Done.
-parsing GTF file: /tmp/nxf.MwmX46TKLS/786-O_FFPE_RNA_0001_B23LG7FLT4_2.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.MwmX46TKLS/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.MwmX46TKLS/786-O_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz /tmp/nxf.MwmX46TKLS/786-O_FFPE_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.MwmX46TKLS/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.MwmX46TKLS/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 786-O_FFPE_RNA_0001_B23LG7FLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 786-O_FFPE_RNA_0001_B23LG7FLT4_2.star.sortedByCoord.out.bam
11:16:02 : INFO : Done.
-parsing GTF file: /tmp/nxf.MwmX46TKLS/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_2.gtf
-parsing /tmp/nxf.MwmX46TKLS/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam

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[2360000]   -done parsing /tmp/nxf.MwmX46TKLS/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'per_id < 96' => 13454,
          'low complexity anchor region' => 14,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 7,
          'exons hit < 2' => 7,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 400,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 6,
          'excessive soft clipping' => 15270,
          ' ** passed ** ' => 46940,
          'seq-similar region overlap' => 16,
          'small anchor length' => 242,
          'num genes matched < 2' => 5
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.MwmX46TKLS/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_2.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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[36000]   -fusion SPANNING read extraction for scaff: ARHGEF3--RRP9

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[34000]   -fusion SPANNING read extraction for scaff: ATAD2B--KLHL29

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[49000]   -fusion SPANNING read extraction for scaff: BNC2--AL358117.1

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

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[36000]   -fusion SPANNING read extraction for scaff: CENPU--ENPP6

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[68000]   -fusion SPANNING read extraction for scaff: DHX38--AMPD1

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[20000]   -fusion SPANNING read extraction for scaff: GUSBP13--NAIP

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[284000]   -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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[67000]   -fusion SPANNING read extraction for scaff: HTR7--LINC02653

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[745000]   
[746000]   -fusion SPANNING read extraction for scaff: LMNA--MEX3A

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[195000]   
[196000]   -fusion SPANNING read extraction for scaff: LRP1B--AC078882.1

[1000]   
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[29000]   
[30000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
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[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
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[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
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[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[1000]   
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[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
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[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
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[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
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[6000]   
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[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
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[72000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[216000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[38000]   
[39000]   -fusion SPANNING read extraction for scaff: RNA5SP281--ACO1

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[38000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[7000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[40000]   -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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[24000]   -fusion SPANNING read extraction for scaff: ZKSCAN7--KIF15
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 28911,
          'seq similar region alignment' => 16316
        };
EM: Starting log likelihood: -9344.191719
EM: Round [1] log likelihood: -9339.826043
