Done.
-parsing GTF file: /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.bIDYTem8xp/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.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam
11:25:24 : INFO : Done.
-parsing GTF file: /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf
-parsing /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam

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[2530000]   -done parsing /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'seq-similar region overlap' => 9,
          'low complexity anchor region' => 4,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 12,
          'per_id < 96' => 14739,
          'exons hit < 2' => 24,
          'small anchor length' => 256,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 12,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 26,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
          ' ** passed ** ' => 43594,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 529,
          'num genes matched < 2' => 17,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
          'excessive soft clipping' => 16455
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.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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[43000]   -fusion SPANNING read extraction for scaff: AL391557.1--SPAG17

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[39000]   -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

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

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[69000]   -fusion SPANNING read extraction for scaff: DHX38--AMPD1

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[263000]   
[264000]   -fusion SPANNING read extraction for scaff: HIF1A--SNAPC1

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[38000]   
[39000]   -fusion SPANNING read extraction for scaff: HMGB3P23--ACO1

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[799000]   
[800000]   -fusion SPANNING read extraction for scaff: LMNA--MEX3A

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[196000]   
[197000]   -fusion SPANNING read extraction for scaff: LRP1B--AC078882.1

[1000]   
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[66000]   
[67000]   -fusion SPANNING read extraction for scaff: MB21D2--FGF12

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

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[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
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[12000]   
[13000]   
[14000]   
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[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
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[19000]   
[20000]   -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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[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
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[8000]   
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[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[69000]   
[70000]   
[71000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[217000]   
[218000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   -fusion SPANNING read extraction for scaff: RNA5SP281--ACO1

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[37000]   
[38000]   
[39000]   
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[41000]   
[42000]   
[43000]   -fusion SPANNING read extraction for scaff: RNA5SP56--SPAG17

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[35000]   
[36000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[6000]   
[7000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[37000]   
[38000]   
[39000]   -fusion SPANNING read extraction for scaff: TMED7--TICAM2

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[8000]   
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[20000]   
[21000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

