Done.
-parsing GTF file: /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.e487RzRTjW/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.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam
11:09:46 : INFO : Done.
-parsing GTF file: /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf
-parsing /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam
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[5370000] -done parsing /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
'excessive soft clipping' => 39245,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 2,
'per_id < 96' => 31537,
'exons hit < 2' => 2,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 66,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 3,
' ** passed ** ' => 46873,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 29,
'small anchor length' => 291,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 427,
'seq-similar region overlap' => 260,
'num genes matched < 2' => 53,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 60,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 38,
'low complexity anchor region' => 34,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 20,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[154000] -fusion SPANNING read extraction for scaff: AC002066.1--SYK
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[51000] -fusion SPANNING read extraction for scaff: AC015712.1--FBXL2
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[7000] -fusion SPANNING read extraction for scaff: AC015712.1--FAM13C
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[10000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
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[59000] -fusion SPANNING read extraction for scaff: AL033504.1--SASH1
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[215000] -fusion SPANNING read extraction for scaff: BIRC6--ITGA9
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[24000] -fusion SPANNING read extraction for scaff: CENPP--ASZ1
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[24000] -fusion SPANNING read extraction for scaff: CHST11--SYK
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[18000] -fusion SPANNING read extraction for scaff: CHST11--DIRAS2
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[18000] -fusion SPANNING read extraction for scaff: CHST11--OR7E109P
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[105000] -fusion SPANNING read extraction for scaff: CLASP1--NRCAM
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[37000] -fusion SPANNING read extraction for scaff: COBL--LINC01866
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[37000] -fusion SPANNING read extraction for scaff: COBL--RN7SKP168
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[177000] -fusion SPANNING read extraction for scaff: CUX1--PCBP1-AS1
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[59000] -fusion SPANNING read extraction for scaff: DGCR2--WARS2-AS1
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[58000] -fusion SPANNING read extraction for scaff: EPHB2--TMEM39B
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[54000] -fusion SPANNING read extraction for scaff: ERCC6L2--PPP1R9A
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[46000] -fusion SPANNING read extraction for scaff: ERCC6L2--PPP1R9A-AS1
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[55000] -fusion SPANNING read extraction for scaff: FAF1--CDKN2C
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[38000] -fusion SPANNING read extraction for scaff: FAF1--MIR4421
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[184000] -fusion SPANNING read extraction for scaff: FOSL1--SLC30A8
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[47000] -fusion SPANNING read extraction for scaff: GLIS3--FGF7P4
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[52000] -fusion SPANNING read extraction for scaff: GLIS3--FGF7P6
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[125000] -fusion SPANNING read extraction for scaff: GTF2H2--FAM114A1
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[14000] -fusion SPANNING read extraction for scaff: LPAR1--SUSD1
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[133000] -fusion SPANNING read extraction for scaff: MMP24OS--PTPRT
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[67000] -fusion SPANNING read extraction for scaff: NEK10--CCBE1
-fusion SPANNING read extraction for scaff: NTM-AS1--OPCML
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[59000] -fusion SPANNING read extraction for scaff: PARD3--AL392046.1
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
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[6000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9