EM: Round [2] log likelihood: -9339.798277
EM: Round [3] log likelihood: -9339.781990
EM: Round [4] log likelihood: -9339.766025
EM: Round [5] log likelihood: -9339.750162
EM: Round [6] log likelihood: -9339.734391
EM: Round [7] log likelihood: -9339.718712
EM: Round [8] log likelihood: -9339.703122
EM: Round [9] log likelihood: -9339.687622
EM: Round [10] log likelihood: -9339.672211
EM: Round [11] log likelihood: -9339.656887
EM: Round [12] log likelihood: -9339.641650
EM: Round [13] log likelihood: -9339.626498
EM: Round [14] log likelihood: -9339.611432
EM: Round [15] log likelihood: -9339.596450
EM: Round [16] log likelihood: -9339.581552
EM: Round [17] log likelihood: -9339.566736
EM: Round [18] log likelihood: -9339.552002
EM: Round [19] log likelihood: -9339.537349
EM: Round [20] log likelihood: -9339.522776
EM: Round [21] log likelihood: -9339.508283
EM: Round [22] log likelihood: -9339.493869
EM: Round [23] log likelihood: -9339.479533
EM: Round [24] log likelihood: -9339.465274
EM: Round [25] log likelihood: -9339.451091
EM: Round [26] log likelihood: -9339.436985
EM: Round [27] log likelihood: -9339.422954
EM: Round [28] log likelihood: -9339.408997
EM: Round [29] log likelihood: -9339.395115
EM: Round [30] log likelihood: -9339.381305
EM: Round [31] log likelihood: -9339.367568
EM: Round [32] log likelihood: -9339.353903
EM: Round [33] log likelihood: -9339.340310
EM: Round [34] log likelihood: -9339.326787
EM: Round [35] log likelihood: -9339.313334
EM: Round [36] log likelihood: -9339.299950
EM: Round [37] log likelihood: -9339.286635
EM: Round [38] log likelihood: -9339.273389
EM: Round [39] log likelihood: -9339.260209
EM: Round [40] log likelihood: -9339.247097
EM: Round [41] log likelihood: -9339.234052
EM: Round [42] log likelihood: -9339.221072
EM: Round [43] log likelihood: -9339.208158
EM: Round [44] log likelihood: -9339.195308
EM: Round [45] log likelihood: -9339.182523
EM: Round [46] log likelihood: -9339.169801
EM: Round [47] log likelihood: -9339.157143
EM: Round [48] log likelihood: -9339.144547
EM: Round [49] log likelihood: -9339.132013
EM: Round [50] log likelihood: -9339.119540
EM: Round [51] log likelihood: -9339.107129
EM: Round [52] log likelihood: -9339.094779
EM: Round [53] log likelihood: -9339.082488
EM: Round [54] log likelihood: -9339.070257
EM: Round [55] log likelihood: -9339.058085
EM: Round [56] log likelihood: -9339.045972
EM: Round [57] log likelihood: -9339.033917
EM: Round [58] log likelihood: -9339.021920
EM: Round [59] log likelihood: -9339.009980
EM: Round [60] log likelihood: -9338.998097
EM: Round [61] log likelihood: -9338.986270
EM: Round [62] log likelihood: -9338.974499
EM: Round [63] log likelihood: -9338.962783
EM: Round [64] log likelihood: -9338.951123
EM: Round [65] log likelihood: -9338.939517
EM: Round [66] log likelihood: -9338.927965
EM: Round [67] log likelihood: -9338.916467
EM: Round [68] log likelihood: -9338.905022
EM: Round [69] log likelihood: -9338.893630
EM: Round [70] log likelihood: -9338.882291
EM: Round [71] log likelihood: -9338.871004
EM: Round [72] log likelihood: -9338.859769
EM: Round [73] log likelihood: -9338.848584
EM: Round [74] log likelihood: -9338.837451
EM: Round [75] log likelihood: -9338.826369
EM: Round [76] log likelihood: -9338.815336
EM: Round [77] log likelihood: -9338.804354
EM: Round [78] log likelihood: -9338.793421
EM: Round [79] log likelihood: -9338.782537
EM: Round [80] log likelihood: -9338.771702
EM: Round [81] log likelihood: -9338.760915
EM: Round [82] log likelihood: -9338.750176
EM: Round [83] log likelihood: -9338.739485
EM: Round [84] log likelihood: -9338.728841
EM: Round [85] log likelihood: -9338.718244
EM: Round [86] log likelihood: -9338.707693
EM: Round [87] log likelihood: -9338.697189
EM: Round [88] log likelihood: -9338.686731
EM: Round [89] log likelihood: -9338.676319
EM: Round [90] log likelihood: -9338.665952
EM: Round [91] log likelihood: -9338.655630
EM: Round [92] log likelihood: -9338.645352
EM: Round [93] log likelihood: -9338.635119
EM: Round [94] log likelihood: -9338.624930
EM: Round [95] log likelihood: -9338.614785
EM: Round [96] log likelihood: -9338.604683
EM: Round [97] log likelihood: -9338.594625
EM: Round [98] log likelihood: -9338.584609
EM: Round [99] log likelihood: -9338.574636
EM: Round [100] log likelihood: -9338.564705
EM: Round [101] log likelihood: -9338.554816
EM: Round [102] log likelihood: -9338.544968
EM: Round [103] log likelihood: -9338.535162
EM: Round [104] log likelihood: -9338.525397
EM: Round [105] log likelihood: -9338.515673
EM: Round [106] log likelihood: -9338.505990
EM: Round [107] log likelihood: -9338.496347
EM: Round [108] log likelihood: -9338.486744
