Done.
-parsing GTF file: /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
12:08:18 : INFO : Done.
-parsing GTF file: /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf
-parsing /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam
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[2650000] -done parsing /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 71,
'per_id < 96' => 23779,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 110,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4,
'small anchor length' => 191,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6,
'seq-similar region overlap' => 398,
' ** passed ** ' => 25067,
'num genes matched < 2' => 64,
'excessive soft clipping' => 18690,
'low complexity anchor region' => 22,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 38,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 402,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[10000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
[1000] -fusion SPANNING read extraction for scaff: AC138035.1--SEPTIN14
[1000] -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2
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[245000] -fusion SPANNING read extraction for scaff: EPC1--PHC2
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[165000] -fusion SPANNING read extraction for scaff: EPC1--TLR12P
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[151000] -fusion SPANNING read extraction for scaff: FBXO10--SETD2
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[27000] -fusion SPANNING read extraction for scaff: FP325317.1--BMS1P10
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[43000] -fusion SPANNING read extraction for scaff: FXYD1--FXYD5
[1000]
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[56000] -fusion SPANNING read extraction for scaff: KDM4C--ZCCHC7
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[85000] -fusion SPANNING read extraction for scaff: NPHP3--ACAD11
[1000]
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[12000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
[1000]
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[21000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
[1000]
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[11000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
[1000]
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[252000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC3
[1000]
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[21000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA8
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[24000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6
[1000]
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC5
[1000]
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[43000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA10
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[37000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11
[1000]
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC4
[1000]
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[43000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB7
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[79000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA12
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[65000]
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[71000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA9
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[21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[23000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[26000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[42000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[36000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[27000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
[1000]
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[42000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[77000]
