Done.
-parsing GTF file: /tmp/nxf.cfy5G5uomt/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.cfy5G5uomt/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.cfy5G5uomt/786-O_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.cfy5G5uomt/786-O_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.cfy5G5uomt/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.cfy5G5uomt/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
23:54:05 : INFO : Done.
-parsing GTF file: /tmp/nxf.cfy5G5uomt/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf
-parsing /tmp/nxf.cfy5G5uomt/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam

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[2520000]   -done parsing /tmp/nxf.cfy5G5uomt/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 26,
          'exons hit < 2' => 24,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 12,
          'small anchor length' => 256,
          'num genes matched < 2' => 17,
          'low complexity anchor region' => 4,
          ' ** passed ** ' => 43517,
          'seq-similar region overlap' => 9,
          'per_id < 96' => 14652,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 491,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
          'excessive soft clipping' => 16345,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 12
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.cfy5G5uomt/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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[72000]   -fusion SPANNING read extraction for scaff: GUSB--NAIP

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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

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

[1000]   
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[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[13000]   
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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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[6000]   
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[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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[30000]   
[31000]   
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[34000]   
[35000]   
[36000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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

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[8000]   
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[19000]   
[20000]   
[21000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[22000]   
[23000]   -fusion SPANNING read extraction for scaff: ZKSCAN7--KIF15
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 31849,
          'seq similar region alignment' => 32589
        };
EM: Starting log likelihood: -8471.129082
EM: Round [1] log likelihood: -8464.273431
EM: Round [2] log likelihood: -8464.266906
EM: Round [3] log likelihood: -8464.262965
EM: Round [4] log likelihood: -8464.259042
EM: Round [5] log likelihood: -8464.255137
EM: Round [6] log likelihood: -8464.251248
EM: Round [7] log likelihood: -8464.247377
EM: Round [8] log likelihood: -8464.243522
EM: Round [9] log likelihood: -8464.239683
EM: Round [10] log likelihood: -8464.235861
EM: Round [11] log likelihood: -8464.232055
EM: Round [12] log likelihood: -8464.228265
EM: Round [13] log likelihood: -8464.224491
EM: Round [14] log likelihood: -8464.220733
EM: Round [15] log likelihood: -8464.216991
EM: Round [16] log likelihood: -8464.213264
EM: Round [17] log likelihood: -8464.209553
EM: Round [18] log likelihood: -8464.205857
EM: Round [19] log likelihood: -8464.202177
EM: Round [20] log likelihood: -8464.198512
EM: Round [21] log likelihood: -8464.194861
EM: Round [22] log likelihood: -8464.191226
EM: Round [23] log likelihood: -8464.187605
EM: Round [24] log likelihood: -8464.183999
EM: Round [25] log likelihood: -8464.180407
EM: Round [26] log likelihood: -8464.176830
EM: Round [27] log likelihood: -8464.173267
EM: Round [28] log likelihood: -8464.169719
