Done.
-parsing GTF file: /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.atNtBlHYmi/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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
14:46:38 : INFO : Done.
-parsing GTF file: /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf
-parsing /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam
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[4880000] -done parsing /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
' ** passed ** ' => 9170,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5,
'num genes matched < 2' => 48,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 72,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 62,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 27,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 75,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 92,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 24,
'small anchor length' => 168,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 8,
'low complexity anchor region' => 19,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 32,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 154,
'per_id < 96' => 229729,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1024,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 2,
'exons hit < 2' => 21,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 2,
'excessive soft clipping' => 130892,
'seq-similar region overlap' => 359
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
-fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
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[17000] -fusion SPANNING read extraction for scaff: AC134878.2--AK6
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[90000] -fusion SPANNING read extraction for scaff: NBAS--EFEMP1
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[46000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[53000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[59000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[89000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[83000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[77000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
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[21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[20000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[96000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[46000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[50000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[58000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[65000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[48000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[39000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[55000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[173000] -fusion SPANNING read extraction for scaff: POLR2F--HMGB1
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[169000] -fusion SPANNING read extraction for scaff: POLR2F--MXI1
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[824000] -fusion SPANNING read extraction for scaff: POLR2F--GNAS
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[504000] -fusion SPANNING read extraction for scaff: RPL14--MAML2
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[483000] -fusion SPANNING read extraction for scaff: RPL14--ATN1
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[448000] -fusion SPANNING read extraction for scaff: RPL14--EP400
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[441000] -fusion SPANNING read extraction for scaff: RPL14--MPRIP
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[308000] -fusion SPANNING read extraction for scaff: RPL14--E2F4
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[12000] -fusion SPANNING read extraction for scaff: SKA2--RNFT1-DT