[78000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[70000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[251000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[49000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[22000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[18000] -fusion SPANNING read extraction for scaff: ZCCHC7--AL513412.1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 121957,
'lacks exon overlap' => 6159
};
EM: Starting log likelihood: -7880.709345
EM: Round [1] log likelihood: -7875.243300
EM: Round [2] log likelihood: -7872.563037
EM: Round [3] log likelihood: -7870.373075
EM: Round [4] log likelihood: -7868.569623
EM: Round [5] log likelihood: -7867.074523
EM: Round [6] log likelihood: -7865.827336
EM: Round [7] log likelihood: -7864.780710
EM: Round [8] log likelihood: -7863.897176
EM: Round [9] log likelihood: -7863.146856
EM: Round [10] log likelihood: -7862.505778
EM: Round [11] log likelihood: -7861.954612
EM: Round [12] log likelihood: -7861.477710
EM: Round [13] log likelihood: -7861.062359
EM: Round [14] log likelihood: -7860.698200
EM: Round [15] log likelihood: -7860.376773
EM: Round [16] log likelihood: -7860.091149
EM: Round [17] log likelihood: -7859.835643
EM: Round [18] log likelihood: -7859.605579
EM: Round [19] log likelihood: -7859.397105
EM: Round [20] log likelihood: -7859.207039
EM: Round [21] log likelihood: -7859.032748
EM: Round [22] log likelihood: -7858.872046
EM: Round [23] log likelihood: -7858.723118
EM: Round [24] log likelihood: -7858.584447
EM: Round [25] log likelihood: -7858.454766
EM: Round [26] log likelihood: -7858.333011
EM: Round [27] log likelihood: -7858.218286
EM: Round [28] log likelihood: -7858.109835
EM: Round [29] log likelihood: -7858.007013
EM: Round [30] log likelihood: -7857.909273
EM: Round [31] log likelihood: -7857.816145
EM: Round [32] log likelihood: -7857.727223
EM: Round [33] log likelihood: -7857.642158
EM: Round [34] log likelihood: -7857.560645
EM: Round [35] log likelihood: -7857.482416
EM: Round [36] log likelihood: -7857.407235
EM: Round [37] log likelihood: -7857.334894
EM: Round [38] log likelihood: -7857.265207
EM: Round [39] log likelihood: -7857.198008
EM: Round [40] log likelihood: -7857.133147
EM: Round [41] log likelihood: -7857.070486
EM: Round [42] log likelihood: -7857.009903
EM: Round [43] log likelihood: -7856.951284
EM: Round [44] log likelihood: -7856.894524
EM: Round [45] log likelihood: -7856.839529
EM: Round [46] log likelihood: -7856.786207
EM: Round [47] log likelihood: -7856.734477
EM: Round [48] log likelihood: -7856.684262
EM: Round [49] log likelihood: -7856.635488
EM: Round [50] log likelihood: -7856.588090
EM: Round [51] log likelihood: -7856.542003
EM: Round [52] log likelihood: -7856.497167
EM: Round [53] log likelihood: -7856.453527
EM: Round [54] log likelihood: -7856.411029
EM: Round [55] log likelihood: -7856.369623
EM: Round [56] log likelihood: -7856.329262
EM: Round [57] log likelihood: -7856.289900
EM: Round [58] log likelihood: -7856.251496
EM: Round [59] log likelihood: -7856.214009
EM: Round [60] log likelihood: -7856.177400
EM: Round [61] log likelihood: -7856.141634
EM: Round [62] log likelihood: -7856.106675
EM: Round [63] log likelihood: -7856.072492
EM: Round [64] log likelihood: -7856.039053
EM: Round [65] log likelihood: -7856.006328
EM: Round [66] log likelihood: -7855.974290
EM: Round [67] log likelihood: -7855.942911
EM: Round [68] log likelihood: -7855.912166
EM: Round [69] log likelihood: -7855.882031
EM: Round [70] log likelihood: -7855.852484
EM: Round [71] log likelihood: -7855.823501
EM: Round [72] log likelihood: -7855.795062
EM: Round [73] log likelihood: -7855.767147
EM: Round [74] log likelihood: -7855.739738
EM: Round [75] log likelihood: -7855.712816
EM: Round [76] log likelihood: -7855.686365
EM: Round [77] log likelihood: -7855.660367
EM: Round [78] log likelihood: -7855.634807
EM: Round [79] log likelihood: -7855.609671
EM: Round [80] log likelihood: -7855.584944
EM: Round [81] log likelihood: -7855.560612
EM: Round [82] log likelihood: -7855.536664
EM: Round [83] log likelihood: -7855.513086