[1000]   
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[6000]   
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[8000]   
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[22000]   
[23000]   -fusion SPANNING read extraction for scaff: ZKSCAN7--KIF15
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 32589,
          'lacks exon overlap' => 32167
        };
EM: Starting log likelihood: -8636.895261
EM: Round [1] log likelihood: -8629.873389
EM: Round [2] log likelihood: -8629.865698
EM: Round [3] log likelihood: -8629.861749
EM: Round [4] log likelihood: -8629.857826
EM: Round [5] log likelihood: -8629.853921
EM: Round [6] log likelihood: -8629.850032
EM: Round [7] log likelihood: -8629.846161
EM: Round [8] log likelihood: -8629.842306
EM: Round [9] log likelihood: -8629.838467
EM: Round [10] log likelihood: -8629.834645
EM: Round [11] log likelihood: -8629.830839
EM: Round [12] log likelihood: -8629.827049
EM: Round [13] log likelihood: -8629.823275
EM: Round [14] log likelihood: -8629.819517
EM: Round [15] log likelihood: -8629.815775
EM: Round [16] log likelihood: -8629.812049
EM: Round [17] log likelihood: -8629.808337
EM: Round [18] log likelihood: -8629.804642
EM: Round [19] log likelihood: -8629.800961
EM: Round [20] log likelihood: -8629.797296
EM: Round [21] log likelihood: -8629.793645
EM: Round [22] log likelihood: -8629.790010
EM: Round [23] log likelihood: -8629.786389
EM: Round [24] log likelihood: -8629.782783
EM: Round [25] log likelihood: -8629.779191
EM: Round [26] log likelihood: -8629.775614
EM: Round [27] log likelihood: -8629.772051
EM: Round [28] log likelihood: -8629.768503
EM: Round [29] log likelihood: -8629.764968
EM: Round [30] log likelihood: -8629.761448
EM: Round [31] log likelihood: -8629.757941
EM: Round [32] log likelihood: -8629.754449
EM: Round [33] log likelihood: -8629.750970
EM: Round [34] log likelihood: -8629.747504
EM: Round [35] log likelihood: -8629.744052
EM: Round [36] log likelihood: -8629.740614
EM: Round [37] log likelihood: -8629.737189
EM: Round [38] log likelihood: -8629.733777
EM: Round [39] log likelihood: -8629.730378
EM: Round [40] log likelihood: -8629.726992
EM: Round [41] log likelihood: -8629.723619
EM: Round [42] log likelihood: -8629.720259
EM: Round [43] log likelihood: -8629.716911
EM: Round [44] log likelihood: -8629.713577
EM: Round [45] log likelihood: -8629.710255
EM: Round [46] log likelihood: -8629.706945
EM: Round [47] log likelihood: -8629.703648
EM: Round [48] log likelihood: -8629.700363
EM: Round [49] log likelihood: -8629.697090
EM: Round [50] log likelihood: -8629.693829
EM: Round [51] log likelihood: -8629.690580
EM: Round [52] log likelihood: -8629.687344
EM: Round [53] log likelihood: -8629.684119
EM: Round [54] log likelihood: -8629.680906
EM: Round [55] log likelihood: -8629.677704
EM: Round [56] log likelihood: -8629.674515
EM: Round [57] log likelihood: -8629.671337
EM: Round [58] log likelihood: -8629.668170
EM: Round [59] log likelihood: -8629.665015
EM: Round [60] log likelihood: -8629.661871
EM: Round [61] log likelihood: -8629.658738
EM: Round [62] log likelihood: -8629.655617
EM: Round [63] log likelihood: -8629.652506
EM: Round [64] log likelihood: -8629.649407
EM: Round [65] log likelihood: -8629.646318
EM: Round [66] log likelihood: -8629.643241
EM: Round [67] log likelihood: -8629.640174
EM: Round [68] log likelihood: -8629.637118
EM: Round [69] log likelihood: -8629.634072
EM: Round [70] log likelihood: -8629.631038
EM: Round [71] log likelihood: -8629.628013
EM: Round [72] log likelihood: -8629.625000
EM: Round [73] log likelihood: -8629.621996
EM: Round [74] log likelihood: -8629.619003
EM: Round [75] log likelihood: -8629.616020
EM: Round [76] log likelihood: -8629.613047
EM: Round [77] log likelihood: -8629.610085
EM: Round [78] log likelihood: -8629.607132
EM: Round [79] log likelihood: -8629.604190
EM: Round [80] log likelihood: -8629.601257
EM: Round [81] log likelihood: -8629.598335
EM: Round [82] log likelihood: -8629.595422
EM: Round [83] log likelihood: -8629.592519
EM: Round [84] log likelihood: -8629.589625
EM: Round [85] log likelihood: -8629.586742
EM: Round [86] log likelihood: -8629.583867
EM: Round [87] log likelihood: -8629.581003