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[21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[7000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[30000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[28000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[83000] -fusion SPANNING read extraction for scaff: POLR2J3--KIF16B
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[33000] -fusion SPANNING read extraction for scaff: PSG9--CD177
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[54000] -fusion SPANNING read extraction for scaff: PSMB2--CELF4
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[179000] -fusion SPANNING read extraction for scaff: PXN--PLA2G1B
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[101000] -fusion SPANNING read extraction for scaff: RBBP4--FBXL2
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[13000] -fusion SPANNING read extraction for scaff: SDHAF3--AC025614.2
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[13000] -fusion SPANNING read extraction for scaff: SDHAF3--LINC01985
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[43000] -fusion SPANNING read extraction for scaff: SLC11A2--CASKP1
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[43000] -fusion SPANNING read extraction for scaff: SLC11A2--SFPQP1
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[14000] -fusion SPANNING read extraction for scaff: SLC30A7--UROC1
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[223000] -fusion SPANNING read extraction for scaff: SLC34A2--ROS1
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[71000] -fusion SPANNING read extraction for scaff: SMARCA2--TRIM72
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[53000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408
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[132000] -fusion SPANNING read extraction for scaff: ST7--AC006001.3
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[54000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[29000] -fusion SPANNING read extraction for scaff: TMED7--TICAM2
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[1482000] -fusion SPANNING read extraction for scaff: TRIO--TMEM272
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[68000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[121000] -fusion SPANNING read extraction for scaff: UHRF2--SLC1A1
[1000]
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[10000] -fusion SPANNING read extraction for scaff: WWOX--AL591721.1
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[167000] -fusion SPANNING read extraction for scaff: XYLB--GOLGA4
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[89000] -fusion SPANNING read extraction for scaff: ZBTB40--ZMYM4
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[40000] -fusion SPANNING read extraction for scaff: ZFP62--SIMC1
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[16000] -fusion SPANNING read extraction for scaff: ZNF559--ZNF177
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 27008,
'lacks exon overlap' => 197274
};
EM: Starting log likelihood: -21931.055798
EM: Round [1] log likelihood: -21918.392121
EM: Round [2] log likelihood: -21915.830628
EM: Round [3] log likelihood: -21913.876513
EM: Round [4] log likelihood: -21912.331071
EM: Round [5] log likelihood: -21911.100037
EM: Round [6] log likelihood: -21910.113802
EM: Round [7] log likelihood: -21909.319452
EM: Round [8] log likelihood: -21908.676371
EM: Round [9] log likelihood: -21908.153142
EM: Round [10] log likelihood: -21907.725297
EM: Round [11] log likelihood: -21907.373677
EM: Round [12] log likelihood: -21907.083200
EM: Round [13] log likelihood: -21906.841944
EM: Round [14] log likelihood: -21906.640444
EM: Round [15] log likelihood: -21906.471159
EM: Round [16] log likelihood: -21906.328060
EM: Round [17] log likelihood: -21906.206311
EM: Round [18] log likelihood: -21906.102018
EM: Round [19] log likelihood: -21906.012042
EM: Round [20] log likelihood: -21905.933841
EM: Round [21] log likelihood: -21905.865350
EM: Round [22] log likelihood: -21905.804891
EM: Round [23] log likelihood: -21905.751093
EM: Round [24] log likelihood: -21905.702836
EM: Round [25] log likelihood: -21905.659200
EM: Round [26] log likelihood: -21905.619430
EM: Round [27] log likelihood: -21905.582903
EM: Round [28] log likelihood: -21905.549106
EM: Round [29] log likelihood: -21905.517611
EM: Round [30] log likelihood: -21905.488068
EM: Round [31] log likelihood: -21905.460182
EM: Round [32] log likelihood: -21905.433709
EM: Round [33] log likelihood: -21905.408446
EM: Round [34] log likelihood: -21905.384222
EM: Round [35] log likelihood: -21905.360895
EM: Round [36] log likelihood: -21905.338345
EM: Round [37] log likelihood: -21905.316472
EM: Round [38] log likelihood: -21905.295190
EM: Round [39] log likelihood: -21905.274429
EM: Round [40] log likelihood: -21905.254129
EM: Round [41] log likelihood: -21905.234238