EM: Round [109] log likelihood: -9338.477180
EM: Round [110] log likelihood: -9338.467656
EM: Round [111] log likelihood: -9338.458172
EM: Round [112] log likelihood: -9338.448726
EM: Round [113] log likelihood: -9338.439319
EM: Round [114] log likelihood: -9338.429950
EM: Round [115] log likelihood: -9338.420620
EM: Round [116] log likelihood: -9338.411328
EM: Round [117] log likelihood: -9338.402073
EM: Round [118] log likelihood: -9338.392856
EM: Round [119] log likelihood: -9338.383676
EM: Round [120] log likelihood: -9338.374533
EM: Round [121] log likelihood: -9338.365427
EM: Round [122] log likelihood: -9338.356357
EM: Round [123] log likelihood: -9338.347324
EM: Round [124] log likelihood: -9338.338326
EM: Round [125] log likelihood: -9338.329365
EM: Round [126] log likelihood: -9338.320439
EM: Round [127] log likelihood: -9338.311548
EM: Round [128] log likelihood: -9338.302693
EM: Round [129] log likelihood: -9338.293872
EM: Round [130] log likelihood: -9338.285086
EM: Round [131] log likelihood: -9338.276335
EM: Round [132] log likelihood: -9338.267618
EM: Round [133] log likelihood: -9338.258935
EM: Round [134] log likelihood: -9338.250286
EM: Round [135] log likelihood: -9338.241670
EM: Round [136] log likelihood: -9338.233088
EM: Round [137] log likelihood: -9338.224539
EM: Round [138] log likelihood: -9338.216023
EM: Round [139] log likelihood: -9338.207540
EM: Round [140] log likelihood: -9338.199090
EM: Round [141] log likelihood: -9338.190672
EM: Round [142] log likelihood: -9338.182287
EM: Round [143] log likelihood: -9338.173933
EM: Round [144] log likelihood: -9338.165611
EM: Round [145] log likelihood: -9338.157321
EM: Round [146] log likelihood: -9338.149063
EM: Round [147] log likelihood: -9338.140835
EM: Round [148] log likelihood: -9338.132639
EM: Round [149] log likelihood: -9338.124474
EM: Round [150] log likelihood: -9338.116339
EM: Round [151] log likelihood: -9338.108235
EM: Round [152] log likelihood: -9338.100161
EM: Round [153] log likelihood: -9338.092118
EM: Round [154] log likelihood: -9338.084105
EM: Round [155] log likelihood: -9338.076121
EM: Round [156] log likelihood: -9338.068167
EM: Round [157] log likelihood: -9338.060243
EM: Round [158] log likelihood: -9338.052348
EM: Round [159] log likelihood: -9338.044482
EM: Round [160] log likelihood: -9338.036645
EM: Round [161] log likelihood: -9338.028837
EM: Round [162] log likelihood: -9338.021057
EM: Round [163] log likelihood: -9338.013306
EM: Round [164] log likelihood: -9338.005584
EM: Round [165] log likelihood: -9337.997889
EM: Round [166] log likelihood: -9337.990223
EM: Round [167] log likelihood: -9337.982584
EM: Round [168] log likelihood: -9337.974974
EM: Round [169] log likelihood: -9337.967390
EM: Round [170] log likelihood: -9337.959834
EM: Round [171] log likelihood: -9337.952306
EM: Round [172] log likelihood: -9337.944804
EM: Round [173] log likelihood: -9337.937330
EM: Round [174] log likelihood: -9337.929882
EM: Round [175] log likelihood: -9337.922461
EM: Round [176] log likelihood: -9337.915066
EM: Round [177] log likelihood: -9337.907698
EM: Round [178] log likelihood: -9337.900356
EM: Round [179] log likelihood: -9337.893040
EM: Round [180] log likelihood: -9337.885750
EM: Round [181] log likelihood: -9337.878485
EM: Round [182] log likelihood: -9337.871247
EM: Round [183] log likelihood: -9337.864033
EM: Round [184] log likelihood: -9337.856846
EM: Round [185] log likelihood: -9337.849683
EM: Round [186] log likelihood: -9337.842546
EM: Round [187] log likelihood: -9337.835433
EM: Round [188] log likelihood: -9337.828345
EM: Round [189] log likelihood: -9337.821282
EM: Round [190] log likelihood: -9337.814244
EM: Round [191] log likelihood: -9337.807230
EM: Round [192] log likelihood: -9337.800240
EM: Round [193] log likelihood: -9337.793275
EM: Round [194] log likelihood: -9337.786333
EM: Round [195] log likelihood: -9337.779416
EM: Round [196] log likelihood: -9337.772522
EM: Round [197] log likelihood: -9337.765652
EM: Round [198] log likelihood: -9337.758806
EM: Round [199] log likelihood: -9337.751982
EM: Round [200] log likelihood: -9337.745183
EM: Round [201] log likelihood: -9337.738406
EM: Round [202] log likelihood: -9337.731653
EM: Round [203] log likelihood: -9337.724922
EM: Round [204] log likelihood: -9337.718214
EM: Round [205] log likelihood: -9337.711529
EM: Round [206] log likelihood: -9337.704867
EM: Round [207] log likelihood: -9337.698227
EM: Round [208] log likelihood: -9337.691609
EM: Round [209] log likelihood: -9337.685014
EM: Round [210] log likelihood: -9337.678441
EM: Round [211] log likelihood: -9337.671890
EM: Round [212] log likelihood: -9337.665360
EM: Round [213] log likelihood: -9337.658853