EM: Round [88] log likelihood: -8629.578147
EM: Round [89] log likelihood: -8629.575302
EM: Round [90] log likelihood: -8629.572465
EM: Round [91] log likelihood: -8629.569638
EM: Round [92] log likelihood: -8629.566820
EM: Round [93] log likelihood: -8629.564011
EM: Round [94] log likelihood: -8629.561211
EM: Round [95] log likelihood: -8629.558420
EM: Round [96] log likelihood: -8629.555639
EM: Round [97] log likelihood: -8629.552866
EM: Round [98] log likelihood: -8629.550102
EM: Round [99] log likelihood: -8629.547347
EM: Round [100] log likelihood: -8629.544601
EM: Round [101] log likelihood: -8629.541863
EM: Round [102] log likelihood: -8629.539135
EM: Round [103] log likelihood: -8629.536414
EM: Round [104] log likelihood: -8629.533703
EM: Round [105] log likelihood: -8629.531000
EM: Round [106] log likelihood: -8629.528305
EM: Round [107] log likelihood: -8629.525619
EM: Round [108] log likelihood: -8629.522941
EM: Round [109] log likelihood: -8629.520272
EM: Round [110] log likelihood: -8629.517611
EM: Round [111] log likelihood: -8629.514958
EM: Round [112] log likelihood: -8629.512313
EM: Round [113] log likelihood: -8629.509677
EM: Round [114] log likelihood: -8629.507048
EM: Round [115] log likelihood: -8629.504428
EM: Round [116] log likelihood: -8629.501816
EM: Round [117] log likelihood: -8629.499211
EM: Round [118] log likelihood: -8629.496615
EM: Round [119] log likelihood: -8629.494026
EM: Round [120] log likelihood: -8629.491445
EM: Round [121] log likelihood: -8629.488872
EM: Round [122] log likelihood: -8629.486307
EM: Round [123] log likelihood: -8629.483749
EM: Round [124] log likelihood: -8629.481199
EM: Round [125] log likelihood: -8629.478657
EM: Round [126] log likelihood: -8629.476122
EM: Round [127] log likelihood: -8629.473595
EM: Round [128] log likelihood: -8629.471076
EM: Round [129] log likelihood: -8629.468563
EM: Round [130] log likelihood: -8629.466058
EM: Round [131] log likelihood: -8629.463561
EM: Round [132] log likelihood: -8629.461071
EM: Round [133] log likelihood: -8629.458588
EM: Round [134] log likelihood: -8629.456112
EM: Round [135] log likelihood: -8629.453644
EM: Round [136] log likelihood: -8629.451183
EM: Round [137] log likelihood: -8629.448729
EM: Round [138] log likelihood: -8629.446282
EM: Round [139] log likelihood: -8629.443842
EM: Round [140] log likelihood: -8629.441409
EM: Round [141] log likelihood: -8629.438983
EM: Round [142] log likelihood: -8629.436564
EM: Round [143] log likelihood: -8629.434152
EM: Round [144] log likelihood: -8629.431746
EM: Round [145] log likelihood: -8629.429348
EM: Round [146] log likelihood: -8629.426956
EM: Round [147] log likelihood: -8629.424572
EM: Round [148] log likelihood: -8629.422194
EM: Round [149] log likelihood: -8629.419822
EM: Round [150] log likelihood: -8629.417457
EM: Round [151] log likelihood: -8629.415099
EM: Round [152] log likelihood: -8629.412748
EM: Round [153] log likelihood: -8629.410403
EM: Round [154] log likelihood: -8629.408064
EM: Round [155] log likelihood: -8629.405733
EM: Round [156] log likelihood: -8629.403407
EM: Round [157] log likelihood: -8629.401088
EM: Round [158] log likelihood: -8629.398775
EM: Round [159] log likelihood: -8629.396469
EM: Round [160] log likelihood: -8629.394169
EM: Round [161] log likelihood: -8629.391875
EM: Round [162] log likelihood: -8629.389588
EM: Round [163] log likelihood: -8629.387307
EM: Round [164] log likelihood: -8629.385032
EM: Round [165] log likelihood: -8629.382763
EM: Round [166] log likelihood: -8629.380500
EM: Round [167] log likelihood: -8629.378244
EM: Round [168] log likelihood: -8629.375993
EM: Round [169] log likelihood: -8629.373749
EM: Round [170] log likelihood: -8629.371510
EM: Round [171] log likelihood: -8629.369278
EM: Round [172] log likelihood: -8629.367052
EM: Round [173] log likelihood: -8629.364831
EM: Round [174] log likelihood: -8629.362616
EM: Round [175] log likelihood: -8629.360408
EM: Round [176] log likelihood: -8629.358205
EM: Round [177] log likelihood: -8629.356008
EM: Round [178] log likelihood: -8629.353816
EM: Round [179] log likelihood: -8629.351631
EM: Round [180] log likelihood: -8629.349451
EM: Round [181] log likelihood: -8629.347277
EM: Round [182] log likelihood: -8629.345109