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[78000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[20000] -fusion SPANNING read extraction for scaff: TAS2R14--PRR4
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[90000] -fusion SPANNING read extraction for scaff: TCEAL4--MTRNR2L12
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[15000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[81000] -fusion SPANNING read extraction for scaff: TTC26--HIPK2
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[52000] -fusion SPANNING read extraction for scaff: WDR91--AC008163.1
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 7305,
'seq similar region alignment' => 89484
};
EM: Starting log likelihood: -6038.855409
EM: Round [1] log likelihood: -6038.155514
EM: Round [2] log likelihood: -6037.805726
EM: Round [3] log likelihood: -6037.493492
EM: Round [4] log likelihood: -6037.213398
EM: Round [5] log likelihood: -6036.961260
EM: Round [6] log likelihood: -6036.733581
EM: Round [7] log likelihood: -6036.527408
EM: Round [8] log likelihood: -6036.340229
EM: Round [9] log likelihood: -6036.169890
EM: Round [10] log likelihood: -6036.014531
EM: Round [11] log likelihood: -6035.872542
EM: Round [12] log likelihood: -6035.742516
EM: Round [13] log likelihood: -6035.623224
EM: Round [14] log likelihood: -6035.513584
EM: Round [15] log likelihood: -6035.412639
EM: Round [16] log likelihood: -6035.319545
EM: Round [17] log likelihood: -6035.233552
EM: Round [18] log likelihood: -6035.153989
EM: Round [19] log likelihood: -6035.080260
EM: Round [20] log likelihood: -6035.011830
EM: Round [21] log likelihood: -6034.948222
EM: Round [22] log likelihood: -6034.889003
EM: Round [23] log likelihood: -6034.833787
EM: Round [24] log likelihood: -6034.782226
EM: Round [25] log likelihood: -6034.734002
EM: Round [26] log likelihood: -6034.688833
EM: Round [27] log likelihood: -6034.646461
EM: Round [28] log likelihood: -6034.606651
EM: Round [29] log likelihood: -6034.569193
EM: Round [30] log likelihood: -6034.533893
EM: Round [31] log likelihood: -6034.500578
EM: Round [32] log likelihood: -6034.469088
EM: Round [33] log likelihood: -6034.439279
EM: Round [34] log likelihood: -6034.411020
EM: Round [35] log likelihood: -6034.384190
EM: Round [36] log likelihood: -6034.358680
EM: Round [37] log likelihood: -6034.334389
EM: Round [38] log likelihood: -6034.311228
EM: Round [39] log likelihood: -6034.289112
EM: Round [40] log likelihood: -6034.267965
EM: Round [41] log likelihood: -6034.247717
EM: Round [42] log likelihood: -6034.228305
EM: Round [43] log likelihood: -6034.209670
EM: Round [44] log likelihood: -6034.191759
EM: Round [45] log likelihood: -6034.174523
EM: Round [46] log likelihood: -6034.157916
EM: Round [47] log likelihood: -6034.141897
EM: Round [48] log likelihood: -6034.126428
EM: Round [49] log likelihood: -6034.111474
EM: Round [50] log likelihood: -6034.097004
EM: Round [51] log likelihood: -6034.082987
EM: Round [52] log likelihood: -6034.069397
EM: Round [53] log likelihood: -6034.056208
EM: Round [54] log likelihood: -6034.043397
EM: Round [55] log likelihood: -6034.030944
EM: Round [56] log likelihood: -6034.018828
EM: Round [57] log likelihood: -6034.007032
EM: Round [58] log likelihood: -6033.995538
EM: Round [59] log likelihood: -6033.984331
EM: Round [60] log likelihood: -6033.973398
EM: Round [61] log likelihood: -6033.962723
EM: Round [62] log likelihood: -6033.952296
EM: Round [63] log likelihood: -6033.942105
EM: Round [64] log likelihood: -6033.932139
EM: Round [65] log likelihood: -6033.922388
EM: Round [66] log likelihood: -6033.912844
EM: Round [67] log likelihood: -6033.903497
EM: Round [68] log likelihood: -6033.894339
EM: Round [69] log likelihood: -6033.885364
EM: Round [70] log likelihood: -6033.876564
EM: Round [71] log likelihood: -6033.867933
EM: Round [72] log likelihood: -6033.859464
