Done.
-parsing GTF file: /tmp/nxf.UnzyqYWreQ/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.UnzyqYWreQ/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.UnzyqYWreQ/786-O_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.UnzyqYWreQ/786-O_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.UnzyqYWreQ/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.UnzyqYWreQ/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam
* Running CMD: samtools index 786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam
00:27:43 : INFO : Done.
-parsing GTF file: /tmp/nxf.UnzyqYWreQ/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gtf
-parsing /tmp/nxf.UnzyqYWreQ/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam

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[2360000]   -done parsing /tmp/nxf.UnzyqYWreQ/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 6,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 463,
          'small anchor length' => 277,
          'excessive soft clipping' => 15273,
          ' ** passed ** ' => 47523,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 9,
          'per_id < 96' => 13903,
          'exons hit < 2' => 13,
          'num genes matched < 2' => 14,
          'seq-similar region overlap' => 28,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 16,
          'low complexity anchor region' => 26
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.UnzyqYWreQ/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[159000]   -fusion SPANNING read extraction for scaff: AC008969.1--SMARCA4

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[38000]   -fusion SPANNING read extraction for scaff: ARHGEF3--RRP9

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[33000]   -fusion SPANNING read extraction for scaff: ATAD2B--KLHL29

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[47000]   -fusion SPANNING read extraction for scaff: BNC2--AL358117.1

[1000]   -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2

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[34000]   -fusion SPANNING read extraction for scaff: CENPU--ENPP6

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[70000]   -fusion SPANNING read extraction for scaff: DHX38--AMPD1

[1000]   -fusion SPANNING read extraction for scaff: GTF2A1L--STON1-GTF2A1L

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[18000]   -fusion SPANNING read extraction for scaff: GUSBP13--NAIP

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[267000]   -fusion SPANNING read extraction for scaff: HIF1A--SNAPC1

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[38000]   -fusion SPANNING read extraction for scaff: HMGB3P23--ACO1

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[15000]   -fusion SPANNING read extraction for scaff: LHCGR--STON1

[1000]   -fusion SPANNING read extraction for scaff: LHCGR--GTF2A1L

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[772000]   
[773000]   -fusion SPANNING read extraction for scaff: LMNA--MEX3A

[1000]   
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[194000]   
[195000]   -fusion SPANNING read extraction for scaff: LRP1B--AC078882.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
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[8000]   
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[30000]   
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[32000]   
[33000]   
[34000]   -fusion SPANNING read extraction for scaff: MTAP--AL157937.1

[1000]   
[2000]   
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[4000]   
[5000]   
[6000]   
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[8000]   
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[25000]   
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[27000]   
[28000]   
[29000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[14000]   
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[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
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[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
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[12000]   
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[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[1000]   
[2000]   
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[5000]   
[6000]   
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[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
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[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
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[71000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[219000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[39000]   -fusion SPANNING read extraction for scaff: RNA5SP281--ACO1

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[14000]   -fusion SPANNING read extraction for scaff: TAS2R14--PRH2

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[36000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[39000]   -fusion SPANNING read extraction for scaff: TMED7--TICAM2