EM: Round [84] log likelihood: -7855.489867
EM: Round [85] log likelihood: -7855.466996
EM: Round [86] log likelihood: -7855.444462
EM: Round [87] log likelihood: -7855.422254
EM: Round [88] log likelihood: -7855.400364
EM: Round [89] log likelihood: -7855.378782
EM: Round [90] log likelihood: -7855.357499
EM: Round [91] log likelihood: -7855.336506
EM: Round [92] log likelihood: -7855.315795
EM: Round [93] log likelihood: -7855.295359
EM: Round [94] log likelihood: -7855.275191
EM: Round [95] log likelihood: -7855.255282
EM: Round [96] log likelihood: -7855.235627
EM: Round [97] log likelihood: -7855.216218
EM: Round [98] log likelihood: -7855.197050
EM: Round [99] log likelihood: -7855.178117
EM: Round [100] log likelihood: -7855.159412
EM: Round [101] log likelihood: -7855.140931
EM: Round [102] log likelihood: -7855.122667
EM: Round [103] log likelihood: -7855.104617
EM: Round [104] log likelihood: -7855.086775
EM: Round [105] log likelihood: -7855.069136
EM: Round [106] log likelihood: -7855.051696
EM: Round [107] log likelihood: -7855.034450
EM: Round [108] log likelihood: -7855.017395
EM: Round [109] log likelihood: -7855.000527
EM: Round [110] log likelihood: -7854.983841
EM: Round [111] log likelihood: -7854.967334
EM: Round [112] log likelihood: -7854.951002
EM: Round [113] log likelihood: -7854.934842
EM: Round [114] log likelihood: -7854.918850
EM: Round [115] log likelihood: -7854.903024
EM: Round [116] log likelihood: -7854.887360
EM: Round [117] log likelihood: -7854.871855
EM: Round [118] log likelihood: -7854.856506
EM: Round [119] log likelihood: -7854.841311
EM: Round [120] log likelihood: -7854.826267
EM: Round [121] log likelihood: -7854.811370
EM: Round [122] log likelihood: -7854.796619
EM: Round [123] log likelihood: -7854.782012
EM: Round [124] log likelihood: -7854.767545
EM: Round [125] log likelihood: -7854.753216
EM: Round [126] log likelihood: -7854.739024
EM: Round [127] log likelihood: -7854.724966
EM: Round [128] log likelihood: -7854.711039
EM: Round [129] log likelihood: -7854.697243
EM: Round [130] log likelihood: -7854.683574
EM: Round [131] log likelihood: -7854.670031
EM: Round [132] log likelihood: -7854.656612
EM: Round [133] log likelihood: -7854.643315
EM: Round [134] log likelihood: -7854.630138
EM: Round [135] log likelihood: -7854.617081
EM: Round [136] log likelihood: -7854.604140
EM: Round [137] log likelihood: -7854.591314
EM: Round [138] log likelihood: -7854.578602
EM: Round [139] log likelihood: -7854.566002
EM: Round [140] log likelihood: -7854.553513
EM: Round [141] log likelihood: -7854.541132
EM: Round [142] log likelihood: -7854.528859
EM: Round [143] log likelihood: -7854.516693
EM: Round [144] log likelihood: -7854.504631
EM: Round [145] log likelihood: -7854.492672
EM: Round [146] log likelihood: -7854.480816
EM: Round [147] log likelihood: -7854.469060
EM: Round [148] log likelihood: -7854.457403
EM: Round [149] log likelihood: -7854.445845
EM: Round [150] log likelihood: -7854.434384
EM: Round [151] log likelihood: -7854.423019
EM: Round [152] log likelihood: -7854.411748
EM: Round [153] log likelihood: -7854.400571
EM: Round [154] log likelihood: -7854.389486
EM: Round [155] log likelihood: -7854.378492
EM: Round [156] log likelihood: -7854.367588
EM: Round [157] log likelihood: -7854.356774
EM: Round [158] log likelihood: -7854.346047
EM: Round [159] log likelihood: -7854.335408
EM: Round [160] log likelihood: -7854.324854
EM: Round [161] log likelihood: -7854.314386
EM: Round [162] log likelihood: -7854.304001
EM: Round [163] log likelihood: -7854.293700
EM: Round [164] log likelihood: -7854.283481
EM: Round [165] log likelihood: -7854.273343
EM: Round [166] log likelihood: -7854.263285
EM: Round [167] log likelihood: -7854.253307
EM: Round [168] log likelihood: -7854.243408
EM: Round [169] log likelihood: -7854.233586
EM: Round [170] log likelihood: -7854.223841
EM: Round [171] log likelihood: -7854.214172
EM: Round [172] log likelihood: -7854.204579
EM: Round [173] log likelihood: -7854.195060
EM: Round [174] log likelihood: -7854.185614