EM: Round [73] log likelihood: -6033.851153
EM: Round [74] log likelihood: -6033.842993
EM: Round [75] log likelihood: -6033.834980
EM: Round [76] log likelihood: -6033.827108
EM: Round [77] log likelihood: -6033.819374
EM: Round [78] log likelihood: -6033.811774
EM: Round [79] log likelihood: -6033.804302
EM: Round [80] log likelihood: -6033.796956
EM: Round [81] log likelihood: -6033.789733
EM: Round [82] log likelihood: -6033.782627
EM: Round [83] log likelihood: -6033.775638
EM: Round [84] log likelihood: -6033.768761
EM: Round [85] log likelihood: -6033.761993
EM: Round [86] log likelihood: -6033.755333
EM: Round [87] log likelihood: -6033.748776
EM: Round [88] log likelihood: -6033.742322
EM: Round [89] log likelihood: -6033.735967
EM: Round [90] log likelihood: -6033.729709
EM: Round [91] log likelihood: -6033.723546
EM: Round [92] log likelihood: -6033.717476
EM: Round [93] log likelihood: -6033.711497
EM: Round [94] log likelihood: -6033.705607
EM: Round [95] log likelihood: -6033.699804
EM: Round [96] log likelihood: -6033.694086
EM: Round [97] log likelihood: -6033.688452
EM: Round [98] log likelihood: -6033.682900
EM: Round [99] log likelihood: -6033.677429
EM: Round [100] log likelihood: -6033.672037
EM: Round [101] log likelihood: -6033.666721
EM: Round [102] log likelihood: -6033.661482
EM: Round [103] log likelihood: -6033.656318
EM: Round [104] log likelihood: -6033.651227
EM: Round [105] log likelihood: -6033.646207
EM: Round [106] log likelihood: -6033.641258
EM: Round [107] log likelihood: -6033.636379
EM: Round [108] log likelihood: -6033.631568
EM: Round [109] log likelihood: -6033.626824
EM: Round [110] log likelihood: -6033.622146
EM: Round [111] log likelihood: -6033.617533
EM: Round [112] log likelihood: -6033.612983
EM: Round [113] log likelihood: -6033.608496
EM: Round [114] log likelihood: -6033.604071
EM: Round [115] log likelihood: -6033.599706
EM: Round [116] log likelihood: -6033.595401
EM: Round [117] log likelihood: -6033.591155
EM: Round [118] log likelihood: -6033.586966
EM: Round [119] log likelihood: -6033.582835
EM: Round [120] log likelihood: -6033.578759
EM: Round [121] log likelihood: -6033.574738
EM: Round [122] log likelihood: -6033.570772
EM: Round [123] log likelihood: -6033.566859
EM: Round [124] log likelihood: -6033.562999
EM: Round [125] log likelihood: -6033.559190
EM: Round [126] log likelihood: -6033.555433
EM: Round [127] log likelihood: -6033.551726
EM: Round [128] log likelihood: -6033.548068
EM: Round [129] log likelihood: -6033.544459
EM: Round [130] log likelihood: -6033.540898
EM: Round [131] log likelihood: -6033.537384
EM: Round [132] log likelihood: -6033.533917
EM: Round [133] log likelihood: -6033.530496
EM: Round [134] log likelihood: -6033.527120
EM: Round [135] log likelihood: -6033.523789
EM: Round [136] log likelihood: -6033.520501
EM: Round [137] log likelihood: -6033.517257
EM: Round [138] log likelihood: -6033.514056
EM: Round [139] log likelihood: -6033.510897
EM: Round [140] log likelihood: -6033.507779
EM: Round [141] log likelihood: -6033.504702
EM: Round [142] log likelihood: -6033.501665
EM: Round [143] log likelihood: -6033.498668
EM: Round [144] log likelihood: -6033.495711
EM: Round [145] log likelihood: -6033.492792
EM: Round [146] log likelihood: -6033.489910
EM: Round [147] log likelihood: -6033.487067
EM: Round [148] log likelihood: -6033.484260
EM: Round [149] log likelihood: -6033.481490
EM: Round [150] log likelihood: -6033.478756
EM: Round [151] log likelihood: -6033.476057
EM: Round [152] log likelihood: -6033.473394
EM: Round [153] log likelihood: -6033.470764
EM: Round [154] log likelihood: -6033.468169
EM: Round [155] log likelihood: -6033.465608
EM: Round [156] log likelihood: -6033.463079
EM: Round [157] log likelihood: -6033.460583
EM: Round [158] log likelihood: -6033.458119
EM: Round [159] log likelihood: -6033.455687
