Round [324] log likelihood: -17875.382260
EM: Round [325] log likelihood: -17875.380758
EM: Round [326] log likelihood: -17875.379272
EM: Round [327] log likelihood: -17875.377801
EM: Round [328] log likelihood: -17875.376344
EM: Round [329] log likelihood: -17875.374901
EM: Round [330] log likelihood: -17875.373473
EM: Round [331] log likelihood: -17875.372059
EM: Round [332] log likelihood: -17875.370659
EM: Round [333] log likelihood: -17875.369273
EM: Round [334] log likelihood: -17875.367900
EM: Round [335] log likelihood: -17875.366541
EM: Round [336] log likelihood: -17875.365196
EM: Round [337] log likelihood: -17875.363863
EM: Round [338] log likelihood: -17875.362544
EM: Round [339] log likelihood: -17875.361238
EM: Round [340] log likelihood: -17875.359945
EM: Round [341] log likelihood: -17875.358664
EM: Round [342] log likelihood: -17875.357396
EM: Round [343] log likelihood: -17875.356141
EM: Round [344] log likelihood: -17875.354897
EM: Round [345] log likelihood: -17875.353667
EM: Round [346] log likelihood: -17875.352448
EM: Round [347] log likelihood: -17875.351241
EM: Round [348] log likelihood: -17875.350046
EM: Round [349] log likelihood: -17875.348863
EM: Round [350] log likelihood: -17875.347691
EM: Round [351] log likelihood: -17875.346531
EM: Round [352] log likelihood: -17875.345382
EM: Round [353] log likelihood: -17875.344245
EM: Round [354] log likelihood: -17875.343119
EM: Round [355] log likelihood: -17875.342004
EM: Round [356] log likelihood: -17875.340899
EM: Round [357] log likelihood: -17875.339806
EM: Round [358] log likelihood: -17875.338723
EM: Round [359] log likelihood: -17875.337651
EM: Round [360] log likelihood: -17875.336589
EM: Round [361] log likelihood: -17875.335538
EM: Round [362] log likelihood: -17875.334497
EM: Round [363] log likelihood: -17875.333466
EM: Round [364] log likelihood: -17875.332446
EM: Round [365] log likelihood: -17875.331435
EM: Round [366] log likelihood: -17875.330434
EM: Round [367] log likelihood: -17875.329443
EM: Round [368] log likelihood: -17875.328461
EM: Round [369] log likelihood: -17875.327490
EM: Round [370] log likelihood: -17875.326527
EM: Round [371] log likelihood: -17875.325574
EM: Round [372] log likelihood: -17875.324631
EM: Round [373] log likelihood: -17875.323696
EM: Round [374] log likelihood: -17875.322771
EM: Round [375] log likelihood: -17875.321855
EM: Round [376] log likelihood: -17875.320947
EM: Round [377] log likelihood: -17875.320049
EM: Round [378] log likelihood: -17875.319159
EM: Round [379] log likelihood: -17875.318278
EM: Round [380] log likelihood: -17875.317405
EM: Round [381] log likelihood: -17875.316541
EM: Round [382] log likelihood: -17875.315686
EM: Round [383] log likelihood: -17875.314838
EM: Round [384] log likelihood: -17875.313999
EM: Round [385] log likelihood: -17875.313169
EM: Round [386] log likelihood: -17875.312346
EM: Round [387] log likelihood: -17875.311531
EM: Round [388] log likelihood: -17875.310724
EM: Round [389] log likelihood: -17875.309925
EM: Round [390] log likelihood: -17875.309134
EM: Round [391] log likelihood: -17875.308350
EM: Round [392] log likelihood: -17875.307574
EM: Round [393] log likelihood: -17875.306806
EM: Round [394] log likelihood: -17875.306044
EM: Round [395] log likelihood: -17875.305291
EM: Round [396] log likelihood: -17875.304545
EM: Round [397] log likelihood: -17875.303805
EM: Round [398] log likelihood: -17875.303074
EM: Round [399] log likelihood: -17875.302349
EM: Round [400] log likelihood: -17875.301631
EM: Round [401] log likelihood: -17875.300920
EM: Round [402] log likelihood: -17875.300216
EM: Round [403] log likelihood: -17875.299519