EM: Round [175] log likelihood: -7854.176241
EM: Round [176] log likelihood: -7854.166941
EM: Round [177] log likelihood: -7854.157712
EM: Round [178] log likelihood: -7854.148553
EM: Round [179] log likelihood: -7854.139465
EM: Round [180] log likelihood: -7854.130445
EM: Round [181] log likelihood: -7854.121494
EM: Round [182] log likelihood: -7854.112611
EM: Round [183] log likelihood: -7854.103795
EM: Round [184] log likelihood: -7854.095045
EM: Round [185] log likelihood: -7854.086361
EM: Round [186] log likelihood: -7854.077742
EM: Round [187] log likelihood: -7854.069188
EM: Round [188] log likelihood: -7854.060697
EM: Round [189] log likelihood: -7854.052269
EM: Round [190] log likelihood: -7854.043904
EM: Round [191] log likelihood: -7854.035601
EM: Round [192] log likelihood: -7854.027359
EM: Round [193] log likelihood: -7854.019178
EM: Round [194] log likelihood: -7854.011058
EM: Round [195] log likelihood: -7854.002996
EM: Round [196] log likelihood: -7853.994994
EM: Round [197] log likelihood: -7853.987050
EM: Round [198] log likelihood: -7853.979164
EM: Round [199] log likelihood: -7853.971335
EM: Round [200] log likelihood: -7853.963563
EM: Round [201] log likelihood: -7853.955848
EM: Round [202] log likelihood: -7853.948188
EM: Round [203] log likelihood: -7853.940583
EM: Round [204] log likelihood: -7853.933033
EM: Round [205] log likelihood: -7853.925537
EM: Round [206] log likelihood: -7853.918095
EM: Round [207] log likelihood: -7853.910706
EM: Round [208] log likelihood: -7853.903370
EM: Round [209] log likelihood: -7853.896086
EM: Round [210] log likelihood: -7853.888853
EM: Round [211] log likelihood: -7853.881672
EM: Round [212] log likelihood: -7853.874542
EM: Round [213] log likelihood: -7853.867462
EM: Round [214] log likelihood: -7853.860432
EM: Round [215] log likelihood: -7853.853452
EM: Round [216] log likelihood: -7853.846520
EM: Round [217] log likelihood: -7853.839637
EM: Round [218] log likelihood: -7853.832802
EM: Round [219] log likelihood: -7853.826015
EM: Round [220] log likelihood: -7853.819275
EM: Round [221] log likelihood: -7853.812582
EM: Round [222] log likelihood: -7853.805936
EM: Round [223] log likelihood: -7853.799336
EM: Round [224] log likelihood: -7853.792781
EM: Round [225] log likelihood: -7853.786271
EM: Round [226] log likelihood: -7853.779807
EM: Round [227] log likelihood: -7853.773386
EM: Round [228] log likelihood: -7853.767010
EM: Round [229] log likelihood: -7853.760678
EM: Round [230] log likelihood: -7853.754389
EM: Round [231] log likelihood: -7853.748143
EM: Round [232] log likelihood: -7853.741940
EM: Round [233] log likelihood: -7853.735778
EM: Round [234] log likelihood: -7853.729659
EM: Round [235] log likelihood: -7853.723581
EM: Round [236] log likelihood: -7853.717545
EM: Round [237] log likelihood: -7853.711549
EM: Round [238] log likelihood: -7853.705594
EM: Round [239] log likelihood: -7853.699679
EM: Round [240] log likelihood: -7853.693803
EM: Round [241] log likelihood: -7853.687968
EM: Round [242] log likelihood: -7853.682171
EM: Round [243] log likelihood: -7853.676413
EM: Round [244] log likelihood: -7853.670694
EM: Round [245] log likelihood: -7853.665013
EM: Round [246] log likelihood: -7853.659370
EM: Round [247] log likelihood: -7853.653764
EM: Round [248] log likelihood: -7853.648196
EM: Round [249] log likelihood: -7853.642665
EM: Round [250] log likelihood: -7853.637170
EM: Round [251] log likelihood: -7853.631712
EM: Round [252] log likelihood: -7853.626290
EM: Round [253] log likelihood: -7853.620903
EM: Round [254] log likelihood: -7853.615552
EM: Round [255] log likelihood: -7853.610237
EM: Round [256] log likelihood: -7853.604956
EM: Round [257] log likelihood: -7853.599710
EM: Round [258] log likelihood: -7853.594498
EM: Round [259] log likelihood: -7853.589321
EM: Round [260] log likelihood: -7853.584177
EM: Round [261] log likelihood: -7853.579067
EM: Round [262] log likelihood: -7853.573990
EM: Round [263] log likelihood: -7853.568946
EM: Round [264] log likelihood: -7853.563935
EM: Round [265] log likelihood: -7853.558956