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[21000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[23000]   -fusion SPANNING read extraction for scaff: ZKSCAN7--KIF15
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 30926,
          'seq similar region alignment' => 16635
        };
EM: Starting log likelihood: -9094.063994
EM: Round [1] log likelihood: -9092.960778
EM: Round [2] log likelihood: -9092.956805
EM: Round [3] log likelihood: -9092.953158
EM: Round [4] log likelihood: -9092.949527
EM: Round [5] log likelihood: -9092.945910
EM: Round [6] log likelihood: -9092.942308
EM: Round [7] log likelihood: -9092.938721
EM: Round [8] log likelihood: -9092.935147
EM: Round [9] log likelihood: -9092.931588
EM: Round [10] log likelihood: -9092.928043
EM: Round [11] log likelihood: -9092.924512
EM: Round [12] log likelihood: -9092.920995
EM: Round [13] log likelihood: -9092.917491
EM: Round [14] log likelihood: -9092.914001
EM: Round [15] log likelihood: -9092.910525
EM: Round [16] log likelihood: -9092.907062
EM: Round [17] log likelihood: -9092.903613
EM: Round [18] log likelihood: -9092.900177
EM: Round [19] log likelihood: -9092.896754
EM: Round [20] log likelihood: -9092.893344
EM: Round [21] log likelihood: -9092.889947
EM: Round [22] log likelihood: -9092.886563
EM: Round [23] log likelihood: -9092.883191
EM: Round [24] log likelihood: -9092.879833
EM: Round [25] log likelihood: -9092.876487
EM: Round [26] log likelihood: -9092.873153
EM: Round [27] log likelihood: -9092.869832
EM: Round [28] log likelihood: -9092.866524
EM: Round [29] log likelihood: -9092.863227
EM: Round [30] log likelihood: -9092.859943
EM: Round [31] log likelihood: -9092.856671
EM: Round [32] log likelihood: -9092.853411
EM: Round [33] log likelihood: -9092.850163
EM: Round [34] log likelihood: -9092.846927
EM: Round [35] log likelihood: -9092.843702
EM: Round [36] log likelihood: -9092.840489
EM: Round [37] log likelihood: -9092.837288
EM: Round [38] log likelihood: -9092.834098
EM: Round [39] log likelihood: -9092.830920
EM: Round [40] log likelihood: -9092.827753
EM: Round [41] log likelihood: -9092.824597
EM: Round [42] log likelihood: -9092.821453
EM: Round [43] log likelihood: -9092.818320
EM: Round [44] log likelihood: -9092.815197
EM: Round [45] log likelihood: -9092.812086
EM: Round [46] log likelihood: -9092.808986
EM: Round [47] log likelihood: -9092.805897
EM: Round [48] log likelihood: -9092.802818
EM: Round [49] log likelihood: -9092.799750
EM: Round [50] log likelihood: -9092.796693
EM: Round [51] log likelihood: -9092.793646
EM: Round [52] log likelihood: -9092.790610
EM: Round [53] log likelihood: -9092.787584
EM: Round [54] log likelihood: -9092.784568
EM: Round [55] log likelihood: -9092.781563
EM: Round [56] log likelihood: -9092.778568
EM: Round [57] log likelihood: -9092.775584
EM: Round [58] log likelihood: -9092.772609
EM: Round [59] log likelihood: -9092.769644
EM: Round [60] log likelihood: -9092.766690
EM: Round [61] log likelihood: -9092.763745
EM: Round [62] log likelihood: -9092.760810
EM: Round [63] log likelihood: -9092.757885
EM: Round [64] log likelihood: -9092.754970
EM: Round [65] log likelihood: -9092.752064
EM: Round [66] log likelihood: -9092.749168
EM: Round [67] log likelihood: -9092.746281
EM: Round [68] log likelihood: -9092.743404
EM: Round [69] log likelihood: -9092.740537
EM: Round [70] log likelihood: -9092.737678
EM: Round [71] log likelihood: -9092.734830
EM: Round [72] log likelihood: -9092.731990
EM: Round [73] log likelihood: -9092.729159
EM: Round [74] log likelihood: -9092.726338
EM: Round [75] log likelihood: -9092.723526
EM: Round [76] log likelihood: -9092.720723
EM: Round [77] log likelihood: -9092.717929
EM: Round [78] log likelihood: -9092.715143
EM: Round [79] log likelihood: -9092.712367
EM: Round [80] log likelihood: -9092.709599
EM: Round [81] log likelihood: -9092.706840
EM: Round [82] log likelihood: -9092.704090
EM: Round [83] log likelihood: -9092.701349
EM: Round [84] log likelihood: -9092.698616
EM: Round [85] log likelihood: -9092.695892
EM: Round [86] log likelihood: -9092.693176
EM: Round [87] log likelihood: -9092.690469
EM: Round [88] log likelihood: -9092.687770
EM: Round [89] log likelihood: -9092.685080
EM: Round [90] log likelihood: -9092.682398
EM: Round [91] log likelihood: -9092.679724
EM: Round [92] log likelihood: -9092.677058
EM: Round [93] log likelihood: -9092.674401
EM: Round [94] log likelihood: -9092.671751
EM: Round [95] log likelihood: -9092.669110
EM: Round [96] log likelihood: -9092.666477
EM: Round [97] log likelihood: -9092.663852
EM: Round [98] log likelihood: -9092.661234
EM: Round [99] log likelihood: -9092.658625
EM: Round [100] log likelihood: -9092.656023
EM: Round [101] log likelihood: -9092.653430
EM: Round [102] log likelihood: -9092.650844
EM: Round [103] log likelihood: -9092.648266
EM: Round [104] log likelihood: -9092.645695
EM: Round [105] log likelihood: -9092.643132