EM: Round [214] log likelihood: -9337.652367
EM: Round [215] log likelihood: -9337.645903
EM: Round [216] log likelihood: -9337.639460
EM: Round [217] log likelihood: -9337.633039
EM: Round [218] log likelihood: -9337.626639
EM: Round [219] log likelihood: -9337.620260
EM: Round [220] log likelihood: -9337.613902
EM: Round [221] log likelihood: -9337.607566
EM: Round [222] log likelihood: -9337.601250
EM: Round [223] log likelihood: -9337.594954
EM: Round [224] log likelihood: -9337.588680
EM: Round [225] log likelihood: -9337.582426
EM: Round [226] log likelihood: -9337.576192
EM: Round [227] log likelihood: -9337.569979
EM: Round [228] log likelihood: -9337.563786
EM: Round [229] log likelihood: -9337.557613
EM: Round [230] log likelihood: -9337.551460
EM: Round [231] log likelihood: -9337.545327
EM: Round [232] log likelihood: -9337.539214
EM: Round [233] log likelihood: -9337.533121
EM: Round [234] log likelihood: -9337.527047
EM: Round [235] log likelihood: -9337.520993
EM: Round [236] log likelihood: -9337.514959
EM: Round [237] log likelihood: -9337.508944
EM: Round [238] log likelihood: -9337.502948
EM: Round [239] log likelihood: -9337.496971
EM: Round [240] log likelihood: -9337.491014
EM: Round [241] log likelihood: -9337.485075
EM: Round [242] log likelihood: -9337.479155
EM: Round [243] log likelihood: -9337.473255
EM: Round [244] log likelihood: -9337.467373
EM: Round [245] log likelihood: -9337.461509
EM: Round [246] log likelihood: -9337.455665
EM: Round [247] log likelihood: -9337.449838
EM: Round [248] log likelihood: -9337.444030
EM: Round [249] log likelihood: -9337.438241
EM: Round [250] log likelihood: -9337.432470
EM: Round [251] log likelihood: -9337.426716
EM: Round [252] log likelihood: -9337.420981
EM: Round [253] log likelihood: -9337.415264
EM: Round [254] log likelihood: -9337.409565
EM: Round [255] log likelihood: -9337.403884
EM: Round [256] log likelihood: -9337.398220
EM: Round [257] log likelihood: -9337.392574
EM: Round [258] log likelihood: -9337.386945
EM: Round [259] log likelihood: -9337.381334
EM: Round [260] log likelihood: -9337.375741
EM: Round [261] log likelihood: -9337.370165
EM: Round [262] log likelihood: -9337.364606
EM: Round [263] log likelihood: -9337.359064
EM: Round [264] log likelihood: -9337.353539
EM: Round [265] log likelihood: -9337.348032
EM: Round [266] log likelihood: -9337.342541
EM: Round [267] log likelihood: -9337.337067
EM: Round [268] log likelihood: -9337.331610
EM: Round [269] log likelihood: -9337.326170
EM: Round [270] log likelihood: -9337.320746
EM: Round [271] log likelihood: -9337.315339
EM: Round [272] log likelihood: -9337.309948
EM: Round [273] log likelihood: -9337.304574
EM: Round [274] log likelihood: -9337.299216
EM: Round [275] log likelihood: -9337.293875
EM: Round [276] log likelihood: -9337.288550
EM: Round [277] log likelihood: -9337.283240
EM: Round [278] log likelihood: -9337.277947
EM: Round [279] log likelihood: -9337.272670
EM: Round [280] log likelihood: -9337.267409
EM: Round [281] log likelihood: -9337.262163
EM: Round [282] log likelihood: -9337.256934
EM: Round [283] log likelihood: -9337.251720
EM: Round [284] log likelihood: -9337.246522
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EM: Round [744] log likelihood: -9335.859274
EM: Round [745] log likelihood: -9335.857590
EM: Round [746] log likelihood: -9335.855910
EM: Round [747] log likelihood: -9335.854233
EM: Round [748] log likelihood: -9335.852560
EM: Round [749] log likelihood: -9335.850890
EM: Round [750] log likelihood: -9335.849224
EM: Round [751] log likelihood: -9335.847562
EM: Round [752] log likelihood: -9335.845902
EM: Round [753] log likelihood: -9335.844247
EM: Round [754] log likelihood: -9335.842595
EM: Round [755] log likelihood: -9335.840946
EM: Round [756] log likelihood: -9335.839301
EM: Round [757] log likelihood: -9335.837659
EM: Round [758] log likelihood: -9335.836020
EM: Round [759] log likelihood: -9335.834385
EM: Round [760] log likelihood: -9335.832754
EM: Round [761] log likelihood: -9335.831126
EM: Round [762] log likelihood: -9335.829501
EM: Round [763] log likelihood: -9335.827879
EM: Round [764] log likelihood: -9335.826262
EM: Round [765] log likelihood: -9335.824647
EM: Round [766] log likelihood: -9335.823036
EM: Round [767] log likelihood: -9335.821428
EM: Round [768] log likelihood: -9335.819823
EM: Round [769] log likelihood: -9335.818222
EM: Round [770] log likelihood: -9335.816624
EM: Round [771] log likelihood: -9335.815030
EM: Round [772] log likelihood: -9335.813439
EM: Round [773] log likelihood: -9335.811851
EM: Round [774] log likelihood: -9335.810266
EM: Round [775] log likelihood: -9335.808685