EM: Round [183] log likelihood: -8629.342946
EM: Round [184] log likelihood: -8629.340789
EM: Round [185] log likelihood: -8629.338637
EM: Round [186] log likelihood: -8629.336491
EM: Round [187] log likelihood: -8629.334351
EM: Round [188] log likelihood: -8629.332216
EM: Round [189] log likelihood: -8629.330087
EM: Round [190] log likelihood: -8629.327963
EM: Round [191] log likelihood: -8629.325844
EM: Round [192] log likelihood: -8629.323731
EM: Round [193] log likelihood: -8629.321623
EM: Round [194] log likelihood: -8629.319521
EM: Round [195] log likelihood: -8629.317424
EM: Round [196] log likelihood: -8629.315333
EM: Round [197] log likelihood: -8629.313246
EM: Round [198] log likelihood: -8629.311165
EM: Round [199] log likelihood: -8629.309089
EM: Round [200] log likelihood: -8629.307019
EM: Round [201] log likelihood: -8629.304953
EM: Round [202] log likelihood: -8629.302893
EM: Round [203] log likelihood: -8629.300838
EM: Round [204] log likelihood: -8629.298788
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EM: Round [663] log likelihood: -8628.683554
EM: Round [664] log likelihood: -8628.682652
EM: Round [665] log likelihood: -8628.681752
EM: Round [666] log likelihood: -8628.680852
EM: Round [667] log likelihood: -8628.679954
EM: Round [668] log likelihood: -8628.679057
EM: Round [669] log likelihood: -8628.678162
EM: Round [670] log likelihood: -8628.677267
EM: Round [671] log likelihood: -8628.676374
EM: Round [672] log likelihood: -8628.675482
EM: Round [673] log likelihood: -8628.674591
EM: Round [674] log likelihood: -8628.673701
EM: Round [675] log likelihood: -8628.672812
EM: Round [676] log likelihood: -8628.671925
EM: Round [677] log likelihood: -8628.671039
EM: Round [678] log likelihood: -8628.670153
EM: Round [679] log likelihood: -8628.669270
EM: Round [680] log likelihood: -8628.668387
EM: Round [681] log likelihood: -8628.667505
EM: Round [682] log likelihood: -8628.666625
EM: Round [683] log likelihood: -8628.665746
EM: Round [684] log likelihood: -8628.664868
EM: Round [685] log likelihood: -8628.663991
EM: Round [686] log likelihood: -8628.663115
EM: Round [687] log likelihood: -8628.662241
EM: Round [688] log likelihood: -8628.661367
EM: Round [689] log likelihood: -8628.660495
EM: Round [690] log likelihood: -8628.659624
EM: Round [691] log likelihood: -8628.658754
EM: Round [692] log likelihood: -8628.657885
EM: Round [693] log likelihood: -8628.657017
EM: Round [694] log likelihood: -8628.656151
EM: Round [695] log likelihood: -8628.655285
EM: Round [696] log likelihood: -8628.654421
EM: Round [697] log likelihood: -8628.653558
EM: Round [698] log likelihood: -8628.652696
EM: Round [699] log likelihood: -8628.651835
EM: Round [700] log likelihood: -8628.650975
EM: Round [701] log likelihood: -8628.650117
EM: Round [702] log likelihood: -8628.649259
EM: Round [703] log likelihood: -8628.648403
EM: Round [704] log likelihood: -8628.647547
EM: Round [705] log likelihood: -8628.646693
EM: Round [706] log likelihood: -8628.645840
EM: Round [707] log likelihood: -8628.644988
EM: Round [708] log likelihood: -8628.644137
EM: Round [709] log likelihood: -8628.643287
EM: Round [710] log likelihood: -8628.642439
EM: Round [711] log likelihood: -8628.641591
EM: Round [712] log likelihood: -8628.640745
EM: Round [713] log likelihood: -8628.639899
EM: Round [714] log likelihood: -8628.639055
EM: Round [715] log likelihood: -8628.638212
EM: Round [716] log likelihood: -8628.637369
EM: Round [717] log likelihood: -8628.636528
EM: Round [718] log likelihood: -8628.635688
EM: Round [719] log likelihood: -8628.634850
EM: Round [720] log likelihood: -8628.634012
EM: Round [721] log likelihood: -8628.633175
EM: Round [722] log likelihood: -8628.632339
EM: Round [723] log likelihood: -8628.631505
EM: Round [724] log likelihood: -8628.630671
EM: Round [725] log likelihood: -8628.629839
EM: Round [726] log likelihood: -8628.629007
EM: Round [727] log likelihood: -8628.628177
EM: Round [728] log likelihood: -8628.627348
EM: Round [729] log likelihood: -8628.626519
EM: Round [730] log likelihood: -8628.625692
EM: Round [731] log likelihood: -8628.624866
EM: Round [732] log likelihood: -8628.624041
EM: Round [733] log likelihood: -8628.623217