EM: Round [106] log likelihood: -9092.640577
EM: Round [107] log likelihood: -9092.638029
EM: Round [108] log likelihood: -9092.635489
EM: Round [109] log likelihood: -9092.632956
EM: Round [110] log likelihood: -9092.630431
EM: Round [111] log likelihood: -9092.627913
EM: Round [112] log likelihood: -9092.625403
EM: Round [113] log likelihood: -9092.622899
EM: Round [114] log likelihood: -9092.620403
EM: Round [115] log likelihood: -9092.617915
EM: Round [116] log likelihood: -9092.615433
EM: Round [117] log likelihood: -9092.612959
EM: Round [118] log likelihood: -9092.610492
EM: Round [119] log likelihood: -9092.608031
EM: Round [120] log likelihood: -9092.605578
EM: Round [121] log likelihood: -9092.603132
EM: Round [122] log likelihood: -9092.600693
EM: Round [123] log likelihood: -9092.598261
EM: Round [124] log likelihood: -9092.595836
EM: Round [125] log likelihood: -9092.593417
EM: Round [126] log likelihood: -9092.591006
EM: Round [127] log likelihood: -9092.588601
EM: Round [128] log likelihood: -9092.586203
EM: Round [129] log likelihood: -9092.583811
EM: Round [130] log likelihood: -9092.581427
EM: Round [131] log likelihood: -9092.579049
EM: Round [132] log likelihood: -9092.576677
EM: Round [133] log likelihood: -9092.574312
EM: Round [134] log likelihood: -9092.571954
EM: Round [135] log likelihood: -9092.569602
EM: Round [136] log likelihood: -9092.567257
EM: Round [137] log likelihood: -9092.564918
EM: Round [138] log likelihood: -9092.562586
EM: Round [139] log likelihood: -9092.560260
EM: Round [140] log likelihood: -9092.557940
EM: Round [141] log likelihood: -9092.555627
EM: Round [142] log likelihood: -9092.553320
EM: Round [143] log likelihood: -9092.551019
EM: Round [144] log likelihood: -9092.548724
EM: Round [145] log likelihood: -9092.546436
EM: Round [146] log likelihood: -9092.544154
EM: Round [147] log likelihood: -9092.541877
EM: Round [148] log likelihood: -9092.539607
EM: Round [149] log likelihood: -9092.537343
EM: Round [150] log likelihood: -9092.535086
EM: Round [151] log likelihood: -9092.532834
EM: Round [152] log likelihood: -9092.530588
EM: Round [153] log likelihood: -9092.528348
EM: Round [154] log likelihood: -9092.526114
EM: Round [155] log likelihood: -9092.523886
EM: Round [156] log likelihood: -9092.521663
EM: Round [157] log likelihood: -9092.519447
EM: Round [158] log likelihood: -9092.517236
EM: Round [159] log likelihood: -9092.515031
EM: Round [160] log likelihood: -9092.512832
EM: Round [161] log likelihood: -9092.510639
EM: Round [162] log likelihood: -9092.508451
EM: Round [163] log likelihood: -9092.506269
EM: Round [164] log likelihood: -9092.504093
EM: Round [165] log likelihood: -9092.501922
EM: Round [166] log likelihood: -9092.499757
EM: Round [167] log likelihood: -9092.497598
EM: Round [168] log likelihood: -9092.495443
EM: Round [169] log likelihood: -9092.493295
EM: Round [170] log likelihood: -9092.491152
EM: Round [171] log likelihood: -9092.489014
EM: Round [172] log likelihood: -9092.486882
EM: Round [173] log likelihood: -9092.484755
EM: Round [174] log likelihood: -9092.482634
EM: Round [175] log likelihood: -9092.480518
EM: Round [176] log likelihood: -9092.478407
EM: Round [177] log likelihood: -9092.476302
EM: Round [178] log likelihood: -9092.474202
EM: Round [179] log likelihood: -9092.472107
EM: Round [180] log likelihood: -9092.470018
EM: Round [181] log likelihood: -9092.467933
EM: Round [182] log likelihood: -9092.465854
EM: Round [183] log likelihood: -9092.463780
EM: Round [184] log likelihood: -9092.461711
EM: Round [185] log likelihood: -9092.459648
EM: Round [186] log likelihood: -9092.457589
EM: Round [187] log likelihood: -9092.455535
EM: Round [188] log likelihood: -9092.453487
EM: Round [189] log likelihood: -9092.451443
EM: Round [190] log likelihood: -9092.449405
EM: Round [191] log likelihood: -9092.447371
EM: Round [192] log likelihood: -9092.445343
EM: Round [193] log likelihood: -9092.443319
EM: Round [194] log likelihood: -9092.441300
EM: Round [195] log likelihood: -9092.439287
EM: Round [196] log likelihood: -9092.437278
EM: Round [197] log likelihood: -9092.435274
EM: Round [198] log likelihood: -9092.433274
EM: Round [199] log likelihood: -9092.431280
EM: Round [200] log likelihood: -9092.429290
EM: Round [201] log likelihood: -9092.427305
EM: Round [202] log likelihood: -9092.425325
EM: Round [203] log likelihood: -9092.423350
EM: Round [204] log likelihood: -9092.421379
EM: Round [205] log likelihood: -9092.419413
EM: Round [206] log likelihood: -9092.417452
EM: Round [207] log likelihood: -9092.415495
EM: Round [208] log likelihood: -9092.413543
EM: Round [209] log likelihood: -9092.411595
EM: Round [210] log likelihood: -9092.409653
EM: Round [211] log likelihood: -9092.407714
EM: Round [212] log likelihood: -9092.405780
EM: Round [213] log likelihood: -9092.403851
EM: Round [214] log likelihood: -9092.401926
EM: Round [215] log likelihood: -9092.400006