EM: Round [776] log likelihood: -9335.807107
EM: Round [777] log likelihood: -9335.805532
EM: Round [778] log likelihood: -9335.803961
EM: Round [779] log likelihood: -9335.802392
EM: Round [780] log likelihood: -9335.800827
EM: Round [781] log likelihood: -9335.799266
EM: Round [782] log likelihood: -9335.797707
EM: Round [783] log likelihood: -9335.796152
EM: Round [784] log likelihood: -9335.794600
EM: Round [785] log likelihood: -9335.793051
EM: Round [786] log likelihood: -9335.791505
EM: Round [787] log likelihood: -9335.789963
EM: Round [788] log likelihood: -9335.788424
EM: Round [789] log likelihood: -9335.786888
EM: Round [790] log likelihood: -9335.785355
EM: Round [791] log likelihood: -9335.783825
EM: Round [792] log likelihood: -9335.782299
EM: Round [793] log likelihood: -9335.780775
EM: Round [794] log likelihood: -9335.779255
EM: Round [795] log likelihood: -9335.777738
EM: Round [796] log likelihood: -9335.776224
EM: Round [797] log likelihood: -9335.774713
EM: Round [798] log likelihood: -9335.773205
EM: Round [799] log likelihood: -9335.771701
EM: Round [800] log likelihood: -9335.770199
EM: Round [801] log likelihood: -9335.768701
EM: Round [802] log likelihood: -9335.767205
EM: Round [803] log likelihood: -9335.765713
EM: Round [804] log likelihood: -9335.764224
EM: Round [805] log likelihood: -9335.762737
EM: Round [806] log likelihood: -9335.761254
EM: Round [807] log likelihood: -9335.759774
EM: Round [808] log likelihood: -9335.758297
EM: Round [809] log likelihood: -9335.756823
EM: Round [810] log likelihood: -9335.755352
EM: Round [811] log likelihood: -9335.753884
EM: Round [812] log likelihood: -9335.752419
EM: Round [813] log likelihood: -9335.750957
EM: Round [814] log likelihood: -9335.749498
EM: Round [815] log likelihood: -9335.748042
EM: Round [816] log likelihood: -9335.746589
EM: Round [817] log likelihood: -9335.745139
EM: Round [818] log likelihood: -9335.743692
EM: Round [819] log likelihood: -9335.742248
EM: Round [820] log likelihood: -9335.740807
EM: Round [821] log likelihood: -9335.739369
EM: Round [822] log likelihood: -9335.737933
EM: Round [823] log likelihood: -9335.736501
EM: Round [824] log likelihood: -9335.735071
EM: Round [825] log likelihood: -9335.733645
EM: Round [826] log likelihood: -9335.732221
EM: Round [827] log likelihood: -9335.730801
EM: Round [828] log likelihood: -9335.729383
EM: Round [829] log likelihood: -9335.727968
EM: Round [830] log likelihood: -9335.726556
EM: Round [831] log likelihood: -9335.725146
EM: Round [832] log likelihood: -9335.723740
EM: Round [833] log likelihood: -9335.722337
EM: Round [834] log likelihood: -9335.720936
EM: Round [835] log likelihood: -9335.719538
EM: Round [836] log likelihood: -9335.718143
EM: Round [837] log likelihood: -9335.716751
EM: Round [838] log likelihood: -9335.715362
EM: Round [839] log likelihood: -9335.713976
EM: Round [840] log likelihood: -9335.712592
EM: Round [841] log likelihood: -9335.711211
EM: Round [842] log likelihood: -9335.709833
EM: Round [843] log likelihood: -9335.708458
EM: Round [844] log likelihood: -9335.707085
EM: Round [845] log likelihood: -9335.705716
EM: Round [846] log likelihood: -9335.704349
EM: Round [847] log likelihood: -9335.702985
EM: Round [848] log likelihood: -9335.701623
EM: Round [849] log likelihood: -9335.700265
EM: Round [850] log likelihood: -9335.698909
EM: Round [851] log likelihood: -9335.697556
EM: Round [852] log likelihood: -9335.696205
EM: Round [853] log likelihood: -9335.694857
EM: Round [854] log likelihood: -9335.693512
EM: Round [855] log likelihood: -9335.692170
EM: Round [856] log likelihood: -9335.690831
EM: Round [857] log likelihood: -9335.689494
EM: Round [858] log likelihood: -9335.688160
EM: Round [859] log likelihood: -9335.686828
EM: Round [860] log likelihood: -9335.685499
EM: Round [861] log likelihood: -9335.684173
EM: Round [862] log likelihood: -9335.682850
EM: Round [863] log likelihood: -9335.681529
EM: Round [864] log likelihood: -9335.680211
EM: Round [865] log likelihood: -9335.678896
EM: Round [866] log likelihood: -9335.677583
EM: Round [867] log likelihood: -9335.676273
EM: Round [868] log likelihood: -9335.674965
EM: Round [869] log likelihood: -9335.673660
EM: Round [870] log likelihood: -9335.672358
EM: Round [871] log likelihood: -9335.671058
EM: Round [872] log likelihood: -9335.669761
EM: Round [873] log likelihood: -9335.668466
EM: Round [874] log likelihood: -9335.667175
EM: Round [875] log likelihood: -9335.665885
EM: Round [876] log likelihood: -9335.664599
EM: Round [877] log likelihood: -9335.663314
EM: Round [878] log likelihood: -9335.662033
EM: Round [879] log likelihood: -9335.660754
EM: Round [880] log likelihood: -9335.659477