EM: Round [734] log likelihood: -8628.622394
EM: Round [735] log likelihood: -8628.621572
EM: Round [736] log likelihood: -8628.620751
EM: Round [737] log likelihood: -8628.619931
EM: Round [738] log likelihood: -8628.619112
EM: Round [739] log likelihood: -8628.618294
EM: Round [740] log likelihood: -8628.617478
EM: Round [741] log likelihood: -8628.616662
EM: Round [742] log likelihood: -8628.615847
EM: Round [743] log likelihood: -8628.615033
EM: Round [744] log likelihood: -8628.614221
EM: Round [745] log likelihood: -8628.613409
EM: Round [746] log likelihood: -8628.612598
EM: Round [747] log likelihood: -8628.611789
EM: Round [748] log likelihood: -8628.610980
EM: Round [749] log likelihood: -8628.610173
EM: Round [750] log likelihood: -8628.609366
EM: Round [751] log likelihood: -8628.608560
EM: Round [752] log likelihood: -8628.607756
EM: Round [753] log likelihood: -8628.606952
EM: Round [754] log likelihood: -8628.606150
EM: Round [755] log likelihood: -8628.605348
EM: Round [756] log likelihood: -8628.604548
EM: Round [757] log likelihood: -8628.603748
EM: Round [758] log likelihood: -8628.602949
EM: Round [759] log likelihood: -8628.602152
EM: Round [760] log likelihood: -8628.601355
EM: Round [761] log likelihood: -8628.600560
EM: Round [762] log likelihood: -8628.599765
EM: Round [763] log likelihood: -8628.598971
EM: Round [764] log likelihood: -8628.598179
EM: Round [765] log likelihood: -8628.597387
EM: Round [766] log likelihood: -8628.596596
EM: Round [767] log likelihood: -8628.595807
EM: Round [768] log likelihood: -8628.595018
EM: Round [769] log likelihood: -8628.594230
EM: Round [770] log likelihood: -8628.593443
EM: Round [771] log likelihood: -8628.592657
EM: Round [772] log likelihood: -8628.591873
EM: Round [773] log likelihood: -8628.591089
EM: Round [774] log likelihood: -8628.590306
EM: Round [775] log likelihood: -8628.589524
EM: Round [776] log likelihood: -8628.588743
EM: Round [777] log likelihood: -8628.587963
EM: Round [778] log likelihood: -8628.587184
EM: Round [779] log likelihood: -8628.586405
EM: Round [780] log likelihood: -8628.585628
EM: Round [781] log likelihood: -8628.584852
EM: Round [782] log likelihood: -8628.584077
EM: Round [783] log likelihood: -8628.583302
EM: Round [784] log likelihood: -8628.582529
EM: Round [785] log likelihood: -8628.581756
EM: Round [786] log likelihood: -8628.580985
EM: Round [787] log likelihood: -8628.580214
EM: Round [788] log likelihood: -8628.579444
EM: Round [789] log likelihood: -8628.578676
EM: Round [790] log likelihood: -8628.577908
EM: Round [791] log likelihood: -8628.577141
EM: Round [792] log likelihood: -8628.576375
EM: Round [793] log likelihood: -8628.575610
EM: Round [794] log likelihood: -8628.574846
EM: Round [795] log likelihood: -8628.574083
EM: Round [796] log likelihood: -8628.573320
EM: Round [797] log likelihood: -8628.572559
EM: Round [798] log likelihood: -8628.571799
EM: Round [799] log likelihood: -8628.571039
EM: Round [800] log likelihood: -8628.570281
EM: Round [801] log likelihood: -8628.569523
EM: Round [802] log likelihood: -8628.568766
EM: Round [803] log likelihood: -8628.568010
EM: Round [804] log likelihood: -8628.567255
EM: Round [805] log likelihood: -8628.566501
EM: Round [806] log likelihood: -8628.565748
EM: Round [807] log likelihood: -8628.564996
EM: Round [808] log likelihood: -8628.564244
EM: Round [809] log likelihood: -8628.563494
EM: Round [810] log likelihood: -8628.562744
EM: Round [811] log likelihood: -8628.561996
EM: Round [812] log likelihood: -8628.561248
EM: Round [813] log likelihood: -8628.560501
EM: Round [814] log likelihood: -8628.559755
EM: Round [815] log likelihood: -8628.559010
EM: Round [816] log likelihood: -8628.558266
EM: Round [817] log likelihood: -8628.557522
EM: Round [818] log likelihood: -8628.556780
EM: Round [819] log likelihood: -8628.556038
EM: Round [820] log likelihood: -8628.555298
EM: Round [821] log likelihood: -8628.554558
EM: Round [822] log likelihood: -8628.553819
EM: Round [823] log likelihood: -8628.553081
EM: Round [824] log likelihood: -8628.552344
EM: Round [825] log likelihood: -8628.551607
EM: Round [826] log likelihood: -8628.550872
EM: Round [827] log likelihood: -8628.550137