EM: Round [42] log likelihood: -21905.214714
EM: Round [43] log likelihood: -21905.195519
EM: Round [44] log likelihood: -21905.176623
EM: Round [45] log likelihood: -21905.157998
EM: Round [46] log likelihood: -21905.139622
EM: Round [47] log likelihood: -21905.121476
EM: Round [48] log likelihood: -21905.103543
EM: Round [49] log likelihood: -21905.085809
EM: Round [50] log likelihood: -21905.068261
EM: Round [51] log likelihood: -21905.050888
EM: Round [52] log likelihood: -21905.033681
EM: Round [53] log likelihood: -21905.016633
EM: Round [54] log likelihood: -21904.999735
EM: Round [55] log likelihood: -21904.982982
EM: Round [56] log likelihood: -21904.966368
EM: Round [57] log likelihood: -21904.949889
EM: Round [58] log likelihood: -21904.933540
EM: Round [59] log likelihood: -21904.917317
EM: Round [60] log likelihood: -21904.901217
EM: Round [61] log likelihood: -21904.885236
EM: Round [62] log likelihood: -21904.869372
EM: Round [63] log likelihood: -21904.853622
EM: Round [64] log likelihood: -21904.837985
EM: Round [65] log likelihood: -21904.822456
EM: Round [66] log likelihood: -21904.807036
EM: Round [67] log likelihood: -21904.791721
EM: Round [68] log likelihood: -21904.776509
EM: Round [69] log likelihood: -21904.761400
EM: Round [70] log likelihood: -21904.746392
EM: Round [71] log likelihood: -21904.731483
EM: Round [72] log likelihood: -21904.716672
EM: Round [73] log likelihood: -21904.701957
EM: Round [74] log likelihood: -21904.687337
EM: Round [75] log likelihood: -21904.672810
EM: Round [76] log likelihood: -21904.658377
EM: Round [77] log likelihood: -21904.644034
EM: Round [78] log likelihood: -21904.629782
EM: Round [79] log likelihood: -21904.615620
EM: Round [80] log likelihood: -21904.601545
EM: Round [81] log likelihood: -21904.587557
EM: Round [82] log likelihood: -21904.573656
EM: Round [83] log likelihood: -21904.559839
EM: Round [84] log likelihood: -21904.546107
EM: Round [85] log likelihood: -21904.532458
EM: Round [86] log likelihood: -21904.518891
EM: Round [87] log likelihood: -21904.505406
EM: Round [88] log likelihood: -21904.492000
EM: Round [89] log likelihood: -21904.478675
EM: Round [90] log likelihood: -21904.465428
EM: Round [91] log likelihood: -21904.452259
EM: Round [92] log likelihood: -21904.439168
EM: Round [93] log likelihood: -21904.426152
EM: Round [94] log likelihood: -21904.413212
EM: Round [95] log likelihood: -21904.400347
EM: Round [96] log likelihood: -21904.387555
EM: Round [97] log likelihood: -21904.374837
EM: Round [98] log likelihood: -21904.362191
EM: Round [99] log likelihood: -21904.349617
EM: Round [100] log likelihood: -21904.337114
EM: Round [101] log likelihood: -21904.324681
EM: Round [102] log likelihood: -21904.312318
EM: Round [103] log likelihood: -21904.300024
EM: Round [104] log likelihood: -21904.287797
EM: Round [105] log likelihood: -21904.275639
EM: Round [106] log likelihood: -21904.263547
EM: Round [107] log likelihood: -21904.251522
EM: Round [108] log likelihood: -21904.239562
EM: Round [109] log likelihood: -21904.227667
EM: Round [110] log likelihood: -21904.215837
EM: Round [111] log likelihood: -21904.204070
EM: Round [112] log likelihood: -21904.192367
EM: Round [113] log likelihood: -21904.180726
EM: Round [114] log likelihood: -21904.169147
EM: Round [115] log likelihood: -21904.157630
EM: Round [116] log likelihood: -21904.146173
EM: Round [117] log likelihood: -21904.134777
EM: Round [118] log likelihood: -21904.123441
EM: Round [119] log likelihood: -21904.112164
EM: Round [120] log likelihood: -21904.100945
EM: Round [121] log likelihood: -21904.089785
EM: Round [122] log likelihood: -21904.078682
EM: Round [123] log likelihood: -21904.067636
EM: Round [124] log likelihood: -21904.056647
EM: Round [125] log likelihood: -21904.045714
EM: Round [126] log likelihood: -21904.034837
EM: Round [127] log likelihood: -21904.024015
EM: Round [128] log likelihood: -21904.013247
EM: Round [129] log likelihood: -21904.002534
EM: Round [130] log likelihood: -21903.991874
EM: Round [131] log likelihood: -21903.981268
EM: Round [132] log likelihood: -21903.970714
EM: Round [133] log likelihood: -21903.960213
EM: Round [134] log likelihood: -21903.949763
EM: Round [135] log likelihood: -21903.939365
EM: Round [136] log likelihood: -21903.929018
EM: Round [137] log likelihood: -21903.918722
EM: Round [138] log likelihood: -21903.908476
EM: Round [139] log likelihood: -21903.898280
EM: Round [140] log likelihood: -21903.888133
EM: Round [141] log likelihood: -21903.878034
EM: Round [142] log likelihood: -21903.867985
EM: Round [143] log likelihood: -21903.857984
EM: Round [144] log likelihood: -21903.848030
EM: Round [145] log likelihood: -21903.838124
EM: Round [146] log likelihood: -21903.828264
EM: Round [147] log likelihood: -21903.818452
EM: Round [148] log likelihood: -21903.808685
EM: Round [149] log likelihood: -21903.798965