EM: Round [881] log likelihood: -9335.658204
EM: Round [882] log likelihood: -9335.656932
EM: Round [883] log likelihood: -9335.655663
EM: Round [884] log likelihood: -9335.654397
EM: Round [885] log likelihood: -9335.653133
EM: Round [886] log likelihood: -9335.651872
EM: Round [887] log likelihood: -9335.650614
EM: Round [888] log likelihood: -9335.649357
EM: Round [889] log likelihood: -9335.648104
EM: Round [890] log likelihood: -9335.646853
EM: Round [891] log likelihood: -9335.645604
EM: Round [892] log likelihood: -9335.644358
EM: Round [893] log likelihood: -9335.643114
EM: Round [894] log likelihood: -9335.641873
EM: Round [895] log likelihood: -9335.640634
EM: Round [896] log likelihood: -9335.639398
EM: Round [897] log likelihood: -9335.638164
EM: Round [898] log likelihood: -9335.636932
EM: Round [899] log likelihood: -9335.635704
EM: Round [900] log likelihood: -9335.634477
EM: Round [901] log likelihood: -9335.633253
EM: Round [902] log likelihood: -9335.632031
EM: Round [903] log likelihood: -9335.630812
EM: Round [904] log likelihood: -9335.629596
EM: Round [905] log likelihood: -9335.628381
EM: Round [906] log likelihood: -9335.627169
EM: Round [907] log likelihood: -9335.625960
EM: Round [908] log likelihood: -9335.624753
EM: Round [909] log likelihood: -9335.623548
EM: Round [910] log likelihood: -9335.622345
EM: Round [911] log likelihood: -9335.621146
EM: Round [912] log likelihood: -9335.619948
EM: Round [913] log likelihood: -9335.618753
EM: Round [914] log likelihood: -9335.617560
EM: Round [915] log likelihood: -9335.616369
EM: Round [916] log likelihood: -9335.615181
EM: Round [917] log likelihood: -9335.613995
EM: Round [918] log likelihood: -9335.612812
EM: Round [919] log likelihood: -9335.611631
EM: Round [920] log likelihood: -9335.610452
EM: Round [921] log likelihood: -9335.609276
EM: Round [922] log likelihood: -9335.608102
EM: Round [923] log likelihood: -9335.606930
EM: Round [924] log likelihood: -9335.605760
EM: Round [925] log likelihood: -9335.604593
EM: Round [926] log likelihood: -9335.603428
EM: Round [927] log likelihood: -9335.602266
EM: Round [928] log likelihood: -9335.601105
EM: Round [929] log likelihood: -9335.599947
EM: Round [930] log likelihood: -9335.598792
EM: Round [931] log likelihood: -9335.597638
EM: Round [932] log likelihood: -9335.596487
EM: Round [933] log likelihood: -9335.595338
EM: Round [934] log likelihood: -9335.594192
EM: Round [935] log likelihood: -9335.593047
EM: Round [936] log likelihood: -9335.591905
EM: Round [937] log likelihood: -9335.590765
EM: Round [938] log likelihood: -9335.589628
EM: Round [939] log likelihood: -9335.588492
EM: Round [940] log likelihood: -9335.587359
EM: Round [941] log likelihood: -9335.586228
EM: Round [942] log likelihood: -9335.585099
EM: Round [943] log likelihood: -9335.583973
EM: Round [944] log likelihood: -9335.582849
EM: Round [945] log likelihood: -9335.581726
EM: Round [946] log likelihood: -9335.580607
EM: Round [947] log likelihood: -9335.579489
EM: Round [948] log likelihood: -9335.578373
EM: Round [949] log likelihood: -9335.577260
EM: Round [950] log likelihood: -9335.576149
EM: Round [951] log likelihood: -9335.575040
EM: Round [952] log likelihood: -9335.573933
EM: Round [953] log likelihood: -9335.572829
EM: Round [954] log likelihood: -9335.571726
EM: Round [955] log likelihood: -9335.570626
EM: Round [956] log likelihood: -9335.569528
EM: Round [957] log likelihood: -9335.568432
EM: Round [958] log likelihood: -9335.567338
EM: Round [959] log likelihood: -9335.566246
EM: Round [960] log likelihood: -9335.565157
EM: Round [961] log likelihood: -9335.564069
EM: Round [962] log likelihood: -9335.562984
EM: Round [963] log likelihood: -9335.561900
EM: Round [964] log likelihood: -9335.560819
EM: Round [965] log likelihood: -9335.559740
EM: Round [966] log likelihood: -9335.558663
EM: Round [967] log likelihood: -9335.557589
EM: Round [968] log likelihood: -9335.556516
EM: Round [969] log likelihood: -9335.555445
EM: Round [970] log likelihood: -9335.554377
EM: Round [971] log likelihood: -9335.553310
EM: Round [972] log likelihood: -9335.552246
EM: Round [973] log likelihood: -9335.551184
EM: Round [974] log likelihood: -9335.550124
EM: Round [975] log likelihood: -9335.549065
EM: Round [976] log likelihood: -9335.548009
EM: Round [977] log likelihood: -9335.546955
EM: Round [978] log likelihood: -9335.545903
EM: Round [979] log likelihood: -9335.544853
EM: Round [980] log likelihood: -9335.543805
EM: Round [981] log likelihood: -9335.542760
EM: Round [982] log likelihood: -9335.541716
EM: Round [983] log likelihood: -9335.540674
EM: Round [984] log likelihood: -9335.539634
EM: Round [985] log likelihood: -9335.538596