EM: Round [828] log likelihood: -8628.549404
EM: Round [829] log likelihood: -8628.548671
EM: Round [830] log likelihood: -8628.547939
EM: Round [831] log likelihood: -8628.547208
EM: Round [832] log likelihood: -8628.546477
EM: Round [833] log likelihood: -8628.545748
EM: Round [834] log likelihood: -8628.545019
EM: Round [835] log likelihood: -8628.544292
EM: Round [836] log likelihood: -8628.543565
EM: Round [837] log likelihood: -8628.542839
EM: Round [838] log likelihood: -8628.542114
EM: Round [839] log likelihood: -8628.541389
EM: Round [840] log likelihood: -8628.540666
EM: Round [841] log likelihood: -8628.539943
EM: Round [842] log likelihood: -8628.539221
EM: Round [843] log likelihood: -8628.538500
EM: Round [844] log likelihood: -8628.537780
EM: Round [845] log likelihood: -8628.537061
EM: Round [846] log likelihood: -8628.536343
EM: Round [847] log likelihood: -8628.535625
EM: Round [848] log likelihood: -8628.534908
EM: Round [849] log likelihood: -8628.534192
EM: Round [850] log likelihood: -8628.533477
EM: Round [851] log likelihood: -8628.532763
EM: Round [852] log likelihood: -8628.532050
EM: Round [853] log likelihood: -8628.531337
EM: Round [854] log likelihood: -8628.530625
EM: Round [855] log likelihood: -8628.529914
EM: Round [856] log likelihood: -8628.529204
EM: Round [857] log likelihood: -8628.528495
EM: Round [858] log likelihood: -8628.527786
EM: Round [859] log likelihood: -8628.527078
EM: Round [860] log likelihood: -8628.526372
EM: Round [861] log likelihood: -8628.525665
EM: Round [862] log likelihood: -8628.524960
EM: Round [863] log likelihood: -8628.524256
EM: Round [864] log likelihood: -8628.523552
EM: Round [865] log likelihood: -8628.522849
EM: Round [866] log likelihood: -8628.522147
EM: Round [867] log likelihood: -8628.521446
EM: Round [868] log likelihood: -8628.520746
EM: Round [869] log likelihood: -8628.520046
EM: Round [870] log likelihood: -8628.519347
EM: Round [871] log likelihood: -8628.518649
EM: Round [872] log likelihood: -8628.517952
EM: Round [873] log likelihood: -8628.517256
EM: Round [874] log likelihood: -8628.516560
EM: Round [875] log likelihood: -8628.515865
EM: Round [876] log likelihood: -8628.515171
EM: Round [877] log likelihood: -8628.514478
EM: Round [878] log likelihood: -8628.513785
EM: Round [879] log likelihood: -8628.513094
EM: Round [880] log likelihood: -8628.512403
EM: Round [881] log likelihood: -8628.511713
EM: Round [882] log likelihood: -8628.511023
EM: Round [883] log likelihood: -8628.510335
EM: Round [884] log likelihood: -8628.509647
EM: Round [885] log likelihood: -8628.508960
EM: Round [886] log likelihood: -8628.508274
EM: Round [887] log likelihood: -8628.507588
EM: Round [888] log likelihood: -8628.506904
EM: Round [889] log likelihood: -8628.506220
EM: Round [890] log likelihood: -8628.505537
EM: Round [891] log likelihood: -8628.504854
EM: Round [892] log likelihood: -8628.504173
EM: Round [893] log likelihood: -8628.503492
EM: Round [894] log likelihood: -8628.502812
EM: Round [895] log likelihood: -8628.502132
EM: Round [896] log likelihood: -8628.501454
EM: Round [897] log likelihood: -8628.500776
EM: Round [898] log likelihood: -8628.500099
EM: Round [899] log likelihood: -8628.499423
EM: Round [900] log likelihood: -8628.498747
EM: Round [901] log likelihood: -8628.498073
EM: Round [902] log likelihood: -8628.497399
EM: Round [903] log likelihood: -8628.496725
EM: Round [904] log likelihood: -8628.496053
EM: Round [905] log likelihood: -8628.495381
EM: Round [906] log likelihood: -8628.494710
EM: Round [907] log likelihood: -8628.494040
EM: Round [908] log likelihood: -8628.493371
EM: Round [909] log likelihood: -8628.492702
EM: Round [910] log likelihood: -8628.492034
EM: Round [911] log likelihood: -8628.491367
EM: Round [912] log likelihood: -8628.490700
EM: Round [913] log likelihood: -8628.490034
EM: Round [914] log likelihood: -8628.489369
EM: Round [915] log likelihood: -8628.488705
EM: Round [916] log likelihood: -8628.488041
EM: Round [917] log likelihood: -8628.487379
EM: Round [918] log likelihood: -8628.486716
EM: Round [919] log likelihood: -8628.486055
EM: Round [920] log likelihood: -8628.485395
EM: Round [921] log likelihood: -8628.484735