EM: Round [160] log likelihood: -6033.453287
EM: Round [161] log likelihood: -6033.450917
EM: Round [162] log likelihood: -6033.448577
EM: Round [163] log likelihood: -6033.446268
EM: Round [164] log likelihood: -6033.443988
EM: Round [165] log likelihood: -6033.441738
EM: Round [166] log likelihood: -6033.439516
EM: Round [167] log likelihood: -6033.437323
EM: Round [168] log likelihood: -6033.435158
EM: Round [169] log likelihood: -6033.433020
EM: Round [170] log likelihood: -6033.430910
EM: Round [171] log likelihood: -6033.428827
EM: Round [172] log likelihood: -6033.426770
EM: Round [173] log likelihood: -6033.424740
EM: Round [174] log likelihood: -6033.422735
EM: Round [175] log likelihood: -6033.420756
EM: Round [176] log likelihood: -6033.418803
EM: Round [177] log likelihood: -6033.416874
EM: Round [178] log likelihood: -6033.414969
EM: Round [179] log likelihood: -6033.413089
EM: Round [180] log likelihood: -6033.411233
EM: Round [181] log likelihood: -6033.409400
EM: Round [182] log likelihood: -6033.407590
EM: Round [183] log likelihood: -6033.405804
EM: Round [184] log likelihood: -6033.404040
EM: Round [185] log likelihood: -6033.402298
EM: Round [186] log likelihood: -6033.400579
EM: Round [187] log likelihood: -6033.398881
EM: Round [188] log likelihood: -6033.397205
EM: Round [189] log likelihood: -6033.395549
EM: Round [190] log likelihood: -6033.393915
EM: Round [191] log likelihood: -6033.392302
EM: Round [192] log likelihood: -6033.390708
EM: Round [193] log likelihood: -6033.389135
EM: Round [194] log likelihood: -6033.387582
EM: Round [195] log likelihood: -6033.386048
EM: Round [196] log likelihood: -6033.384534
EM: Round [197] log likelihood: -6033.383038
EM: Round [198] log likelihood: -6033.381562
EM: Round [199] log likelihood: -6033.380104
EM: Round [200] log likelihood: -6033.378664
EM: Round [201] log likelihood: -6033.377243
EM: Round [202] log likelihood: -6033.375839
EM: Round [203] log likelihood: -6033.374453
EM: Round [204] log likelihood: -6033.373084
EM: Round [205] log likelihood: -6033.371733
EM: Round [206] log likelihood: -6033.370399
EM: Round [207] log likelihood: -6033.369081
EM: Round [208] log likelihood: -6033.367780
EM: Round [209] log likelihood: -6033.366495
EM: Round [210] log likelihood: -6033.365226
EM: Round [211] log likelihood: -6033.363973
EM: Round [212] log likelihood: -6033.362736
EM: Round [213] log likelihood: -6033.361514
EM: Round [214] log likelihood: -6033.360307
EM: Round [215] log likelihood: -6033.359116
EM: Round [216] log likelihood: -6033.357939
EM: Round [217] log likelihood: -6033.356778
EM: Round [218] log likelihood: -6033.355630
EM: Round [219] log likelihood: -6033.354497
EM: Round [220] log likelihood: -6033.353379
EM: Round [221] log likelihood: -6033.352274
EM: Round [222] log likelihood: -6033.351183
EM: Round [223] log likelihood: -6033.350105
EM: Round [224] log likelihood: -6033.349041
EM: Round [225] log likelihood: -6033.347991
EM: Round [226] log likelihood: -6033.346953
EM: Round [227] log likelihood: -6033.345928
EM: Round [228] log likelihood: -6033.344916
EM: Round [229] log likelihood: -6033.343917
EM: Round [230] log likelihood: -6033.342930
EM: Round [231] log likelihood: -6033.341955
EM: Round [232] log likelihood: -6033.340993
EM: Round [233] log likelihood: -6033.340042
EM: Round [234] log likelihood: -6033.339104
EM: Round [235] log likelihood: -6033.338177
EM: Round [236] log likelihood: -6033.337261
EM: Round [237] log likelihood: -6033.336357
EM: Round [238] log likelihood: -6033.335464
EM: Round [239] log likelihood: -6033.334582
EM: Round [240] log likelihood: -6033.333712
EM: Round [241] log likelihood: -6033.332851
EM: Round [242] log likelihood: -6033.332002
EM: Round [243] log likelihood: -6033.331163
EM: Round [244] log likelihood: -6033.330335
EM: Round [245] log likelihood: -6033.329517
EM: Round [246] log likelihood: -6033.328709