EM: Round [266] log likelihood: -7853.554010
EM: Round [267] log likelihood: -7853.549096
EM: Round [268] log likelihood: -7853.544213
EM: Round [269] log likelihood: -7853.539362
EM: Round [270] log likelihood: -7853.534543
EM: Round [271] log likelihood: -7853.529754
EM: Round [272] log likelihood: -7853.524996
EM: Round [273] log likelihood: -7853.520269
EM: Round [274] log likelihood: -7853.515572
EM: Round [275] log likelihood: -7853.510905
EM: Round [276] log likelihood: -7853.506268
EM: Round [277] log likelihood: -7853.501661
EM: Round [278] log likelihood: -7853.497083
EM: Round [279] log likelihood: -7853.492534
EM: Round [280] log likelihood: -7853.488014
EM: Round [281] log likelihood: -7853.483523
EM: Round [282] log likelihood: -7853.479061
EM: Round [283] log likelihood: -7853.474627
EM: Round [284] log likelihood: -7853.470220
EM: Round [285] log likelihood: -7853.465842
EM: Round [286] log likelihood: -7853.461492
EM: Round [287] log likelihood: -7853.457169
EM: Round [288] log likelihood: -7853.452873
EM: Round [289] log likelihood: -7853.448604
EM: Round [290] log likelihood: -7853.444362
EM: Round [291] log likelihood: -7853.440147
EM: Round [292] log likelihood: -7853.435958
EM: Round [293] log likelihood: -7853.431796
EM: Round [294] log likelihood: -7853.427660
EM: Round [295] log likelihood: -7853.423549
EM: Round [296] log likelihood: -7853.419464
EM: Round [297] log likelihood: -7853.415405
EM: Round [298] log likelihood: -7853.411371
EM: Round [299] log likelihood: -7853.407362
EM: Round [300] log likelihood: -7853.403378
EM: Round [301] log likelihood: -7853.399419
EM: Round [302] log likelihood: -7853.395485
EM: Round [303] log likelihood: -7853.391575
EM: Round [304] log likelihood: -7853.387689
EM: Round [305] log likelihood: -7853.383827
EM: Round [306] log likelihood: -7853.379989
EM: Round [307] log likelihood: -7853.376175
EM: Round [308] log likelihood: -7853.372384
EM: Round [309] log likelihood: -7853.368617
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EM: Round [768] log likelihood: -7852.762557
EM: Round [769] log likelihood: -7852.762261
EM: Round [770] log likelihood: -7852.761967
EM: Round [771] log likelihood: -7852.761675
EM: Round [772] log likelihood: -7852.761384
EM: Round [773] log likelihood: -7852.761095
EM: Round [774] log likelihood: -7852.760807
EM: Round [775] log likelihood: -7852.760521
EM: Round [776] log likelihood: -7852.760236
EM: Round [777] log likelihood: -7852.759953
EM: Round [778] log likelihood: -7852.759671
EM: Round [779] log likelihood: -7852.759391
EM: Round [780] log likelihood: -7852.759112
EM: Round [781] log likelihood: -7852.758835
EM: Round [782] log likelihood: -7852.758559
EM: Round [783] log likelihood: -7852.758284
EM: Round [784] log likelihood: -7852.758011
EM: Round [785] log likelihood: -7852.757740
EM: Round [786] log likelihood: -7852.757470
EM: Round [787] log likelihood: -7852.757201
EM: Round [788] log likelihood: -7852.756934
EM: Round [789] log likelihood: -7852.756668
EM: Round [790] log likelihood: -7852.756403
EM: Round [791] log likelihood: -7852.756140
EM: Round [792] log likelihood: -7852.755878
EM: Round [793] log likelihood: -7852.755618
EM: Round [794] log likelihood: -7852.755359
EM: Round [795] log likelihood: -7852.755101
EM: Round [796] log likelihood: -7852.754845
EM: Round [797] log likelihood: -7852.754590
EM: Round [798] log likelihood: -7852.754336
EM: Round [799] log likelihood: -7852.754084
EM: Round [800] log likelihood: -7852.753833
EM: Round [801] log likelihood: -7852.753583
EM: Round [802] log likelihood: -7852.753335
EM: Round [803] log likelihood: -7852.753088
EM: Round [804] log likelihood: -7852.752842
EM: Round [805] log likelihood: -7852.752598
EM: Round [806] log likelihood: -7852.752354
EM: Round [807] log likelihood: -7852.752112
EM: Round [808] log likelihood: -7852.751872
EM: Round [809] log likelihood: -7852.751632
EM: Round [810] log likelihood: -7852.751394
EM: Round [811] log likelihood: -7852.751157
EM: Round [812] log likelihood: -7852.750922