EM: Round [922] log likelihood: -8628.484075
EM: Round [923] log likelihood: -8628.483417
EM: Round [924] log likelihood: -8628.482759
EM: Round [925] log likelihood: -8628.482102
EM: Round [926] log likelihood: -8628.481446
EM: Round [927] log likelihood: -8628.480790
EM: Round [928] log likelihood: -8628.480136
EM: Round [929] log likelihood: -8628.479482
EM: Round [930] log likelihood: -8628.478828
EM: Round [931] log likelihood: -8628.478175
EM: Round [932] log likelihood: -8628.477524
EM: Round [933] log likelihood: -8628.476872
EM: Round [934] log likelihood: -8628.476222
EM: Round [935] log likelihood: -8628.475572
EM: Round [936] log likelihood: -8628.474923
EM: Round [937] log likelihood: -8628.474274
EM: Round [938] log likelihood: -8628.473627
EM: Round [939] log likelihood: -8628.472980
EM: Round [940] log likelihood: -8628.472333
EM: Round [941] log likelihood: -8628.471688
EM: Round [942] log likelihood: -8628.471043
EM: Round [943] log likelihood: -8628.470399
EM: Round [944] log likelihood: -8628.469755
EM: Round [945] log likelihood: -8628.469113
EM: Round [946] log likelihood: -8628.468471
EM: Round [947] log likelihood: -8628.467829
EM: Round [948] log likelihood: -8628.467188
EM: Round [949] log likelihood: -8628.466548
EM: Round [950] log likelihood: -8628.465909
EM: Round [951] log likelihood: -8628.465271
EM: Round [952] log likelihood: -8628.464633
EM: Round [953] log likelihood: -8628.463995
EM: Round [954] log likelihood: -8628.463359
EM: Round [955] log likelihood: -8628.462723
EM: Round [956] log likelihood: -8628.462088
EM: Round [957] log likelihood: -8628.461453
EM: Round [958] log likelihood: -8628.460820
EM: Round [959] log likelihood: -8628.460187
EM: Round [960] log likelihood: -8628.459554
EM: Round [961] log likelihood: -8628.458922
EM: Round [962] log likelihood: -8628.458291
EM: Round [963] log likelihood: -8628.457661
EM: Round [964] log likelihood: -8628.457031
EM: Round [965] log likelihood: -8628.456402
EM: Round [966] log likelihood: -8628.455774
EM: Round [967] log likelihood: -8628.455146
EM: Round [968] log likelihood: -8628.454519
EM: Round [969] log likelihood: -8628.453893
EM: Round [970] log likelihood: -8628.453267
EM: Round [971] log likelihood: -8628.452642
EM: Round [972] log likelihood: -8628.452018
EM: Round [973] log likelihood: -8628.451394
EM: Round [974] log likelihood: -8628.450771
EM: Round [975] log likelihood: -8628.450149
EM: Round [976] log likelihood: -8628.449527
EM: Round [977] log likelihood: -8628.448906
EM: Round [978] log likelihood: -8628.448286
EM: Round [979] log likelihood: -8628.447666
EM: Round [980] log likelihood: -8628.447047
EM: Round [981] log likelihood: -8628.446429
EM: Round [982] log likelihood: -8628.445811
EM: Round [983] log likelihood: -8628.445194
EM: Round [984] log likelihood: -8628.444578
EM: Round [985] log likelihood: -8628.443962
EM: Round [986] log likelihood: -8628.443347
EM: Round [987] log likelihood: -8628.442732
EM: Round [988] log likelihood: -8628.442119
EM: Round [989] log likelihood: -8628.441505
EM: Round [990] log likelihood: -8628.440893
EM: Round [991] log likelihood: -8628.440281
EM: Round [992] log likelihood: -8628.439670
EM: Round [993] log likelihood: -8628.439059
EM: Round [994] log likelihood: -8628.438449
EM: Round [995] log likelihood: -8628.437840
EM: Round [996] log likelihood: -8628.437231
EM: Round [997] log likelihood: -8628.436623
EM: Round [998] log likelihood: -8628.436016
EM: Round [999] log likelihood: -8628.435409
EM: Round [1000] log likelihood: -8628.434803
EM: Round [1001] log likelihood: -8628.434198
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam into /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.bIDYTem8xp/786-O_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.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords > /tmp/nxf.bIDYTem8xp/786-O_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.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.bIDYTem8xp/786-O_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.bIDYTem8xp/fi_workdir/786-O_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.bIDYTem8xp/fi_workdir/786-O_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.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -8170.064007