EM: Round [216] log likelihood: -9092.398090
EM: Round [217] log likelihood: -9092.396179
EM: Round [218] log likelihood: -9092.394272
EM: Round [219] log likelihood: -9092.392369
EM: Round [220] log likelihood: -9092.390471
EM: Round [221] log likelihood: -9092.388577
EM: Round [222] log likelihood: -9092.386688
EM: Round [223] log likelihood: -9092.384803
EM: Round [224] log likelihood: -9092.382922
EM: Round [225] log likelihood: -9092.381046
EM: Round [226] log likelihood: -9092.379173
EM: Round [227] log likelihood: -9092.377306
EM: Round [228] log likelihood: -9092.375442
EM: Round [229] log likelihood: -9092.373582
EM: Round [230] log likelihood: -9092.371727
EM: Round [231] log likelihood: -9092.369876
EM: Round [232] log likelihood: -9092.368029
EM: Round [233] log likelihood: -9092.366187
EM: Round [234] log likelihood: -9092.364348
EM: Round [235] log likelihood: -9092.362514
EM: Round [236] log likelihood: -9092.360683
EM: Round [237] log likelihood: -9092.358857
EM: Round [238] log likelihood: -9092.357035
EM: Round [239] log likelihood: -9092.355217
EM: Round [240] log likelihood: -9092.353403
EM: Round [241] log likelihood: -9092.351593
EM: Round [242] log likelihood: -9092.349787
EM: Round [243] log likelihood: -9092.347985
EM: Round [244] log likelihood: -9092.346187
EM: Round [245] log likelihood: -9092.344393
EM: Round [246] log likelihood: -9092.342603
EM: Round [247] log likelihood: -9092.340817
EM: Round [248] log likelihood: -9092.339035
EM: Round [249] log likelihood: -9092.337256
EM: Round [250] log likelihood: -9092.335482
EM: Round [251] log likelihood: -9092.333711
EM: Round [252] log likelihood: -9092.331944
EM: Round [253] log likelihood: -9092.330181
EM: Round [254] log likelihood: -9092.328422
EM: Round [255] log likelihood: -9092.326667
EM: Round [256] log likelihood: -9092.324916
EM: Round [257] log likelihood: -9092.323168
EM: Round [258] log likelihood: -9092.321424
EM: Round [259] log likelihood: -9092.319684
EM: Round [260] log likelihood: -9092.317947
EM: Round [261] log likelihood: -9092.316215
EM: Round [262] log likelihood: -9092.314486
EM: Round [263] log likelihood: -9092.312760
EM: Round [264] log likelihood: -9092.311039
EM: Round [265] log likelihood: -9092.309321
EM: Round [266] log likelihood: -9092.307606
EM: Round [267] log likelihood: -9092.305896
EM: Round [268] log likelihood: -9092.304189
EM: Round [269] log likelihood: -9092.302485
EM: Round [270] log likelihood: -9092.300785
EM: Round [271] log likelihood: -9092.299089
EM: Round [272] log likelihood: -9092.297396
EM: Round [273] log likelihood: -9092.295707
EM: Round [274] log likelihood: -9092.294022
EM: Round [275] log likelihood: -9092.292340
EM: Round [276] log likelihood: -9092.290661
EM: Round [277] log likelihood: -9092.288986
EM: Round [278] log likelihood: -9092.287314
EM: Round [279] log likelihood: -9092.285646
EM: Round [280] log likelihood: -9092.283982
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EM: Round [742] log likelihood: -9091.753503
EM: Round [743] log likelihood: -9091.752694
EM: Round [744] log likelihood: -9091.751887
EM: Round [745] log likelihood: -9091.751080
EM: Round [746] log likelihood: -9091.750274
EM: Round [747] log likelihood: -9091.749469
EM: Round [748] log likelihood: -9091.748666
EM: Round [749] log likelihood: -9091.747863
EM: Round [750] log likelihood: -9091.747061
EM: Round [751] log likelihood: -9091.746260
EM: Round [752] log likelihood: -9091.745460
EM: Round [753] log likelihood: -9091.744661
EM: Round [754] log likelihood: -9091.743863
EM: Round [755] log likelihood: -9091.743066
EM: Round [756] log likelihood: -9091.742270
EM: Round [757] log likelihood: -9091.741475
EM: Round [758] log likelihood: -9091.740681
EM: Round [759] log likelihood: -9091.739888
EM: Round [760] log likelihood: -9091.739096
EM: Round [761] log likelihood: -9091.738305
EM: Round [762] log likelihood: -9091.737514
EM: Round [763] log likelihood: -9091.736725
EM: Round [764] log likelihood: -9091.735937
EM: Round [765] log likelihood: -9091.735149
EM: Round [766] log likelihood: -9091.734363
EM: Round [767] log likelihood: -9091.733577
EM: Round [768] log likelihood: -9091.732793
EM: Round [769] log likelihood: -9091.732009
EM: Round [770] log likelihood: -9091.731226
EM: Round [771] log likelihood: -9091.730444
EM: Round [772] log likelihood: -9091.729663
EM: Round [773] log likelihood: -9091.728883
EM: Round [774] log likelihood: -9091.728104
EM: Round [775] log likelihood: -9091.727326
EM: Round [776] log likelihood: -9091.726549
EM: Round [777] log likelihood: -9091.725773
EM: Round [778] log likelihood: -9091.724998
EM: Round [779] log likelihood: -9091.724223
EM: Round [780] log likelihood: -9091.723450
EM: Round [781] log likelihood: -9091.722677
EM: Round [782] log likelihood: -9091.721905
EM: Round [783] log likelihood: -9091.721135
EM: Round [784] log likelihood: -9091.720365
EM: Round [785] log likelihood: -9091.719596