EM: Round [150] log likelihood: -21903.789290
EM: Round [151] log likelihood: -21903.779660
EM: Round [152] log likelihood: -21903.770075
EM: Round [153] log likelihood: -21903.760534
EM: Round [154] log likelihood: -21903.751037
EM: Round [155] log likelihood: -21903.741584
EM: Round [156] log likelihood: -21903.732175
EM: Round [157] log likelihood: -21903.722809
EM: Round [158] log likelihood: -21903.713485
EM: Round [159] log likelihood: -21903.704204
EM: Round [160] log likelihood: -21903.694965
EM: Round [161] log likelihood: -21903.685767
EM: Round [162] log likelihood: -21903.676611
EM: Round [163] log likelihood: -21903.667497
EM: Round [164] log likelihood: -21903.658423
EM: Round [165] log likelihood: -21903.649389
EM: Round [166] log likelihood: -21903.640396
EM: Round [167] log likelihood: -21903.631443
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EM: Round [627] log likelihood: -21901.561501
EM: Round [628] log likelihood: -21901.559247
EM: Round [629] log likelihood: -21901.556998
EM: Round [630] log likelihood: -21901.554754
EM: Round [631] log likelihood: -21901.552515
EM: Round [632] log likelihood: -21901.550281
EM: Round [633] log likelihood: -21901.548052
EM: Round [634] log likelihood: -21901.545828
EM: Round [635] log likelihood: -21901.543609
EM: Round [636] log likelihood: -21901.541395
EM: Round [637] log likelihood: -21901.539187
EM: Round [638] log likelihood: -21901.536983
EM: Round [639] log likelihood: -21901.534784
EM: Round [640] log likelihood: -21901.532590
EM: Round [641] log likelihood: -21901.530401
EM: Round [642] log likelihood: -21901.528217
EM: Round [643] log likelihood: -21901.526037
EM: Round [644] log likelihood: -21901.523863
EM: Round [645] log likelihood: -21901.521694
EM: Round [646] log likelihood: -21901.519529
EM: Round [647] log likelihood: -21901.517369
EM: Round [648] log likelihood: -21901.515214
EM: Round [649] log likelihood: -21901.513064
EM: Round [650] log likelihood: -21901.510919
EM: Round [651] log likelihood: -21901.508778
EM: Round [652] log likelihood: -21901.506642
EM: Round [653] log likelihood: -21901.504511
EM: Round [654] log likelihood: -21901.502385
EM: Round [655] log likelihood: -21901.500263
EM: Round [656] log likelihood: -21901.498146
EM: Round [657] log likelihood: -21901.496034
EM: Round [658] log likelihood: -21901.493927
EM: Round [659] log likelihood: -21901.491824
EM: Round [660] log likelihood: -21901.489726
EM: Round [661] log likelihood: -21901.487632
EM: Round [662] log likelihood: -21901.485543
EM: Round [663] log likelihood: -21901.483459
EM: Round [664] log likelihood: -21901.481379
EM: Round [665] log likelihood: -21901.479304
EM: Round [666] log likelihood: -21901.477234
EM: Round [667] log likelihood: -21901.475168
EM: Round [668] log likelihood: -21901.473107
EM: Round [669] log likelihood: -21901.471050
EM: Round [670] log likelihood: -21901.468998
EM: Round [671] log likelihood: -21901.466950
EM: Round [672] log likelihood: -21901.464907
EM: Round [673] log likelihood: -21901.462868
EM: Round [674] log likelihood: -21901.460833
EM: Round [675] log likelihood: -21901.458804
EM: Round [676] log likelihood: -21901.456778
EM: Round [677] log likelihood: -21901.454757
EM: Round [678] log likelihood: -21901.452741
EM: Round [679] log likelihood: -21901.450729
EM: Round [680] log likelihood: -21901.448721
EM: Round [681] log likelihood: -21901.446717
EM: Round [682] log likelihood: -21901.444718
EM: Round [683] log likelihood: -21901.442724
EM: Round [684] log likelihood: -21901.440734
EM: Round [685] log likelihood: -21901.438748
EM: Round [686] log likelihood: -21901.436766
EM: Round [687] log likelihood: -21901.434789
EM: Round [688] log likelihood: -21901.432816
EM: Round [689] log likelihood: -21901.430847
EM: Round [690] log likelihood: -21901.428883
EM: Round [691] log likelihood: -21901.426923
EM: Round [692] log likelihood: -21901.424967
EM: Round [693] log likelihood: -21901.423015
EM: Round [694] log likelihood: -21901.421068
EM: Round [695] log likelihood: -21901.419124
EM: Round [696] log likelihood: -21901.417185
EM: Round [697] log likelihood: -21901.415251
EM: Round [698] log likelihood: -21901.413320
EM: Round [699] log likelihood: -21901.411394
EM: Round [700] log likelihood: -21901.409471
EM: Round [701] log likelihood: -21901.407553
EM: Round [702] log likelihood: -21901.405639
EM: Round [703] log likelihood: -21901.403729
EM: Round [704] log likelihood: -21901.401823
EM: Round [705] log likelihood: -21901.399922
EM: Round [706] log likelihood: -21901.398024
EM: Round [707] log likelihood: -21901.396131
EM: Round [708] log likelihood: -21901.394241
EM: Round [709] log likelihood: -21901.392356
EM: Round [710] log likelihood: -21901.390475
EM: Round [711] log likelihood: -21901.388597
EM: Round [712] log likelihood: -21901.386724
EM: Round [713] log likelihood: -21901.384855