EM: Round [247] log likelihood: -6033.327911
EM: Round [248] log likelihood: -6033.327123
EM: Round [249] log likelihood: -6033.326344
EM: Round [250] log likelihood: -6033.325576
EM: Round [251] log likelihood: -6033.324817
EM: Round [252] log likelihood: -6033.324067
EM: Round [253] log likelihood: -6033.323326
EM: Round [254] log likelihood: -6033.322595
EM: Round [255] log likelihood: -6033.321873
EM: Round [256] log likelihood: -6033.321160
EM: Round [257] log likelihood: -6033.320455
EM: Round [258] log likelihood: -6033.319759
EM: Round [259] log likelihood: -6033.319072
EM: Round [260] log likelihood: -6033.318393
EM: Round [261] log likelihood: -6033.317723
EM: Round [262] log likelihood: -6033.317061
EM: Round [263] log likelihood: -6033.316407
EM: Round [264] log likelihood: -6033.315762
EM: Round [265] log likelihood: -6033.315124
EM: Round [266] log likelihood: -6033.314494
EM: Round [267] log likelihood: -6033.313872
EM: Round [268] log likelihood: -6033.313258
EM: Round [269] log likelihood: -6033.312651
EM: Round [270] log likelihood: -6033.312052
EM: Round [271] log likelihood: -6033.311460
EM: Round [272] log likelihood: -6033.310875
EM: Round [273] log likelihood: -6033.310298
EM: Round [274] log likelihood: -6033.309727
EM: Round [275] log likelihood: -6033.309164
EM: Round [276] log likelihood: -6033.308608
EM: Round [277] log likelihood: -6033.308058
EM: Round [278] log likelihood: -6033.307516
EM: Round [279] log likelihood: -6033.306980
EM: Round [280] log likelihood: -6033.306451
EM: Round [281] log likelihood: -6033.305928
EM: Round [282] log likelihood: -6033.305411
EM: Round [283] log likelihood: -6033.304901
EM: Round [284] log likelihood: -6033.304398
EM: Round [285] log likelihood: -6033.303900
EM: Round [286] log likelihood: -6033.303409
EM: Round [287] log likelihood: -6033.302923
EM: Round [288] log likelihood: -6033.302444
EM: Round [289] log likelihood: -6033.301970
EM: Round [290] log likelihood: -6033.301503
EM: Round [291] log likelihood: -6033.301041
EM: Round [292] log likelihood: -6033.300585
EM: Round [293] log likelihood: -6033.300134
EM: Round [294] log likelihood: -6033.299689
EM: Round [295] log likelihood: -6033.299250
EM: Round [296] log likelihood: -6033.298815
EM: Round [297] log likelihood: -6033.298387
EM: Round [298] log likelihood: -6033.297963
EM: Round [299] log likelihood: -6033.297545
EM: Round [300] log likelihood: -6033.297132
EM: Round [301] log likelihood: -6033.296724
EM: Round [302] log likelihood: -6033.296320
EM: Round [303] log likelihood: -6033.295922
EM: Round [304] log likelihood: -6033.295529
EM: Round [305] log likelihood: -6033.295141
EM: Round [306] log likelihood: -6033.294757
EM: Round [307] log likelihood: -6033.294378
EM: Round [308] log likelihood: -6033.294004
EM: Round [309] log likelihood: -6033.293634
EM: Round [310] log likelihood: -6033.293269
EM: Round [311] log likelihood: -6033.292909
EM: Round [312] log likelihood: -6033.292552
EM: Round [313] log likelihood: -6033.292201
EM: Round [314] log likelihood: -6033.291853
EM: Round [315] log likelihood: -6033.291510
EM: Round [316] log likelihood: -6033.291171
EM: Round [317] log likelihood: -6033.290836
EM: Round [318] log likelihood: -6033.290505
EM: Round [319] log likelihood: -6033.290179
EM: Round [320] log likelihood: -6033.289856
EM: Round [321] log likelihood: -6033.289537
EM: Round [322] log likelihood: -6033.289222
EM: Round [323] log likelihood: -6033.288912
EM: Round [324] log likelihood: -6033.288604
EM: Round [325] log likelihood: -6033.288301
EM: Round [326] log likelihood: -6033.288001
EM: Round [327] log likelihood: -6033.287706
EM: Round [328] log likelihood: -6033.287413
EM: Round [329] log likelihood: -6033.287124
EM: Round [330] log likelihood: -6033.286839
EM: Round [331] log likelihood: -6033.286558
EM: Round [332] log likelihood: -6033.286279