EM: Round [1] log likelihood: -8169.422296
EM: Round [2] log likelihood: -8169.417938
EM: Round [3] log likelihood: -8169.414856
EM: Round [4] log likelihood: -8169.411793
EM: Round [5] log likelihood: -8169.408741
EM: Round [6] log likelihood: -8169.405700
EM: Round [7] log likelihood: -8169.402669
EM: Round [8] log likelihood: -8169.399649
EM: Round [9] log likelihood: -8169.396639
EM: Round [10] log likelihood: -8169.393639
EM: Round [11] log likelihood: -8169.390650
EM: Round [12] log likelihood: -8169.387671
EM: Round [13] log likelihood: -8169.384702
EM: Round [14] log likelihood: -8169.381743
EM: Round [15] log likelihood: -8169.378795
EM: Round [16] log likelihood: -8169.375856
EM: Round [17] log likelihood: -8169.372927
EM: Round [18] log likelihood: -8169.370008
EM: Round [19] log likelihood: -8169.367099
EM: Round [20] log likelihood: -8169.364199
EM: Round [21] log likelihood: -8169.361310
EM: Round [22] log likelihood: -8169.358429
EM: Round [23] log likelihood: -8169.355559
EM: Round [24] log likelihood: -8169.352698
EM: Round [25] log likelihood: -8169.349846
EM: Round [26] log likelihood: -8169.347004
EM: Round [27] log likelihood: -8169.344170
EM: Round [28] log likelihood: -8169.341347
EM: Round [29] log likelihood: -8169.338532
EM: Round [30] log likelihood: -8169.335727
EM: Round [31] log likelihood: -8169.332930
EM: Round [32] log likelihood: -8169.330143
EM: Round [33] log likelihood: -8169.327365
EM: Round [34] log likelihood: -8169.324595
EM: Round [35] log likelihood: -8169.321835
EM: Round [36] log likelihood: -8169.319083
EM: Round [37] log likelihood: -8169.316340
EM: Round [38] log likelihood: -8169.313606
EM: Round [39] log likelihood: -8169.310880
EM: Round [40] log likelihood: -8169.308163
EM: Round [41] log likelihood: -8169.305455
EM: Round [42] log likelihood: -8169.302755
EM: Round [43] log likelihood: -8169.300064
EM: Round [44] log likelihood: -8169.297381
EM: Round [45] log likelihood: -8169.294706
EM: Round [46] log likelihood: -8169.292040
EM: Round [47] log likelihood: -8169.289382
EM: Round [48] log likelihood: -8169.286732
EM: Round [49] log likelihood: -8169.284090
EM: Round [50] log likelihood: -8169.281457
EM: Round [51] log likelihood: -8169.278831
EM: Round [52] log likelihood: -8169.276214
EM: Round [53] log likelihood: -8169.273604
EM: Round [54] log likelihood: -8169.271003
EM: Round [55] log likelihood: -8169.268409
EM: Round [56] log likelihood: -8169.265824
EM: Round [57] log likelihood: -8169.263246
EM: Round [58] log likelihood: -8169.260676
EM: Round [59] log likelihood: -8169.258113
EM: Round [60] log likelihood: -8169.255559
EM: Round [61] log likelihood: -8169.253012
EM: Round [62] log likelihood: -8169.250472
EM: Round [63] log likelihood: -8169.247940
EM: Round [64] log likelihood: -8169.245416
EM: Round [65] log likelihood: -8169.242899
EM: Round [66] log likelihood: -8169.240390
EM: Round [67] log likelihood: -8169.237887
EM: Round [68] log likelihood: -8169.235393
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EM: Round [985] log likelihood: -8168.178985
EM: Round [986] log likelihood: -8168.178409
EM: Round [987] log likelihood: -8168.177833
EM: Round [988] log likelihood: -8168.177259
EM: Round [989] log likelihood: -8168.176685
EM: Round [990] log likelihood: -8168.176111
EM: Round [991] log likelihood: -8168.175538
EM: Round [992] log likelihood: -8168.174966
EM: Round [993] log likelihood: -8168.174394
EM: Round [994] log likelihood: -8168.173823
EM: Round [995] log likelihood: -8168.173252
EM: Round [996] log likelihood: -8168.172682
EM: Round [997] log likelihood: -8168.172113
EM: Round [998] log likelihood: -8168.171544
EM: Round [999] log likelihood: -8168.170975
EM: Round [1000] log likelihood: -8168.170408
EM: Round [1001] log likelihood: -8168.169841
-total frags in /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz: 294468379
Warning - not locating file: /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.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 [ENSG00000285169.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000176593.8]
WARNING, no entry stored in dbm for [ENSG00000176593.8]
ls: cannot access 'IGV_inputs': No such file or directory