EM: Round [714] log likelihood: -21901.382989
EM: Round [715] log likelihood: -21901.381128
EM: Round [716] log likelihood: -21901.379271
EM: Round [717] log likelihood: -21901.377418
EM: Round [718] log likelihood: -21901.375568
EM: Round [719] log likelihood: -21901.373723
EM: Round [720] log likelihood: -21901.371881
EM: Round [721] log likelihood: -21901.370044
EM: Round [722] log likelihood: -21901.368210
EM: Round [723] log likelihood: -21901.366380
EM: Round [724] log likelihood: -21901.364555
EM: Round [725] log likelihood: -21901.362733
EM: Round [726] log likelihood: -21901.360914
EM: Round [727] log likelihood: -21901.359100
EM: Round [728] log likelihood: -21901.357290
EM: Round [729] log likelihood: -21901.355483
EM: Round [730] log likelihood: -21901.353681
EM: Round [731] log likelihood: -21901.351882
EM: Round [732] log likelihood: -21901.350087
EM: Round [733] log likelihood: -21901.348295
EM: Round [734] log likelihood: -21901.346508
EM: Round [735] log likelihood: -21901.344724
EM: Round [736] log likelihood: -21901.342944
EM: Round [737] log likelihood: -21901.341168
EM: Round [738] log likelihood: -21901.339396
EM: Round [739] log likelihood: -21901.337627
EM: Round [740] log likelihood: -21901.335862
EM: Round [741] log likelihood: -21901.334101
EM: Round [742] log likelihood: -21901.332343
EM: Round [743] log likelihood: -21901.330589
EM: Round [744] log likelihood: -21901.328839
EM: Round [745] log likelihood: -21901.327093
EM: Round [746] log likelihood: -21901.325350
EM: Round [747] log likelihood: -21901.323611
EM: Round [748] log likelihood: -21901.321875
EM: Round [749] log likelihood: -21901.320143
EM: Round [750] log likelihood: -21901.318415
EM: Round [751] log likelihood: -21901.316690
EM: Round [752] log likelihood: -21901.314969
EM: Round [753] log likelihood: -21901.313252
EM: Round [754] log likelihood: -21901.311538
EM: Round [755] log likelihood: -21901.309828
EM: Round [756] log likelihood: -21901.308121
EM: Round [757] log likelihood: -21901.306418
EM: Round [758] log likelihood: -21901.304719
EM: Round [759] log likelihood: -21901.303023
EM: Round [760] log likelihood: -21901.301330
EM: Round [761] log likelihood: -21901.299641
EM: Round [762] log likelihood: -21901.297956
EM: Round [763] log likelihood: -21901.296274
EM: Round [764] log likelihood: -21901.294596
EM: Round [765] log likelihood: -21901.292921
EM: Round [766] log likelihood: -21901.291249
EM: Round [767] log likelihood: -21901.289581
EM: Round [768] log likelihood: -21901.287917
EM: Round [769] log likelihood: -21901.286256
EM: Round [770] log likelihood: -21901.284598
EM: Round [771] log likelihood: -21901.282944
EM: Round [772] log likelihood: -21901.281293
EM: Round [773] log likelihood: -21901.279646
EM: Round [774] log likelihood: -21901.278002
EM: Round [775] log likelihood: -21901.276361
EM: Round [776] log likelihood: -21901.274724
EM: Round [777] log likelihood: -21901.273090
EM: Round [778] log likelihood: -21901.271460
EM: Round [779] log likelihood: -21901.269833
EM: Round [780] log likelihood: -21901.268209
EM: Round [781] log likelihood: -21901.266589
EM: Round [782] log likelihood: -21901.264972
EM: Round [783] log likelihood: -21901.263358
EM: Round [784] log likelihood: -21901.261748
EM: Round [785] log likelihood: -21901.260141
EM: Round [786] log likelihood: -21901.258537
EM: Round [787] log likelihood: -21901.256937
EM: Round [788] log likelihood: -21901.255340
EM: Round [789] log likelihood: -21901.253746
EM: Round [790] log likelihood: -21901.252155
EM: Round [791] log likelihood: -21901.250568
EM: Round [792] log likelihood: -21901.248984
EM: Round [793] log likelihood: -21901.247403
EM: Round [794] log likelihood: -21901.245825
EM: Round [795] log likelihood: -21901.244251
EM: Round [796] log likelihood: -21901.242680
EM: Round [797] log likelihood: -21901.241112
EM: Round [798] log likelihood: -21901.239547
EM: Round [799] log likelihood: -21901.237986
EM: Round [800] log likelihood: -21901.236427
EM: Round [801] log likelihood: -21901.234872
EM: Round [802] log likelihood: -21901.233320
EM: Round [803] log likelihood: -21901.231771
EM: Round [804] log likelihood: -21901.230225
EM: Round [805] log likelihood: -21901.228683
EM: Round [806] log likelihood: -21901.227143
EM: Round [807] log likelihood: -21901.225607
EM: Round [808] log likelihood: -21901.224074
EM: Round [809] log likelihood: -21901.222544
EM: Round [810] log likelihood: -21901.221017
EM: Round [811] log likelihood: -21901.219493
EM: Round [812] log likelihood: -21901.217972
EM: Round [813] log likelihood: -21901.216455
EM: Round [814] log likelihood: -21901.214940
EM: Round [815] log likelihood: -21901.213429
EM: Round [816] log likelihood: -21901.211920
EM: Round [817] log likelihood: -21901.210415
EM: Round [818] log likelihood: -21901.208912
EM: Round [819] log likelihood: -21901.207413