EM: Round [786] log likelihood: -9091.718828
EM: Round [787] log likelihood: -9091.718061
EM: Round [788] log likelihood: -9091.717294
EM: Round [789] log likelihood: -9091.716529
EM: Round [790] log likelihood: -9091.715765
EM: Round [791] log likelihood: -9091.715001
EM: Round [792] log likelihood: -9091.714239
EM: Round [793] log likelihood: -9091.713477
EM: Round [794] log likelihood: -9091.712716
EM: Round [795] log likelihood: -9091.711956
EM: Round [796] log likelihood: -9091.711197
EM: Round [797] log likelihood: -9091.710439
EM: Round [798] log likelihood: -9091.709681
EM: Round [799] log likelihood: -9091.708925
EM: Round [800] log likelihood: -9091.708170
EM: Round [801] log likelihood: -9091.707415
EM: Round [802] log likelihood: -9091.706661
EM: Round [803] log likelihood: -9091.705908
EM: Round [804] log likelihood: -9091.705156
EM: Round [805] log likelihood: -9091.704405
EM: Round [806] log likelihood: -9091.703655
EM: Round [807] log likelihood: -9091.702905
EM: Round [808] log likelihood: -9091.702157
EM: Round [809] log likelihood: -9091.701409
EM: Round [810] log likelihood: -9091.700662
EM: Round [811] log likelihood: -9091.699916
EM: Round [812] log likelihood: -9091.699171
EM: Round [813] log likelihood: -9091.698427
EM: Round [814] log likelihood: -9091.697684
EM: Round [815] log likelihood: -9091.696941
EM: Round [816] log likelihood: -9091.696200
EM: Round [817] log likelihood: -9091.695459
EM: Round [818] log likelihood: -9091.694719
EM: Round [819] log likelihood: -9091.693980
EM: Round [820] log likelihood: -9091.693242
EM: Round [821] log likelihood: -9091.692504
EM: Round [822] log likelihood: -9091.691768
EM: Round [823] log likelihood: -9091.691032
EM: Round [824] log likelihood: -9091.690297
EM: Round [825] log likelihood: -9091.689563
EM: Round [826] log likelihood: -9091.688830
EM: Round [827] log likelihood: -9091.688098
EM: Round [828] log likelihood: -9091.687366
EM: Round [829] log likelihood: -9091.686636
EM: Round [830] log likelihood: -9091.685906
EM: Round [831] log likelihood: -9091.685177
EM: Round [832] log likelihood: -9091.684449
EM: Round [833] log likelihood: -9091.683721
EM: Round [834] log likelihood: -9091.682995
EM: Round [835] log likelihood: -9091.682269
EM: Round [836] log likelihood: -9091.681544
EM: Round [837] log likelihood: -9091.680820
EM: Round [838] log likelihood: -9091.680097
EM: Round [839] log likelihood: -9091.679374
EM: Round [840] log likelihood: -9091.678653
EM: Round [841] log likelihood: -9091.677932
EM: Round [842] log likelihood: -9091.677212
EM: Round [843] log likelihood: -9091.676493
EM: Round [844] log likelihood: -9091.675775
EM: Round [845] log likelihood: -9091.675057
EM: Round [846] log likelihood: -9091.674340
EM: Round [847] log likelihood: -9091.673625
EM: Round [848] log likelihood: -9091.672909
EM: Round [849] log likelihood: -9091.672195
EM: Round [850] log likelihood: -9091.671482
EM: Round [851] log likelihood: -9091.670769
EM: Round [852] log likelihood: -9091.670057
EM: Round [853] log likelihood: -9091.669346
EM: Round [854] log likelihood: -9091.668636
EM: Round [855] log likelihood: -9091.667926
EM: Round [856] log likelihood: -9091.667218
EM: Round [857] log likelihood: -9091.666510
EM: Round [858] log likelihood: -9091.665803
EM: Round [859] log likelihood: -9091.665096
EM: Round [860] log likelihood: -9091.664391
EM: Round [861] log likelihood: -9091.663686
EM: Round [862] log likelihood: -9091.662982
EM: Round [863] log likelihood: -9091.662279
EM: Round [864] log likelihood: -9091.661576
EM: Round [865] log likelihood: -9091.660875
EM: Round [866] log likelihood: -9091.660174
EM: Round [867] log likelihood: -9091.659474
EM: Round [868] log likelihood: -9091.658775
EM: Round [869] log likelihood: -9091.658076
EM: Round [870] log likelihood: -9091.657378
EM: Round [871] log likelihood: -9091.656681
EM: Round [872] log likelihood: -9091.655985
EM: Round [873] log likelihood: -9091.655290
EM: Round [874] log likelihood: -9091.654595
EM: Round [875] log likelihood: -9091.653901
EM: Round [876] log likelihood: -9091.653208
EM: Round [877] log likelihood: -9091.652516
EM: Round [878] log likelihood: -9091.651824
EM: Round [879] log likelihood: -9091.651133
EM: Round [880] log likelihood: -9091.650443
EM: Round [881] log likelihood: -9091.649754
EM: Round [882] log likelihood: -9091.649066
EM: Round [883] log likelihood: -9091.648378
EM: Round [884] log likelihood: -9091.647691
EM: Round [885] log likelihood: -9091.647004
EM: Round [886] log likelihood: -9091.646319
EM: Round [887] log likelihood: -9091.645634
EM: Round [888] log likelihood: -9091.644950
EM: Round [889] log likelihood: -9091.644267
EM: Round [890] log likelihood: -9091.643584
EM: Round [891] log likelihood: -9091.642902
EM: Round [892] log likelihood: -9091.642221
EM: Round [893] log likelihood: -9091.641541
EM: Round [894] log likelihood: -9091.640862
EM: Round [895] log likelihood: -9091.640183