EM: Round [404] log likelihood: -17875.298829
EM: Round [405] log likelihood: -17875.298145
EM: Round [406] log likelihood: -17875.297468
EM: Round [407] log likelihood: -17875.296797
EM: Round [408] log likelihood: -17875.296133
EM: Round [409] log likelihood: -17875.295476
EM: Round [410] log likelihood: -17875.294824
EM: Round [411] log likelihood: -17875.294179
EM: Round [412] log likelihood: -17875.293541
EM: Round [413] log likelihood: -17875.292908
EM: Round [414] log likelihood: -17875.292282
EM: Round [415] log likelihood: -17875.291661
EM: Round [416] log likelihood: -17875.291047
EM: Round [417] log likelihood: -17875.290438
EM: Round [418] log likelihood: -17875.289836
EM: Round [419] log likelihood: -17875.289239
EM: Round [420] log likelihood: -17875.288648
EM: Round [421] log likelihood: -17875.288063
EM: Round [422] log likelihood: -17875.287483
EM: Round [423] log likelihood: -17875.286909
EM: Round [424] log likelihood: -17875.286340
EM: Round [425] log likelihood: -17875.285777
EM: Round [426] log likelihood: -17875.285220
EM: Round [427] log likelihood: -17875.284668
EM: Round [428] log likelihood: -17875.284121
EM: Round [429] log likelihood: -17875.283579
EM: Round [430] log likelihood: -17875.283043
EM: Round [431] log likelihood: -17875.282511
EM: Round [432] log likelihood: -17875.281985
EM: Round [433] log likelihood: -17875.281464
EM: Round [434] log likelihood: -17875.280948
EM: Round [435] log likelihood: -17875.280437
EM: Round [436] log likelihood: -17875.279931
EM: Round [437] log likelihood: -17875.279430
EM: Round [438] log likelihood: -17875.278933
EM: Round [439] log likelihood: -17875.278441
EM: Round [440] log likelihood: -17875.277954
EM: Round [441] log likelihood: -17875.277472
EM: Round [442] log likelihood: -17875.276995
EM: Round [443] log likelihood: -17875.276522
EM: Round [444] log likelihood: -17875.276053
EM: Round [445] log likelihood: -17875.275589
EM: Round [446] log likelihood: -17875.275130
EM: Round [447] log likelihood: -17875.274674
EM: Round [448] log likelihood: -17875.274224
EM: Round [449] log likelihood: -17875.273777
EM: Round [450] log likelihood: -17875.273335
EM: Round [451] log likelihood: -17875.272897
EM: Round [452] log likelihood: -17875.272464
EM: Round [453] log likelihood: -17875.272034
EM: Round [454] log likelihood: -17875.271609
EM: Round [455] log likelihood: -17875.271188
EM: Round [456] log likelihood: -17875.270770
EM: Round [457] log likelihood: -17875.270357
EM: Round [458] log likelihood: -17875.269948
EM: Round [459] log likelihood: -17875.269542
EM: Round [460] log likelihood: -17875.269141
EM: Round [461] log likelihood: -17875.268743
EM: Round [462] log likelihood: -17875.268350
EM: Round [463] log likelihood: -17875.267960
EM: Round [464] log likelihood: -17875.267573
EM: Round [465] log likelihood: -17875.267191
EM: Round [466] log likelihood: -17875.266812
EM: Round [467] log likelihood: -17875.266437
EM: Round [468] log likelihood: -17875.266065
EM: Round [469] log likelihood: -17875.265697
EM: Round [470] log likelihood: -17875.265332
EM: Round [471] log likelihood: -17875.264971
EM: Round [472] log likelihood: -17875.264613
EM: Round [473] log likelihood: -17875.264259
EM: Round [474] log likelihood: -17875.263908
EM: Round [475] log likelihood: -17875.263561
EM: Round [476] log likelihood: -17875.263217
EM: Round [477] log likelihood: -17875.262876
EM: Round [478] log likelihood: -17875.262538
EM: Round [479] log likelihood: -17875.262204
EM: Round [480] log likelihood: -17875.261873
EM: Round [481] log likelihood: -17875.261545
EM: Round [482] log likelihood: -17875.261220
EM: Round [483] log likelihood: -17875.260898