EM: Round [820] log likelihood: -21901.205917
EM: Round [821] log likelihood: -21901.204424
EM: Round [822] log likelihood: -21901.202933
EM: Round [823] log likelihood: -21901.201446
EM: Round [824] log likelihood: -21901.199962
EM: Round [825] log likelihood: -21901.198480
EM: Round [826] log likelihood: -21901.197002
EM: Round [827] log likelihood: -21901.195527
EM: Round [828] log likelihood: -21901.194055
EM: Round [829] log likelihood: -21901.192585
EM: Round [830] log likelihood: -21901.191119
EM: Round [831] log likelihood: -21901.189655
EM: Round [832] log likelihood: -21901.188195
EM: Round [833] log likelihood: -21901.186737
EM: Round [834] log likelihood: -21901.185282
EM: Round [835] log likelihood: -21901.183831
EM: Round [836] log likelihood: -21901.182382
EM: Round [837] log likelihood: -21901.180936
EM: Round [838] log likelihood: -21901.179493
EM: Round [839] log likelihood: -21901.178053
EM: Round [840] log likelihood: -21901.176615
EM: Round [841] log likelihood: -21901.175181
EM: Round [842] log likelihood: -21901.173749
EM: Round [843] log likelihood: -21901.172321
EM: Round [844] log likelihood: -21901.170895
EM: Round [845] log likelihood: -21901.169472
EM: Round [846] log likelihood: -21901.168052
EM: Round [847] log likelihood: -21901.166634
EM: Round [848] log likelihood: -21901.165220
EM: Round [849] log likelihood: -21901.163808
EM: Round [850] log likelihood: -21901.162399
EM: Round [851] log likelihood: -21901.160993
EM: Round [852] log likelihood: -21901.159590
EM: Round [853] log likelihood: -21901.158190
EM: Round [854] log likelihood: -21901.156792
EM: Round [855] log likelihood: -21901.155397
EM: Round [856] log likelihood: -21901.154005
EM: Round [857] log likelihood: -21901.152616
EM: Round [858] log likelihood: -21901.151229
EM: Round [859] log likelihood: -21901.149845
EM: Round [860] log likelihood: -21901.148464
EM: Round [861] log likelihood: -21901.147086
EM: Round [862] log likelihood: -21901.145710
EM: Round [863] log likelihood: -21901.144337
EM: Round [864] log likelihood: -21901.142967
EM: Round [865] log likelihood: -21901.141599
EM: Round [866] log likelihood: -21901.140234
EM: Round [867] log likelihood: -21901.138872
EM: Round [868] log likelihood: -21901.137513
EM: Round [869] log likelihood: -21901.136156
EM: Round [870] log likelihood: -21901.134802
EM: Round [871] log likelihood: -21901.133451
EM: Round [872] log likelihood: -21901.132102
EM: Round [873] log likelihood: -21901.130756
EM: Round [874] log likelihood: -21901.129413
EM: Round [875] log likelihood: -21901.128072
EM: Round [876] log likelihood: -21901.126734
EM: Round [877] log likelihood: -21901.125398
EM: Round [878] log likelihood: -21901.124065
EM: Round [879] log likelihood: -21901.122735
EM: Round [880] log likelihood: -21901.121407
EM: Round [881] log likelihood: -21901.120082
EM: Round [882] log likelihood: -21901.118760
EM: Round [883] log likelihood: -21901.117440
EM: Round [884] log likelihood: -21901.116123
EM: Round [885] log likelihood: -21901.114808
EM: Round [886] log likelihood: -21901.113496
EM: Round [887] log likelihood: -21901.112187
EM: Round [888] log likelihood: -21901.110880
EM: Round [889] log likelihood: -21901.109575
EM: Round [890] log likelihood: -21901.108274
EM: Round [891] log likelihood: -21901.106974
EM: Round [892] log likelihood: -21901.105678
EM: Round [893] log likelihood: -21901.104383
EM: Round [894] log likelihood: -21901.103092
EM: Round [895] log likelihood: -21901.101802
EM: Round [896] log likelihood: -21901.100516
EM: Round [897] log likelihood: -21901.099232
EM: Round [898] log likelihood: -21901.097950
EM: Round [899] log likelihood: -21901.096671
EM: Round [900] log likelihood: -21901.095394
EM: Round [901] log likelihood: -21901.094120
EM: Round [902] log likelihood: -21901.092848
EM: Round [903] log likelihood: -21901.091579
EM: Round [904] log likelihood: -21901.090312
EM: Round [905] log likelihood: -21901.089048
EM: Round [906] log likelihood: -21901.087786
EM: Round [907] log likelihood: -21901.086527
EM: Round [908] log likelihood: -21901.085270
EM: Round [909] log likelihood: -21901.084016
EM: Round [910] log likelihood: -21901.082763
EM: Round [911] log likelihood: -21901.081514
EM: Round [912] log likelihood: -21901.080267
EM: Round [913] log likelihood: -21901.079022
EM: Round [914] log likelihood: -21901.077779
EM: Round [915] log likelihood: -21901.076540
EM: Round [916] log likelihood: -21901.075302
EM: Round [917] log likelihood: -21901.074067
EM: Round [918] log likelihood: -21901.072834
EM: Round [919] log likelihood: -21901.071604
EM: Round [920] log likelihood: -21901.070376
EM: Round [921] log likelihood: -21901.069150
EM: Round [922] log likelihood: -21901.067927
EM: Round [923] log likelihood: -21901.066706
EM: Round [924] log likelihood: -21901.065487
EM: Round [925] log likelihood: -21901.064271