EM: Round [896] log likelihood: -9091.639505
EM: Round [897] log likelihood: -9091.638827
EM: Round [898] log likelihood: -9091.638151
EM: Round [899] log likelihood: -9091.637475
EM: Round [900] log likelihood: -9091.636800
EM: Round [901] log likelihood: -9091.636125
EM: Round [902] log likelihood: -9091.635452
EM: Round [903] log likelihood: -9091.634779
EM: Round [904] log likelihood: -9091.634107
EM: Round [905] log likelihood: -9091.633435
EM: Round [906] log likelihood: -9091.632764
EM: Round [907] log likelihood: -9091.632094
EM: Round [908] log likelihood: -9091.631425
EM: Round [909] log likelihood: -9091.630756
EM: Round [910] log likelihood: -9091.630088
EM: Round [911] log likelihood: -9091.629421
EM: Round [912] log likelihood: -9091.628755
EM: Round [913] log likelihood: -9091.628089
EM: Round [914] log likelihood: -9091.627424
EM: Round [915] log likelihood: -9091.626760
EM: Round [916] log likelihood: -9091.626096
EM: Round [917] log likelihood: -9091.625433
EM: Round [918] log likelihood: -9091.624771
EM: Round [919] log likelihood: -9091.624110
EM: Round [920] log likelihood: -9091.623449
EM: Round [921] log likelihood: -9091.622789
EM: Round [922] log likelihood: -9091.622130
EM: Round [923] log likelihood: -9091.621471
EM: Round [924] log likelihood: -9091.620813
EM: Round [925] log likelihood: -9091.620156
EM: Round [926] log likelihood: -9091.619500
EM: Round [927] log likelihood: -9091.618844
EM: Round [928] log likelihood: -9091.618189
EM: Round [929] log likelihood: -9091.617534
EM: Round [930] log likelihood: -9091.616881
EM: Round [931] log likelihood: -9091.616228
EM: Round [932] log likelihood: -9091.615575
EM: Round [933] log likelihood: -9091.614924
EM: Round [934] log likelihood: -9091.614273
EM: Round [935] log likelihood: -9091.613623
EM: Round [936] log likelihood: -9091.612973
EM: Round [937] log likelihood: -9091.612324
EM: Round [938] log likelihood: -9091.611676
EM: Round [939] log likelihood: -9091.611028
EM: Round [940] log likelihood: -9091.610382
EM: Round [941] log likelihood: -9091.609736
EM: Round [942] log likelihood: -9091.609090
EM: Round [943] log likelihood: -9091.608445
EM: Round [944] log likelihood: -9091.607801
EM: Round [945] log likelihood: -9091.607158
EM: Round [946] log likelihood: -9091.606515
EM: Round [947] log likelihood: -9091.605873
EM: Round [948] log likelihood: -9091.605232
EM: Round [949] log likelihood: -9091.604591
EM: Round [950] log likelihood: -9091.603951
EM: Round [951] log likelihood: -9091.603312
EM: Round [952] log likelihood: -9091.602673
EM: Round [953] log likelihood: -9091.602035
EM: Round [954] log likelihood: -9091.601398
EM: Round [955] log likelihood: -9091.600761
EM: Round [956] log likelihood: -9091.600125
EM: Round [957] log likelihood: -9091.599490
EM: Round [958] log likelihood: -9091.598855
EM: Round [959] log likelihood: -9091.598221
EM: Round [960] log likelihood: -9091.597588
EM: Round [961] log likelihood: -9091.596955
EM: Round [962] log likelihood: -9091.596323
EM: Round [963] log likelihood: -9091.595692
EM: Round [964] log likelihood: -9091.595061
EM: Round [965] log likelihood: -9091.594431
EM: Round [966] log likelihood: -9091.593801
EM: Round [967] log likelihood: -9091.593173
EM: Round [968] log likelihood: -9091.592544
EM: Round [969] log likelihood: -9091.591917
EM: Round [970] log likelihood: -9091.591290
EM: Round [971] log likelihood: -9091.590664
EM: Round [972] log likelihood: -9091.590039
EM: Round [973] log likelihood: -9091.589414
EM: Round [974] log likelihood: -9091.588790
EM: Round [975] log likelihood: -9091.588166
EM: Round [976] log likelihood: -9091.587543
EM: Round [977] log likelihood: -9091.586921
EM: Round [978] log likelihood: -9091.586299
EM: Round [979] log likelihood: -9091.585678
EM: Round [980] log likelihood: -9091.585058
EM: Round [981] log likelihood: -9091.584438
EM: Round [982] log likelihood: -9091.583819
EM: Round [983] log likelihood: -9091.583201
EM: Round [984] log likelihood: -9091.582583
EM: Round [985] log likelihood: -9091.581966
EM: Round [986] log likelihood: -9091.581349
EM: Round [987] log likelihood: -9091.580733
EM: Round [988] log likelihood: -9091.580118
EM: Round [989] log likelihood: -9091.579503
EM: Round [990] log likelihood: -9091.578889
EM: Round [991] log likelihood: -9091.578276
EM: Round [992] log likelihood: -9091.577663
EM: Round [993] log likelihood: -9091.577051
EM: Round [994] log likelihood: -9091.576440
EM: Round [995] log likelihood: -9091.575829
EM: Round [996] log likelihood: -9091.575219
EM: Round [997] log likelihood: -9091.574609
EM: Round [998] log likelihood: -9091.574000
EM: Round [999] log likelihood: -9091.573392
EM: Round [1000] log likelihood: -9091.572784
EM: Round [1001] log likelihood: -9091.572177
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.UnzyqYWreQ/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam into /tmp/nxf.UnzyqYWreQ/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords

CMD: touch /tmp/nxf.UnzyqYWreQ/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.UnzyqYWreQ/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords > /tmp/nxf.UnzyqYWreQ/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.UnzyqYWreQ/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.UnzyqYWreQ/786-O_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.UnzyqYWreQ/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.UnzyqYWreQ/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.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.UnzyqYWreQ/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.UnzyqYWreQ/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.UnzyqYWreQ/786-O_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -8526.691053
EM: Round [1] log likelihood: -8526.483673
EM: Round [2] log likelihood: -8526.480720
EM: Round [3] log likelihood: -8526.477876
EM: Round [4] log likelihood: -8526.475042
EM: Round [5] log likelihood: -8526.472217
EM: Round [6] log likelihood: -8526.469400
EM: Round [7] log likelihood: -8526.466593
EM: Round [8] log likelihood: -8526.463795
EM: Round [9] log likelihood: -8526.461006
EM: Round [10] log likelihood: -8526.458225
EM: Round [11] log likelihood: -8526.455454
EM: Round [12] log likelihood: -8526.452691
EM: Round [13] log likelihood: -8526.449937
EM: Round [14] log likelihood: -8526.447192
EM: Round [15] log likelihood: -8526.444455
EM: Round [16] log likelihood: -8526.441727
EM: Round [17] log likelihood: -8526.439008
EM: Round [18] log likelihood: -8526.436297
EM: Round [19] log likelihood: -8526.433594
EM: Round [20] log likelihood: -8526.430900
EM: Round [21] log likelihood: -8526.428214
EM: Round [22] log likelihood: -8526.425537
EM: Round [23] log likelihood: -8526.422867
EM: Round [24] log likelihood: -8526.420206
EM: Round [25] log likelihood: -8526.417553
EM: Round [26] log likelihood: -8526.414908
EM: Round [27] log likelihood: -8526.412272
EM: Round [28] log likelihood: -8526.409643
EM: Round [29] log likelihood: -8526.407022
EM: Round [30] log likelihood: -8526.404409
EM: Round [31] log likelihood: -8526.401804
EM: Round [32] log likelihood: -8526.399207
EM: Round [33] log likelihood: -8526.396618
EM: Round [34] log likelihood: -8526.394036
EM: Round [35] log likelihood: -8526.391462
EM: Round [36] log likelihood: -8526.388896
EM: Round [37] log likelihood: -8526.386337
EM: Round [38] log likelihood: -8526.383786
EM: Round [39] log likelihood: -8526.381243
EM: Round [40] log likelihood: -8526.378706
EM: Round [41] log likelihood: -8526.376178
EM: Round [42] log likelihood: -8526.373657
EM: Round [43] log likelihood: -8526.371143
EM: Round [44] log likelihood: -8526.368636
EM: Round [45] log likelihood: -8526.366137
EM: Round [46] log likelihood: -8526.363645
EM: Round [47] log likelihood: -8526.361161
EM: Round [48] log likelihood: -8526.358683
EM: Round [49] log likelihood: -8526.356213
EM: Round [50] log likelihood: -8526.353749
EM: Round [51] log likelihood: -8526.351293
EM: Round [52] log likelihood: -8526.348844
EM: Round [53] log likelihood: -8526.346402
EM: Round [54] log likelihood: -8526.343966
EM: Round [55] log likelihood: -8526.341538
EM: Round [56] log likelihood: -8526.339117
EM: Round [57] log likelihood: -8526.336702
EM: Round [58] log likelihood: -8526.334294
EM: Round [59] log likelihood: -8526.331893
EM: Round [60] log likelihood: -8526.329499
EM: Round [61] log likelihood: -8526.327111
EM: Round [62] log likelihood: -8526.324730
EM: Round [63] log likelihood: -8526.322356
EM: Round [64] log likelihood: -8526.319988
EM: Round [65] log likelihood: -8526.317627
EM: Round [66] log likelihood: -8526.315272
EM: Round [67] log likelihood: -8526.312924
EM: Round [68] log likelihood: -8526.310582
EM: Round [69] log likelihood: -8526.308247
EM: Round [70] log likelihood: -8526.305918
EM: Round [71] log likelihood: -8526.303596
EM: Round [72] log likelihood: -8526.301279
EM: Round [73] log likelihood: -8526.298970
EM: Round [74] log likelihood: -8526.296666