EM: Round [484] log likelihood: -17875.260580
EM: Round [485] log likelihood: -17875.260264
EM: Round [486] log likelihood: -17875.259952
EM: Round [487] log likelihood: -17875.259642
EM: Round [488] log likelihood: -17875.259335
EM: Round [489] log likelihood: -17875.259032
EM: Round [490] log likelihood: -17875.258731
EM: Round [491] log likelihood: -17875.258433
EM: Round [492] log likelihood: -17875.258138
EM: Round [493] log likelihood: -17875.257846
EM: Round [494] log likelihood: -17875.257556
EM: Round [495] log likelihood: -17875.257269
EM: Round [496] log likelihood: -17875.256985
EM: Round [497] log likelihood: -17875.256704
EM: Round [498] log likelihood: -17875.256426
EM: Round [499] log likelihood: -17875.256150
EM: Round [500] log likelihood: -17875.255876
EM: Round [501] log likelihood: -17875.255606
EM: Round [502] log likelihood: -17875.255338
EM: Round [503] log likelihood: -17875.255072
EM: Round [504] log likelihood: -17875.254809
EM: Round [505] log likelihood: -17875.254549
EM: Round [506] log likelihood: -17875.254291
EM: Round [507] log likelihood: -17875.254035
EM: Round [508] log likelihood: -17875.253782
EM: Round [509] log likelihood: -17875.253531
EM: Round [510] log likelihood: -17875.253283
EM: Round [511] log likelihood: -17875.253037
EM: Round [512] log likelihood: -17875.252794
EM: Round [513] log likelihood: -17875.252552
EM: Round [514] log likelihood: -17875.252313
EM: Round [515] log likelihood: -17875.252077
EM: Round [516] log likelihood: -17875.251842
EM: Round [517] log likelihood: -17875.251610
EM: Round [518] log likelihood: -17875.251380
EM: Round [519] log likelihood: -17875.251152
EM: Round [520] log likelihood: -17875.250927
EM: Round [521] log likelihood: -17875.250703
EM: Round [522] log likelihood: -17875.250482
EM: Round [523] log likelihood: -17875.250263
EM: Round [524] log likelihood: -17875.250046
EM: Round [525] log likelihood: -17875.249831
EM: Round [526] log likelihood: -17875.249618
EM: Round [527] log likelihood: -17875.249407
EM: Round [528] log likelihood: -17875.249198
EM: Round [529] log likelihood: -17875.248991
EM: Round [530] log likelihood: -17875.248786
EM: Round [531] log likelihood: -17875.248583
EM: Round [532] log likelihood: -17875.248381
EM: Round [533] log likelihood: -17875.248182
EM: Round [534] log likelihood: -17875.247985
EM: Round [535] log likelihood: -17875.247789
EM: Round [536] log likelihood: -17875.247596
EM: Round [537] log likelihood: -17875.247404
EM: Round [538] log likelihood: -17875.247214
EM: Round [539] log likelihood: -17875.247026
EM: Round [540] log likelihood: -17875.246840
EM: Round [541] log likelihood: -17875.246655
EM: Round [542] log likelihood: -17875.246472
EM: Round [543] log likelihood: -17875.246291
EM: Round [544] log likelihood: -17875.246112
EM: Round [545] log likelihood: -17875.245934
EM: Round [546] log likelihood: -17875.245758
EM: Round [547] log likelihood: -17875.245584
EM: Round [548] log likelihood: -17875.245411
EM: Round [549] log likelihood: -17875.245240
EM: Round [550] log likelihood: -17875.245071
EM: Round [551] log likelihood: -17875.244903
EM: Round [552] log likelihood: -17875.244737
EM: Round [553] log likelihood: -17875.244573
EM: Round [554] log likelihood: -17875.244410
EM: Round [555] log likelihood: -17875.244248
EM: Round [556] log likelihood: -17875.244088
EM: Round [557] log likelihood: -17875.243930
EM: Round [558] log likelihood: -17875.243773
EM: Round [559] log likelihood: -17875.243618
EM: Round [560] log likelihood: -17875.243464
EM: Round [561] log likelihood: -17875.243311
EM: Round [562] log likelihood: -17875.243160
EM: Round [563] log likelihood: -17875.243010
EM: Round [564] log likelihood: -17875.242862