EM: Round [926] log likelihood: -21901.063057
EM: Round [927] log likelihood: -21901.061845
EM: Round [928] log likelihood: -21901.060636
EM: Round [929] log likelihood: -21901.059429
EM: Round [930] log likelihood: -21901.058225
EM: Round [931] log likelihood: -21901.057022
EM: Round [932] log likelihood: -21901.055822
EM: Round [933] log likelihood: -21901.054625
EM: Round [934] log likelihood: -21901.053430
EM: Round [935] log likelihood: -21901.052236
EM: Round [936] log likelihood: -21901.051046
EM: Round [937] log likelihood: -21901.049857
EM: Round [938] log likelihood: -21901.048671
EM: Round [939] log likelihood: -21901.047487
EM: Round [940] log likelihood: -21901.046306
EM: Round [941] log likelihood: -21901.045126
EM: Round [942] log likelihood: -21901.043949
EM: Round [943] log likelihood: -21901.042774
EM: Round [944] log likelihood: -21901.041602
EM: Round [945] log likelihood: -21901.040431
EM: Round [946] log likelihood: -21901.039263
EM: Round [947] log likelihood: -21901.038097
EM: Round [948] log likelihood: -21901.036933
EM: Round [949] log likelihood: -21901.035772
EM: Round [950] log likelihood: -21901.034613
EM: Round [951] log likelihood: -21901.033456
EM: Round [952] log likelihood: -21901.032301
EM: Round [953] log likelihood: -21901.031148
EM: Round [954] log likelihood: -21901.029998
EM: Round [955] log likelihood: -21901.028850
EM: Round [956] log likelihood: -21901.027704
EM: Round [957] log likelihood: -21901.026560
EM: Round [958] log likelihood: -21901.025418
EM: Round [959] log likelihood: -21901.024278
EM: Round [960] log likelihood: -21901.023141
EM: Round [961] log likelihood: -21901.022006
EM: Round [962] log likelihood: -21901.020873
EM: Round [963] log likelihood: -21901.019742
EM: Round [964] log likelihood: -21901.018613
EM: Round [965] log likelihood: -21901.017487
EM: Round [966] log likelihood: -21901.016362
EM: Round [967] log likelihood: -21901.015240
EM: Round [968] log likelihood: -21901.014120
EM: Round [969] log likelihood: -21901.013002
EM: Round [970] log likelihood: -21901.011886
EM: Round [971] log likelihood: -21901.010772
EM: Round [972] log likelihood: -21901.009660
EM: Round [973] log likelihood: -21901.008551
EM: Round [974] log likelihood: -21901.007443
EM: Round [975] log likelihood: -21901.006338
EM: Round [976] log likelihood: -21901.005234
EM: Round [977] log likelihood: -21901.004133
EM: Round [978] log likelihood: -21901.003034
EM: Round [979] log likelihood: -21901.001937
EM: Round [980] log likelihood: -21901.000842
EM: Round [981] log likelihood: -21900.999749
EM: Round [982] log likelihood: -21900.998658
EM: Round [983] log likelihood: -21900.997569
EM: Round [984] log likelihood: -21900.996482
EM: Round [985] log likelihood: -21900.995397
EM: Round [986] log likelihood: -21900.994315
EM: Round [987] log likelihood: -21900.993234
EM: Round [988] log likelihood: -21900.992155
EM: Round [989] log likelihood: -21900.991079
EM: Round [990] log likelihood: -21900.990004
EM: Round [991] log likelihood: -21900.988932
EM: Round [992] log likelihood: -21900.987861
EM: Round [993] log likelihood: -21900.986792
EM: Round [994] log likelihood: -21900.985726
EM: Round [995] log likelihood: -21900.984661
EM: Round [996] log likelihood: -21900.983599
EM: Round [997] log likelihood: -21900.982538
EM: Round [998] log likelihood: -21900.981480
EM: Round [999] log likelihood: -21900.980423
EM: Round [1000] log likelihood: -21900.979369
EM: Round [1001] log likelihood: -21900.978316
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam into /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.e487RzRTjW/Hs746T_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.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords > /tmp/nxf.e487RzRTjW/Hs746T_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.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.e487RzRTjW/Hs746T_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.e487RzRTjW/fi_workdir/Hs746T_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.e487RzRTjW/fi_workdir/Hs746T_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.e487RzRTjW/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -21223.674809
EM: Round [1] log likelihood: -21222.676840
EM: Round [2] log likelihood: -21222.631061
EM: Round [3] log likelihood: -21222.596451
EM: Round [4] log likelihood: -21222.567885
EM: Round [5] log likelihood: -21222.543016
EM: Round [6] log likelihood: -21222.520433
EM: Round [7] log likelihood: -21222.499284
EM: Round [8] log likelihood: -21222.479054
EM: Round [9] log likelihood: -21222.459435
EM: Round [10] log likelihood: -21222.440242
EM: Round [11] log likelihood: -21222.421361
EM: Round [12] log likelihood: -21222.402725
EM: Round [13] log likelihood: -21222.384294
EM: Round [14] log likelihood: -21222.366042
EM: Round [15] log likelihood: -21222.347952