EM: Round [813] log likelihood: -7852.750687
EM: Round [814] log likelihood: -7852.750454
EM: Round [815] log likelihood: -7852.750222
EM: Round [816] log likelihood: -7852.749991
EM: Round [817] log likelihood: -7852.749762
EM: Round [818] log likelihood: -7852.749533
EM: Round [819] log likelihood: -7852.749306
EM: Round [820] log likelihood: -7852.749080
EM: Round [821] log likelihood: -7852.748855
EM: Round [822] log likelihood: -7852.748632
EM: Round [823] log likelihood: -7852.748409
EM: Round [824] log likelihood: -7852.748188
EM: Round [825] log likelihood: -7852.747968
EM: Round [826] log likelihood: -7852.747749
EM: Round [827] log likelihood: -7852.747531
EM: Round [828] log likelihood: -7852.747314
EM: Round [829] log likelihood: -7852.747099
EM: Round [830] log likelihood: -7852.746884
EM: Round [831] log likelihood: -7852.746671
EM: Round [832] log likelihood: -7852.746459
EM: Round [833] log likelihood: -7852.746248
EM: Round [834] log likelihood: -7852.746038
EM: Round [835] log likelihood: -7852.745829
EM: Round [836] log likelihood: -7852.745621
EM: Round [837] log likelihood: -7852.745414
EM: Round [838] log likelihood: -7852.745209
EM: Round [839] log likelihood: -7852.745004
EM: Round [840] log likelihood: -7852.744801
EM: Round [841] log likelihood: -7852.744598
EM: Round [842] log likelihood: -7852.744397
EM: Round [843] log likelihood: -7852.744196
EM: Round [844] log likelihood: -7852.743997
EM: Round [845] log likelihood: -7852.743799
EM: Round [846] log likelihood: -7852.743602
EM: Round [847] log likelihood: -7852.743406
EM: Round [848] log likelihood: -7852.743210
EM: Round [849] log likelihood: -7852.743016
EM: Round [850] log likelihood: -7852.742823
EM: Round [851] log likelihood: -7852.742631
EM: Round [852] log likelihood: -7852.742440
EM: Round [853] log likelihood: -7852.742250
EM: Round [854] log likelihood: -7852.742061
EM: Round [855] log likelihood: -7852.741873
EM: Round [856] log likelihood: -7852.741686
EM: Round [857] log likelihood: -7852.741499
EM: Round [858] log likelihood: -7852.741314
EM: Round [859] log likelihood: -7852.741130
EM: Round [860] log likelihood: -7852.740947
EM: Round [861] log likelihood: -7852.740764
EM: Round [862] log likelihood: -7852.740583
EM: Round [863] log likelihood: -7852.740403
EM: Round [864] log likelihood: -7852.740223
EM: Round [865] log likelihood: -7852.740045
EM: Round [866] log likelihood: -7852.739867
EM: Round [867] log likelihood: -7852.739690
EM: Round [868] log likelihood: -7852.739515
EM: Round [869] log likelihood: -7852.739340
EM: Round [870] log likelihood: -7852.739166
EM: Round [871] log likelihood: -7852.738993
EM: Round [872] log likelihood: -7852.738821
EM: Round [873] log likelihood: -7852.738649
EM: Round [874] log likelihood: -7852.738479
EM: Round [875] log likelihood: -7852.738310
EM: Round [876] log likelihood: -7852.738141
EM: Round [877] log likelihood: -7852.737974
EM: Round [878] log likelihood: -7852.737807
EM: Round [879] log likelihood: -7852.737641
EM: Round [880] log likelihood: -7852.737476
EM: Round [881] log likelihood: -7852.737312
EM: Round [882] log likelihood: -7852.737148
EM: Round [883] log likelihood: -7852.736986
EM: Round [884] log likelihood: -7852.736824
EM: Round [885] log likelihood: -7852.736663
EM: Round [886] log likelihood: -7852.736503
EM: Round [887] log likelihood: -7852.736344
EM: Round [888] log likelihood: -7852.736186
EM: Round [889] log likelihood: -7852.736028
EM: Round [890] log likelihood: -7852.735872
EM: Round [891] log likelihood: -7852.735716
EM: Round [892] log likelihood: -7852.735561
EM: Round [893] log likelihood: -7852.735407
EM: Round [894] log likelihood: -7852.735253
EM: Round [895] log likelihood: -7852.735101
EM: Round [896] log likelihood: -7852.734949
EM: Round [897] log likelihood: -7852.734798
EM: Round [898] log likelihood: -7852.734648
EM: Round [899] log likelihood: -7852.734498
EM: Round [900] log likelihood: -7852.734349
EM: Round [901] log likelihood: -7852.734202
EM: Round [902] log likelihood: -7852.734054
EM: Round [903] log likelihood: -7852.733908