EM: Round [565] log likelihood: -17875.242716
EM: Round [566] log likelihood: -17875.242570
EM: Round [567] log likelihood: -17875.242426
EM: Round [568] log likelihood: -17875.242283
EM: Round [569] log likelihood: -17875.242142
EM: Round [570] log likelihood: -17875.242002
EM: Round [571] log likelihood: -17875.241864
EM: Round [572] log likelihood: -17875.241726
EM: Round [573] log likelihood: -17875.241590
EM: Round [574] log likelihood: -17875.241456
EM: Round [575] log likelihood: -17875.241322
EM: Round [576] log likelihood: -17875.241190
EM: Round [577] log likelihood: -17875.241059
EM: Round [578] log likelihood: -17875.240929
EM: Round [579] log likelihood: -17875.240801
EM: Round [580] log likelihood: -17875.240674
EM: Round [581] log likelihood: -17875.240548
EM: Round [582] log likelihood: -17875.240423
EM: Round [583] log likelihood: -17875.240299
EM: Round [584] log likelihood: -17875.240177
EM: Round [585] log likelihood: -17875.240055
EM: Round [586] log likelihood: -17875.239935
EM: Round [587] log likelihood: -17875.239816
EM: Round [588] log likelihood: -17875.239698
EM: Round [589] log likelihood: -17875.239582
EM: Round [590] log likelihood: -17875.239466
EM: Round [591] log likelihood: -17875.239351
EM: Round [592] log likelihood: -17875.239238
EM: Round [593] log likelihood: -17875.239125
EM: Round [594] log likelihood: -17875.239014
EM: Round [595] log likelihood: -17875.238904
EM: Round [596] log likelihood: -17875.238794
EM: Round [597] log likelihood: -17875.238686
EM: Round [598] log likelihood: -17875.238579
EM: Round [599] log likelihood: -17875.238473
EM: Round [600] log likelihood: -17875.238368
EM: Round [601] log likelihood: -17875.238263
EM: Round [602] log likelihood: -17875.238160
EM: Round [603] log likelihood: -17875.238058
EM: Round [604] log likelihood: -17875.237957
EM: Round [605] log likelihood: -17875.237856
EM: Round [606] log likelihood: -17875.237757
EM: Stopping iterations at round 606 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.rvUREQo5zB/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam into /tmp/nxf.rvUREQo5zB/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.rvUREQo5zB/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.rvUREQo5zB/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords > /tmp/nxf.rvUREQo5zB/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.rvUREQo5zB/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.rvUREQo5zB/A673_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.rvUREQo5zB/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_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.rvUREQo5zB/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_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.rvUREQo5zB/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.rvUREQo5zB/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.rvUREQo5zB/A673_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -11058.803437
EM: Round [1] log likelihood: -11056.042573
EM: Round [2] log likelihood: -11056.042416
EM: Round [3] log likelihood: -11056.042415
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.rvUREQo5zB/A673_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz: 295019057
Warning - not locating file: /tmp/nxf.rvUREQo5zB/A673_FFPE_RNA_0001_B23LG7FLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000253554.7]
WARNING, no entry stored in dbm for [ENSG00000253554.7]
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 [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000241621.1]
WARNING, no entry stored in dbm for [ENSG00000232211.1]
ls: cannot access 'IGV_inputs': No such file or directory