EM: Round [29] log likelihood: -8464.166184
EM: Round [30] log likelihood: -8464.162664
EM: Round [31] log likelihood: -8464.159157
EM: Round [32] log likelihood: -8464.155665
EM: Round [33] log likelihood: -8464.152186
EM: Round [34] log likelihood: -8464.148720
EM: Round [35] log likelihood: -8464.145268
EM: Round [36] log likelihood: -8464.141830
EM: Round [37] log likelihood: -8464.138405
EM: Round [38] log likelihood: -8464.134993
EM: Round [39] log likelihood: -8464.131594
EM: Round [40] log likelihood: -8464.128208
EM: Round [41] log likelihood: -8464.124835
EM: Round [42] log likelihood: -8464.121475
EM: Round [43] log likelihood: -8464.118127
EM: Round [44] log likelihood: -8464.114793
EM: Round [45] log likelihood: -8464.111470
EM: Round [46] log likelihood: -8464.108161
EM: Round [47] log likelihood: -8464.104863
EM: Round [48] log likelihood: -8464.101578
EM: Round [49] log likelihood: -8464.098306
EM: Round [50] log likelihood: -8464.095045
EM: Round [51] log likelihood: -8464.091796
EM: Round [52] log likelihood: -8464.088560
EM: Round [53] log likelihood: -8464.085335
EM: Round [54] log likelihood: -8464.082122
EM: Round [55] log likelihood: -8464.078920
EM: Round [56] log likelihood: -8464.075731
EM: Round [57] log likelihood: -8464.072553
EM: Round [58] log likelihood: -8464.069386
EM: Round [59] log likelihood: -8464.066231
EM: Round [60] log likelihood: -8464.063087
EM: Round [61] log likelihood: -8464.059954
EM: Round [62] log likelihood: -8464.056832
EM: Round [63] log likelihood: -8464.053722
EM: Round [64] log likelihood: -8464.050623
EM: Round [65] log likelihood: -8464.047534
EM: Round [66] log likelihood: -8464.044457
EM: Round [67] log likelihood: -8464.041390
EM: Round [68] log likelihood: -8464.038334
EM: Round [69] log likelihood: -8464.035288
EM: Round [70] log likelihood: -8464.032254
EM: Round [71] log likelihood: -8464.029229
EM: Round [72] log likelihood: -8464.026215
EM: Round [73] log likelihood: -8464.023212
EM: Round [74] log likelihood: -8464.020219
EM: Round [75] log likelihood: -8464.017236
EM: Round [76] log likelihood: -8464.014263
EM: Round [77] log likelihood: -8464.011301
EM: Round [78] log likelihood: -8464.008348
EM: Round [79] log likelihood: -8464.005406
EM: Round [80] log likelihood: -8464.002473
EM: Round [81] log likelihood: -8463.999551
EM: Round [82] log likelihood: -8463.996638
EM: Round [83] log likelihood: -8463.993735
EM: Round [84] log likelihood: -8463.990841
EM: Round [85] log likelihood: -8463.987958
EM: Round [86] log likelihood: -8463.985083
EM: Round [87] log likelihood: -8463.982219
EM: Round [88] log likelihood: -8463.979363
EM: Round [89] log likelihood: -8463.976518
EM: Round [90] log likelihood: -8463.973681
EM: Round [91] log likelihood: -8463.970854
EM: Round [92] log likelihood: -8463.968036
EM: Round [93] log likelihood: -8463.965227
EM: Round [94] log likelihood: -8463.962427
EM: Round [95] log likelihood: -8463.959636
EM: Round [96] log likelihood: -8463.956855
EM: Round [97] log likelihood: -8463.954082
EM: Round [98] log likelihood: -8463.951318
EM: Round [99] log likelihood: -8463.948563
EM: Round [100] log likelihood: -8463.945817
EM: Round [101] log likelihood: -8463.943079
EM: Round [102] log likelihood: -8463.940351
EM: Round [103] log likelihood: -8463.937630
EM: Round [104] log likelihood: -8463.934919
EM: Round [105] log likelihood: -8463.932216
EM: Round [106] log likelihood: -8463.929521
EM: Round [107] log likelihood: -8463.926835
EM: Round [108] log likelihood: -8463.924157
EM: Round [109] log likelihood: -8463.921488
EM: Round [110] log likelihood: -8463.918827
EM: Round [111] log likelihood: -8463.916174
EM: Round [112] log likelihood: -8463.913529
EM: Round [113] log likelihood: -8463.910893
EM: Round [114] log likelihood: -8463.908264
EM: Round [115] log likelihood: -8463.905644
EM: Round [116] log likelihood: -8463.903031
EM: Round [117] log likelihood: -8463.900427
EM: Round [118] log likelihood: -8463.897831
EM: Round [119] log likelihood: -8463.895242
EM: Round [120] log likelihood: -8463.892661