EM: Round [75] log likelihood: -8526.294369
EM: Round [76] log likelihood: -8526.292077
EM: Round [77] log likelihood: -8526.289792
EM: Round [78] log likelihood: -8526.287514
EM: Round [79] log likelihood: -8526.285241
EM: Round [80] log likelihood: -8526.282974
EM: Round [81] log likelihood: -8526.280714
EM: Round [82] log likelihood: -8526.278459
EM: Round [83] log likelihood: -8526.276211
EM: Round [84] log likelihood: -8526.273968
EM: Round [85] log likelihood: -8526.271731
EM: Round [86] log likelihood: -8526.269501
EM: Round [87] log likelihood: -8526.267276
EM: Round [88] log likelihood: -8526.265057
EM: Round [89] log likelihood: -8526.262843
EM: Round [90] log likelihood: -8526.260636
EM: Round [91] log likelihood: -8526.258434
EM: Round [92] log likelihood: -8526.256238
EM: Round [93] log likelihood: -8526.254048
EM: Round [94] log likelihood: -8526.251864
EM: Round [95] log likelihood: -8526.249685
EM: Round [96] log likelihood: -8526.247512
EM: Round [97] log likelihood: -8526.245344
EM: Round [98] log likelihood: -8526.243182
EM: Round [99] log likelihood: -8526.241025
EM: Round [100] log likelihood: -8526.238874
EM: Round [101] log likelihood: -8526.236729
EM: Round [102] log likelihood: -8526.234589
EM: Round [103] log likelihood: -8526.232454
EM: Round [104] log likelihood: -8526.230325
EM: Round [105] log likelihood: -8526.228202
EM: Round [106] log likelihood: -8526.226083
EM: Round [107] log likelihood: -8526.223970
EM: Round [108] log likelihood: -8526.221862
EM: Round [109] log likelihood: -8526.219760
EM: Round [110] log likelihood: -8526.217663
EM: Round [111] log likelihood: -8526.215571
EM: Round [112] log likelihood: -8526.213484
EM: Round [113] log likelihood: -8526.211403
EM: Round [114] log likelihood: -8526.209326
EM: Round [115] log likelihood: -8526.207255
EM: Round [116] log likelihood: -8526.205189
EM: Round [117] log likelihood: -8526.203128
EM: Round [118] log likelihood: -8526.201073
EM: Round [119] log likelihood: -8526.199022
EM: Round [120] log likelihood: -8526.196976
EM: Round [121] log likelihood: -8526.194935
EM: Round [122] log likelihood: -8526.192900
EM: Round [123] log likelihood: -8526.190869
EM: Round [124] log likelihood: -8526.188843
EM: Round [125] log likelihood: -8526.186822
EM: Round [126] log likelihood: -8526.184806
EM: Round [127] log likelihood: -8526.182795
EM: Round [128] log likelihood: -8526.180789
EM: Round [129] log likelihood: -8526.178788
EM: Round [130] log likelihood: -8526.176791
EM: Round [131] log likelihood: -8526.174799
EM: Round [132] log likelihood: -8526.172812
EM: Round [133] log likelihood: -8526.170830
EM: Round [134] log likelihood: -8526.168852
EM: Round [135] log likelihood: -8526.166880
EM: Round [136] log likelihood: -8526.164911
EM: Round [137] log likelihood: -8526.162948
EM: Round [138] log likelihood: -8526.160989
EM: Round [139] log likelihood: -8526.159035
EM: Round [140] log likelihood: -8526.157086
EM: Round [141] log likelihood: -8526.155141
EM: Round [142] log likelihood: -8526.153200
EM: Round [143] log likelihood: -8526.151264
EM: Round [144] log likelihood: -8526.149333
EM: Round [145] log likelihood: -8526.147406
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-total frags in /tmp/nxf.UnzyqYWreQ/786-O_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz: 294645782
Warning - not locating file: /tmp/nxf.UnzyqYWreQ/786-O_FFPE_RNA_0001_B23LG7FLT4_3.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000198237.8]
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WARNING, no entry stored in dbm for [ENSG00000198237.8]
WARNING, no entry stored in dbm for [ENSG00000198237.8]
WARNING, no entry stored in dbm for [ENSG00000285169.2]
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WARNING, no entry stored in dbm for [ENSG00000176593.8]
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WARNING, no entry stored in dbm for [ENSG00000068781.21]
ls: cannot access 'IGV_inputs': No such file or directory