EM: Round [904] log likelihood: -7852.733762
EM: Round [905] log likelihood: -7852.733618
EM: Round [906] log likelihood: -7852.733473
EM: Round [907] log likelihood: -7852.733330
EM: Round [908] log likelihood: -7852.733188
EM: Round [909] log likelihood: -7852.733046
EM: Round [910] log likelihood: -7852.732905
EM: Round [911] log likelihood: -7852.732764
EM: Round [912] log likelihood: -7852.732625
EM: Round [913] log likelihood: -7852.732486
EM: Round [914] log likelihood: -7852.732347
EM: Round [915] log likelihood: -7852.732210
EM: Round [916] log likelihood: -7852.732073
EM: Round [917] log likelihood: -7852.731937
EM: Round [918] log likelihood: -7852.731802
EM: Round [919] log likelihood: -7852.731667
EM: Round [920] log likelihood: -7852.731533
EM: Round [921] log likelihood: -7852.731400
EM: Round [922] log likelihood: -7852.731267
EM: Round [923] log likelihood: -7852.731136
EM: Round [924] log likelihood: -7852.731004
EM: Round [925] log likelihood: -7852.730874
EM: Round [926] log likelihood: -7852.730744
EM: Round [927] log likelihood: -7852.730615
EM: Round [928] log likelihood: -7852.730487
EM: Round [929] log likelihood: -7852.730359
EM: Round [930] log likelihood: -7852.730232
EM: Round [931] log likelihood: -7852.730105
EM: Round [932] log likelihood: -7852.729979
EM: Round [933] log likelihood: -7852.729854
EM: Round [934] log likelihood: -7852.729730
EM: Round [935] log likelihood: -7852.729606
EM: Round [936] log likelihood: -7852.729483
EM: Round [937] log likelihood: -7852.729360
EM: Round [938] log likelihood: -7852.729238
EM: Round [939] log likelihood: -7852.729117
EM: Round [940] log likelihood: -7852.728996
EM: Round [941] log likelihood: -7852.728876
EM: Round [942] log likelihood: -7852.728757
EM: Round [943] log likelihood: -7852.728638
EM: Round [944] log likelihood: -7852.728520
EM: Round [945] log likelihood: -7852.728402
EM: Round [946] log likelihood: -7852.728285
EM: Round [947] log likelihood: -7852.728169
EM: Round [948] log likelihood: -7852.728053
EM: Round [949] log likelihood: -7852.727938
EM: Round [950] log likelihood: -7852.727824
EM: Round [951] log likelihood: -7852.727710
EM: Round [952] log likelihood: -7852.727596
EM: Round [953] log likelihood: -7852.727484
EM: Round [954] log likelihood: -7852.727371
EM: Round [955] log likelihood: -7852.727260
EM: Round [956] log likelihood: -7852.727149
EM: Round [957] log likelihood: -7852.727038
EM: Round [958] log likelihood: -7852.726929
EM: Round [959] log likelihood: -7852.726819
EM: Round [960] log likelihood: -7852.726711
EM: Round [961] log likelihood: -7852.726602
EM: Round [962] log likelihood: -7852.726495
EM: Round [963] log likelihood: -7852.726388
EM: Round [964] log likelihood: -7852.726281
EM: Round [965] log likelihood: -7852.726175
EM: Round [966] log likelihood: -7852.726070
EM: Round [967] log likelihood: -7852.725965
EM: Round [968] log likelihood: -7852.725861
EM: Round [969] log likelihood: -7852.725757
EM: Round [970] log likelihood: -7852.725654
EM: Round [971] log likelihood: -7852.725551
EM: Round [972] log likelihood: -7852.725449
EM: Round [973] log likelihood: -7852.725348
EM: Round [974] log likelihood: -7852.725247
EM: Round [975] log likelihood: -7852.725146
EM: Round [976] log likelihood: -7852.725046
EM: Round [977] log likelihood: -7852.724947
EM: Stopping iterations at round 977 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords
CMD: touch /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -7097.961224
EM: Round [1] log likelihood: -7097.914278
EM: Round [2] log likelihood: -7097.914258
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 295604458
Warning - not locating file: /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000277737.3]
WARNING, no entry stored in dbm for [ENSG00000237238.3]
WARNING, no entry stored in dbm for [ENSG00000277737.3]
WARNING, no entry stored in dbm for [ENSG00000237238.3]
WARNING, no entry stored in dbm for [ENSG00000277737.3]
WARNING, no entry stored in dbm for [ENSG00000237238.3]
ls: cannot access 'IGV_inputs': No such file or directory