EM: Round [986] log likelihood: -9335.537561
EM: Round [987] log likelihood: -9335.536527
EM: Round [988] log likelihood: -9335.535495
EM: Round [989] log likelihood: -9335.534465
EM: Round [990] log likelihood: -9335.533438
EM: Round [991] log likelihood: -9335.532412
EM: Round [992] log likelihood: -9335.531388
EM: Round [993] log likelihood: -9335.530366
EM: Round [994] log likelihood: -9335.529346
EM: Round [995] log likelihood: -9335.528329
EM: Round [996] log likelihood: -9335.527313
EM: Round [997] log likelihood: -9335.526299
EM: Round [998] log likelihood: -9335.525287
EM: Round [999] log likelihood: -9335.524277
EM: Round [1000] log likelihood: -9335.523269
EM: Round [1001] log likelihood: -9335.522263
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.MwmX46TKLS/786-O_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam into /tmp/nxf.MwmX46TKLS/786-O_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.MwmX46TKLS/786-O_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.MwmX46TKLS/786-O_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.read_coords > /tmp/nxf.MwmX46TKLS/786-O_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.MwmX46TKLS/786-O_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.frag_coords > /tmp/nxf.MwmX46TKLS/786-O_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.MwmX46TKLS/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.MwmX46TKLS/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.MwmX46TKLS/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.MwmX46TKLS/786-O_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.MwmX46TKLS/786-O_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -8861.512261
EM: Round [1] log likelihood: -8860.974928
EM: Round [2] log likelihood: -8860.943769
EM: Round [3] log likelihood: -8860.917689
EM: Round [4] log likelihood: -8860.891920
EM: Round [5] log likelihood: -8860.866391
EM: Round [6] log likelihood: -8860.841095
EM: Round [7] log likelihood: -8860.816028
EM: Round [8] log likelihood: -8860.791188
EM: Round [9] log likelihood: -8860.766569
EM: Round [10] log likelihood: -8860.742169
EM: Round [11] log likelihood: -8860.717984
EM: Round [12] log likelihood: -8860.694010
EM: Round [13] log likelihood: -8860.670244
EM: Round [14] log likelihood: -8860.646682
EM: Round [15] log likelihood: -8860.623322
EM: Round [16] log likelihood: -8860.600160
EM: Round [17] log likelihood: -8860.577193
EM: Round [18] log likelihood: -8860.554418
EM: Round [19] log likelihood: -8860.531832
EM: Round [20] log likelihood: -8860.509432
EM: Round [21] log likelihood: -8860.487216
EM: Round [22] log likelihood: -8860.465180
EM: Round [23] log likelihood: -8860.443321
EM: Round [24] log likelihood: -8860.421639
EM: Round [25] log likelihood: -8860.400128
EM: Round [26] log likelihood: -8860.378788
EM: Round [27] log likelihood: -8860.357616
EM: Round [28] log likelihood: -8860.336609
EM: Round [29] log likelihood: -8860.315765
EM: Round [30] log likelihood: -8860.295082
EM: Round [31] log likelihood: -8860.274556
EM: Round [32] log likelihood: -8860.254187
EM: Round [33] log likelihood: -8860.233972
EM: Round [34] log likelihood: -8860.213909
EM: Round [35] log likelihood: -8860.193996
EM: Round [36] log likelihood: -8860.174230
EM: Round [37] log likelihood: -8860.154611
EM: Round [38] log likelihood: -8860.135135
EM: Round [39] log likelihood: -8860.115800
EM: Round [40] log likelihood: -8860.096606
EM: Round [41] log likelihood: -8860.077551
EM: Round [42] log likelihood: -8860.058631
EM: Round [43] log likelihood: -8860.039846
EM: Round [44] log likelihood: -8860.021194
EM: Round [45] log likelihood: -8860.002674
EM: Round [46] log likelihood: -8859.984282
EM: Round [47] log likelihood: -8859.966019
EM: Round [48] log likelihood: -8859.947882
EM: Round [49] log likelihood: -8859.929870
EM: Round [50] log likelihood: -8859.911981
EM: Round [51] log likelihood: -8859.894213
EM: Round [52] log likelihood: -8859.876566
EM: Round [53] log likelihood: -8859.859038
EM: Round [54] log likelihood: -8859.841626
EM: Round [55] log likelihood: -8859.824331
EM: Round [56] log likelihood: -8859.807150
EM: Round [57] log likelihood: -8859.790083
EM: Round [58] log likelihood: -8859.773127
EM: Round [59] log likelihood: -8859.756282
EM: Round [60] log likelihood: -8859.739546
EM: Round [61] log likelihood: -8859.722918
EM: Round [62] log likelihood: -8859.706397
EM: Round [63] log likelihood: -8859.689981
EM: Round [64] log likelihood: -8859.673669
EM: Round [65] log likelihood: -8859.657461
EM: Round [66] log likelihood: -8859.641355
EM: Round [67] log likelihood: -8859.625349
EM: Round [68] log likelihood: -8859.609443
EM: Round [69] log likelihood: -8859.593636