EM: Round [16] log likelihood: -21222.330015
EM: Round [17] log likelihood: -21222.312224
EM: Round [18] log likelihood: -21222.294573
EM: Round [19] log likelihood: -21222.277060
EM: Round [20] log likelihood: -21222.259681
EM: Round [21] log likelihood: -21222.242433
EM: Round [22] log likelihood: -21222.225315
EM: Round [23] log likelihood: -21222.208325
EM: Round [24] log likelihood: -21222.191460
EM: Round [25] log likelihood: -21222.174719
EM: Round [26] log likelihood: -21222.158101
EM: Round [27] log likelihood: -21222.141602
EM: Round [28] log likelihood: -21222.125223
EM: Round [29] log likelihood: -21222.108960
EM: Round [30] log likelihood: -21222.092813
EM: Round [31] log likelihood: -21222.076780
EM: Round [32] log likelihood: -21222.060860
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EM: Round [951] log likelihood: -21218.189869
EM: Round [952] log likelihood: -21218.188765
EM: Round [953] log likelihood: -21218.187663
EM: Round [954] log likelihood: -21218.186563
EM: Round [955] log likelihood: -21218.185465
EM: Round [956] log likelihood: -21218.184370
EM: Round [957] log likelihood: -21218.183276
EM: Round [958] log likelihood: -21218.182184
EM: Round [959] log likelihood: -21218.181095
EM: Round [960] log likelihood: -21218.180007
EM: Round [961] log likelihood: -21218.178922
EM: Round [962] log likelihood: -21218.177838
EM: Round [963] log likelihood: -21218.176756
EM: Round [964] log likelihood: -21218.175677
EM: Round [965] log likelihood: -21218.174599
EM: Round [966] log likelihood: -21218.173524
EM: Round [967] log likelihood: -21218.172450
EM: Round [968] log likelihood: -21218.171379
EM: Round [969] log likelihood: -21218.170309
EM: Round [970] log likelihood: -21218.169241
EM: Round [971] log likelihood: -21218.168176
EM: Round [972] log likelihood: -21218.167112
EM: Round [973] log likelihood: -21218.166050
EM: Round [974] log likelihood: -21218.164991
EM: Round [975] log likelihood: -21218.163933
EM: Round [976] log likelihood: -21218.162877
EM: Round [977] log likelihood: -21218.161823
EM: Round [978] log likelihood: -21218.160771
EM: Round [979] log likelihood: -21218.159721
EM: Round [980] log likelihood: -21218.158673
EM: Round [981] log likelihood: -21218.157627
EM: Round [982] log likelihood: -21218.156583
EM: Round [983] log likelihood: -21218.155541
EM: Round [984] log likelihood: -21218.154500
EM: Round [985] log likelihood: -21218.153462
EM: Round [986] log likelihood: -21218.152425
EM: Round [987] log likelihood: -21218.151390
EM: Round [988] log likelihood: -21218.150358
EM: Round [989] log likelihood: -21218.149327
EM: Round [990] log likelihood: -21218.148298
EM: Round [991] log likelihood: -21218.147271
EM: Round [992] log likelihood: -21218.146246
EM: Round [993] log likelihood: -21218.145222
EM: Round [994] log likelihood: -21218.144201
EM: Round [995] log likelihood: -21218.143181
EM: Round [996] log likelihood: -21218.142164
EM: Round [997] log likelihood: -21218.141148
EM: Round [998] log likelihood: -21218.140134
EM: Round [999] log likelihood: -21218.139122
EM: Round [1000] log likelihood: -21218.138112
EM: Round [1001] log likelihood: -21218.137103
-total frags in /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz: 294765771
Warning - not locating file: /tmp/nxf.e487RzRTjW/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000231365.6]
WARNING, no entry stored in dbm for [ENSG00000231365.6]
WARNING, no entry stored in dbm for [ENSG00000231365.6]
WARNING, no entry stored in dbm for [ENSG00000230534.6]
WARNING, no entry stored in dbm for [ENSG00000216829.6]
WARNING, no entry stored in dbm for [ENSG00000216829.6]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000229180.7]
WARNING, no entry stored in dbm for [ENSG00000229180.7]
WARNING, no entry stored in dbm for [ENSG00000227681.5]
WARNING, no entry stored in dbm for [ENSG00000227681.5]
WARNING, no entry stored in dbm for [ENSG00000227681.5]
WARNING, no entry stored in dbm for [ENSG00000227681.5]
WARNING, no entry stored in dbm for [ENSG00000227681.5]
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 [ENSG00000267052.3]
WARNING, no entry stored in dbm for [ENSG00000267052.3]
WARNING, no entry stored in dbm for [ENSG00000267052.3]
WARNING, no entry stored in dbm for [ENSG00000237813.4]
WARNING, no entry stored in dbm for [ENSG00000237813.4]
WARNING, no entry stored in dbm for [ENSG00000237813.4]
WARNING, no entry stored in dbm for [ENSG00000243797.6]
WARNING, no entry stored in dbm for [ENSG00000243797.6]
WARNING, no entry stored in dbm for [ENSG00000243797.6]
WARNING, no entry stored in dbm for [ENSG00000243797.6]
WARNING, no entry stored in dbm for [ENSG00000232386.9]
WARNING, no entry stored in dbm for [ENSG00000232386.9]
WARNING, no entry stored in dbm for [ENSG00000236031.1]
WARNING, no entry stored in dbm for [ENSG00000236197.4]
ls: cannot access 'IGV_inputs': No such file or directory