EM: Round [333] log likelihood: -6033.286005
EM: Round [334] log likelihood: -6033.285733
EM: Round [335] log likelihood: -6033.285465
EM: Round [336] log likelihood: -6033.285200
EM: Round [337] log likelihood: -6033.284939
EM: Round [338] log likelihood: -6033.284680
EM: Round [339] log likelihood: -6033.284425
EM: Round [340] log likelihood: -6033.284173
EM: Round [341] log likelihood: -6033.283924
EM: Round [342] log likelihood: -6033.283678
EM: Round [343] log likelihood: -6033.283435
EM: Round [344] log likelihood: -6033.283195
EM: Round [345] log likelihood: -6033.282958
EM: Round [346] log likelihood: -6033.282724
EM: Round [347] log likelihood: -6033.282493
EM: Round [348] log likelihood: -6033.282264
EM: Round [349] log likelihood: -6033.282039
EM: Round [350] log likelihood: -6033.281816
EM: Round [351] log likelihood: -6033.281596
EM: Round [352] log likelihood: -6033.281378
EM: Round [353] log likelihood: -6033.281163
EM: Round [354] log likelihood: -6033.280951
EM: Round [355] log likelihood: -6033.280742
EM: Round [356] log likelihood: -6033.280535
EM: Round [357] log likelihood: -6033.280330
EM: Round [358] log likelihood: -6033.280129
EM: Round [359] log likelihood: -6033.279929
EM: Round [360] log likelihood: -6033.279732
EM: Round [361] log likelihood: -6033.279537
EM: Round [362] log likelihood: -6033.279345
EM: Round [363] log likelihood: -6033.279155
EM: Round [364] log likelihood: -6033.278968
EM: Round [365] log likelihood: -6033.278783
EM: Round [366] log likelihood: -6033.278600
EM: Round [367] log likelihood: -6033.278419
EM: Round [368] log likelihood: -6033.278240
EM: Round [369] log likelihood: -6033.278064
EM: Round [370] log likelihood: -6033.277890
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EM: Round [379] log likelihood: -6033.276415
EM: Round [380] log likelihood: -6033.276261
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EM: Round [382] log likelihood: -6033.275959
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EM: Round [388] log likelihood: -6033.275095
EM: Round [389] log likelihood: -6033.274957
EM: Round [390] log likelihood: -6033.274821
EM: Round [391] log likelihood: -6033.274686
EM: Round [392] log likelihood: -6033.274554
EM: Round [393] log likelihood: -6033.274422
EM: Round [394] log likelihood: -6033.274293
EM: Round [395] log likelihood: -6033.274165
EM: Round [396] log likelihood: -6033.274038
EM: Round [397] log likelihood: -6033.273913
EM: Round [398] log likelihood: -6033.273790
EM: Round [399] log likelihood: -6033.273668
EM: Round [400] log likelihood: -6033.273548
EM: Round [401] log likelihood: -6033.273429
EM: Round [402] log likelihood: -6033.273311
EM: Round [403] log likelihood: -6033.273195
EM: Round [404] log likelihood: -6033.273080
EM: Round [405] log likelihood: -6033.272967
EM: Round [406] log likelihood: -6033.272855
EM: Round [407] log likelihood: -6033.272745
EM: Round [408] log likelihood: -6033.272636
EM: Round [409] log likelihood: -6033.272528
EM: Round [410] log likelihood: -6033.272421
EM: Round [411] log likelihood: -6033.272316
EM: Round [412] log likelihood: -6033.272212
EM: Round [413] log likelihood: -6033.272110
EM: Round [414] log likelihood: -6033.272008
EM: Round [415] log likelihood: -6033.271908
EM: Round [416] log likelihood: -6033.271809
EM: Stopping iterations at round 416 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -4709.957846
EM: Round [1] log likelihood: -4709.947075
EM: Round [2] log likelihood: -4709.947056
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 265946703
Warning - not locating file: /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000198237.8]
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 [ENSG00000267302.5]
WARNING, no entry stored in dbm for [ENSG00000267302.5]
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 [ENSG00000278212.2]
ls: cannot access 'IGV_inputs': No such file or directory