EM: Round [70] log likelihood: -8859.577927
EM: Round [71] log likelihood: -8859.562314
EM: Round [72] log likelihood: -8859.546796
EM: Round [73] log likelihood: -8859.531373
EM: Round [74] log likelihood: -8859.516043
EM: Round [75] log likelihood: -8859.500805
EM: Round [76] log likelihood: -8859.485659
EM: Round [77] log likelihood: -8859.470603
EM: Round [78] log likelihood: -8859.455637
EM: Round [79] log likelihood: -8859.440760
EM: Round [80] log likelihood: -8859.425970
EM: Round [81] log likelihood: -8859.411267
EM: Round [82] log likelihood: -8859.396649
EM: Round [83] log likelihood: -8859.382117
EM: Round [84] log likelihood: -8859.367668
EM: Round [85] log likelihood: -8859.353303
EM: Round [86] log likelihood: -8859.339021
EM: Round [87] log likelihood: -8859.324820
EM: Round [88] log likelihood: -8859.310699
EM: Round [89] log likelihood: -8859.296659
EM: Round [90] log likelihood: -8859.282698
EM: Round [91] log likelihood: -8859.268815
EM: Round [92] log likelihood: -8859.255010
EM: Round [93] log likelihood: -8859.241282
EM: Round [94] log likelihood: -8859.227630
EM: Round [95] log likelihood: -8859.214054
EM: Round [96] log likelihood: -8859.200552
EM: Round [97] log likelihood: -8859.187124
EM: Round [98] log likelihood: -8859.173769
EM: Round [99] log likelihood: -8859.160487
EM: Round [100] log likelihood: -8859.147277
EM: Round [101] log likelihood: -8859.134138
EM: Round [102] log likelihood: -8859.121069
EM: Round [103] log likelihood: -8859.108071
EM: Round [104] log likelihood: -8859.095142
EM: Round [105] log likelihood: -8859.082281
EM: Round [106] log likelihood: -8859.069489
EM: Round [107] log likelihood: -8859.056763
EM: Round [108] log likelihood: -8859.044105
EM: Round [109] log likelihood: -8859.031513
EM: Round [110] log likelihood: -8859.018986
EM: Round [111] log likelihood: -8859.006525
EM: Round [112] log likelihood: -8858.994127
EM: Round [113] log likelihood: -8858.981794
EM: Round [114] log likelihood: -8858.969524
EM: Round [115] log likelihood: -8858.957317
EM: Round [116] log likelihood: -8858.945171
EM: Round [117] log likelihood: -8858.933088
EM: Round [118] log likelihood: -8858.921066
EM: Round [119] log likelihood: -8858.909104
EM: Round [120] log likelihood: -8858.897202
EM: Round [121] log likelihood: -8858.885360
EM: Round [122] log likelihood: -8858.873577
EM: Round [123] log likelihood: -8858.861852
EM: Round [124] log likelihood: -8858.850186
EM: Round [125] log likelihood: -8858.838577
EM: Round [126] log likelihood: -8858.827025
EM: Round [127] log likelihood: -8858.815530
EM: Round [128] log likelihood: -8858.804090
EM: Round [129] log likelihood: -8858.792707
EM: Round [130] log likelihood: -8858.781379
EM: Round [131] log likelihood: -8858.770105
EM: Round [132] log likelihood: -8858.758886
EM: Round [133] log likelihood: -8858.747721
EM: Round [134] log likelihood: -8858.736609
EM: Round [135] log likelihood: -8858.725551
EM: Round [136] log likelihood: -8858.714544
EM: Round [137] log likelihood: -8858.703590
EM: Round [138] log likelihood: -8858.692688
EM: Round [139] log likelihood: -8858.681837
EM: Round [140] log likelihood: -8858.671037
EM: Round [141] log likelihood: -8858.660288
EM: Round [142] log likelihood: -8858.649588
EM: Round [143] log likelihood: -8858.638939
EM: Round [144] log likelihood: -8858.628339
EM: Round [145] log likelihood: -8858.617788
EM: Round [146] log likelihood: -8858.607285
EM: Round [147] log likelihood: -8858.596831
EM: Round [148] log likelihood: -8858.586424
EM: Round [149] log likelihood: -8858.576065
EM: Round [150] log likelihood: -8858.565753
EM: Round [151] log likelihood: -8858.555488
EM: Round [152] log likelihood: -8858.545270
EM: Round [153] log likelihood: -8858.535097
EM: Round [154] log likelihood: -8858.524970
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-total frags in /tmp/nxf.MwmX46TKLS/786-O_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz: 294873575
Warning - not locating file: /tmp/nxf.MwmX46TKLS/786-O_FFPE_RNA_0001_B23LG7FLT4_2.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000285169.2]
WARNING, no entry stored in dbm for [ENSG00000285169.2]
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 [ENSG00000198237.8]
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 [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000176593.8]
WARNING, no entry stored in dbm for [ENSG00000176593.8]
WARNING, no entry stored in dbm for [ENSG00000176593.8]
WARNING, no entry stored in dbm for [ENSG00000236373.2]
WARNING, no entry stored in dbm for [ENSG00000236373.2]
WARNING, no entry stored in dbm for [ENSG00000236373.2]
ls: cannot access 'IGV_inputs': No such file or directory