EM: Round [121] log likelihood: -8463.890088
EM: Round [122] log likelihood: -8463.887523
EM: Round [123] log likelihood: -8463.884965
EM: Round [124] log likelihood: -8463.882415
EM: Round [125] log likelihood: -8463.879873
EM: Round [126] log likelihood: -8463.877338
EM: Round [127] log likelihood: -8463.874811
EM: Round [128] log likelihood: -8463.872291
EM: Round [129] log likelihood: -8463.869779
EM: Round [130] log likelihood: -8463.867274
EM: Round [131] log likelihood: -8463.864777
EM: Round [132] log likelihood: -8463.862287
EM: Round [133] log likelihood: -8463.859804
EM: Round [134] log likelihood: -8463.857328
EM: Round [135] log likelihood: -8463.854860
EM: Round [136] log likelihood: -8463.852399
EM: Round [137] log likelihood: -8463.849945
EM: Round [138] log likelihood: -8463.847498
EM: Round [139] log likelihood: -8463.845058
EM: Round [140] log likelihood: -8463.842625
EM: Round [141] log likelihood: -8463.840199
EM: Round [142] log likelihood: -8463.837780
EM: Round [143] log likelihood: -8463.835368
EM: Round [144] log likelihood: -8463.832962
EM: Round [145] log likelihood: -8463.830564
EM: Round [146] log likelihood: -8463.828172
EM: Round [147] log likelihood: -8463.825788
EM: Round [148] log likelihood: -8463.823410
EM: Round [149] log likelihood: -8463.821038
EM: Round [150] log likelihood: -8463.818673
EM: Round [151] log likelihood: -8463.816315
EM: Round [152] log likelihood: -8463.813964
EM: Round [153] log likelihood: -8463.811619
EM: Round [154] log likelihood: -8463.809280
EM: Round [155] log likelihood: -8463.806948
EM: Round [156] log likelihood: -8463.804623
EM: Round [157] log likelihood: -8463.802304
EM: Round [158] log likelihood: -8463.799991
EM: Round [159] log likelihood: -8463.797685
EM: Round [160] log likelihood: -8463.795385
EM: Round [161] log likelihood: -8463.793091
EM: Round [162] log likelihood: -8463.790804
EM: Round [163] log likelihood: -8463.788523
EM: Round [164] log likelihood: -8463.786248
EM: Round [165] log likelihood: -8463.783979
EM: Round [166] log likelihood: -8463.781716
EM: Round [167] log likelihood: -8463.779460
EM: Round [168] log likelihood: -8463.777209
EM: Round [169] log likelihood: -8463.774965
EM: Round [170] log likelihood: -8463.772726
EM: Round [171] log likelihood: -8463.770494
EM: Round [172] log likelihood: -8463.768268
EM: Round [173] log likelihood: -8463.766047
EM: Round [174] log likelihood: -8463.763832
EM: Round [175] log likelihood: -8463.761624
EM: Round [176] log likelihood: -8463.759421
EM: Round [177] log likelihood: -8463.757224
EM: Round [178] log likelihood: -8463.755032
EM: Round [179] log likelihood: -8463.752847
EM: Round [180] log likelihood: -8463.750667
EM: Round [181] log likelihood: -8463.748493
EM: Round [182] log likelihood: -8463.746325
EM: Round [183] log likelihood: -8463.744162
EM: Round [184] log likelihood: -8463.742005
EM: Round [185] log likelihood: -8463.739853
EM: Round [186] log likelihood: -8463.737707
EM: Round [187] log likelihood: -8463.735567
EM: Round [188] log likelihood: -8463.733432
EM: Round [189] log likelihood: -8463.731303
EM: Round [190] log likelihood: -8463.729179
EM: Round [191] log likelihood: -8463.727060
EM: Round [192] log likelihood: -8463.724947
EM: Round [193] log likelihood: -8463.722839
EM: Round [194] log likelihood: -8463.720737
EM: Round [195] log likelihood: -8463.718640
EM: Round [196] log likelihood: -8463.716548
EM: Round [197] log likelihood: -8463.714462
EM: Round [198] log likelihood: -8463.712381
EM: Round [199] log likelihood: -8463.710305
EM: Round [200] log likelihood: -8463.708235
EM: Round [201] log likelihood: -8463.706169
EM: Round [202] log likelihood: -8463.704109
EM: Round [203] log likelihood: -8463.702054
EM: Round [204] log likelihood: -8463.700004
EM: Round [205] log likelihood: -8463.697959
EM: Round [206] log likelihood: -8463.695919
EM: Round [207] log likelihood: -8463.693884
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EM: Round [669] log likelihood: -8463.079378
EM: Round [670] log likelihood: -8463.078483
EM: Round [671] log likelihood: -8463.077590
EM: Round [672] log likelihood: -8463.076697
EM: Round [673] log likelihood: -8463.075806
EM: Round [674] log likelihood: -8463.074917
EM: Round [675] log likelihood: -8463.074028
EM: Round [676] log likelihood: -8463.073141
EM: Round [677] log likelihood: -8463.072254
EM: Round [678] log likelihood: -8463.071369
EM: Round [679] log likelihood: -8463.070486
EM: Round [680] log likelihood: -8463.069603
EM: Round [681] log likelihood: -8463.068721
EM: Round [682] log likelihood: -8463.067841
EM: Round [683] log likelihood: -8463.066962
EM: Round [684] log likelihood: -8463.066084
EM: Round [685] log likelihood: -8463.065207
EM: Round [686] log likelihood: -8463.064331
EM: Round [687] log likelihood: -8463.063457
EM: Round [688] log likelihood: -8463.062583
EM: Round [689] log likelihood: -8463.061711
EM: Round [690] log likelihood: -8463.060840
EM: Round [691] log likelihood: -8463.059970
EM: Round [692] log likelihood: -8463.059101
EM: Round [693] log likelihood: -8463.058233
EM: Round [694] log likelihood: -8463.057367
EM: Round [695] log likelihood: -8463.056501
EM: Round [696] log likelihood: -8463.055637
EM: Round [697] log likelihood: -8463.054774
EM: Round [698] log likelihood: -8463.053912
EM: Round [699] log likelihood: -8463.053051
EM: Round [700] log likelihood: -8463.052191
EM: Round [701] log likelihood: -8463.051332
EM: Round [702] log likelihood: -8463.050475
EM: Round [703] log likelihood: -8463.049619
EM: Round [704] log likelihood: -8463.048763
EM: Round [705] log likelihood: -8463.047909
EM: Round [706] log likelihood: -8463.047056
EM: Round [707] log likelihood: -8463.046204
EM: Round [708] log likelihood: -8463.045353
EM: Round [709] log likelihood: -8463.044503
EM: Round [710] log likelihood: -8463.043655
EM: Round [711] log likelihood: -8463.042807
EM: Round [712] log likelihood: -8463.041960
EM: Round [713] log likelihood: -8463.041115
EM: Round [714] log likelihood: -8463.040271
EM: Round [715] log likelihood: -8463.039428
EM: Round [716] log likelihood: -8463.038585
EM: Round [717] log likelihood: -8463.037744
EM: Round [718] log likelihood: -8463.036904
EM: Round [719] log likelihood: -8463.036065
EM: Round [720] log likelihood: -8463.035228
EM: Round [721] log likelihood: -8463.034391
EM: Round [722] log likelihood: -8463.033555
EM: Round [723] log likelihood: -8463.032721
EM: Round [724] log likelihood: -8463.031887
EM: Round [725] log likelihood: -8463.031055
EM: Round [726] log likelihood: -8463.030223
EM: Round [727] log likelihood: -8463.029393
EM: Round [728] log likelihood: -8463.028564
EM: Round [729] log likelihood: -8463.027735
EM: Round [730] log likelihood: -8463.026908
EM: Round [731] log likelihood: -8463.026082
EM: Round [732] log likelihood: -8463.025257
EM: Round [733] log likelihood: -8463.024433
EM: Round [734] log likelihood: -8463.023610
EM: Round [735] log likelihood: -8463.022788
EM: Round [736] log likelihood: -8463.021967
EM: Round [737] log likelihood: -8463.021147
EM: Round [738] log likelihood: -8463.020328
EM: Round [739] log likelihood: -8463.019510
EM: Round [740] log likelihood: -8463.018694
EM: Round [741] log likelihood: -8463.017878
EM: Round [742] log likelihood: -8463.017063
EM: Round [743] log likelihood: -8463.016249
EM: Round [744] log likelihood: -8463.015437
EM: Round [745] log likelihood: -8463.014625
EM: Round [746] log likelihood: -8463.013814
EM: Round [747] log likelihood: -8463.013005
EM: Round [748] log likelihood: -8463.012196
EM: Round [749] log likelihood: -8463.011389
EM: Round [750] log likelihood: -8463.010582
EM: Round [751] log likelihood: -8463.009776
EM: Round [752] log likelihood: -8463.008972
EM: Round [753] log likelihood: -8463.008168
EM: Round [754] log likelihood: -8463.007366
EM: Round [755] log likelihood: -8463.006564
EM: Round [756] log likelihood: -8463.005764
EM: Round [757] log likelihood: -8463.004964
EM: Round [758] log likelihood: -8463.004165
EM: Round [759] log likelihood: -8463.003368
EM: Round [760] log likelihood: -8463.002571
EM: Round [761] log likelihood: -8463.001776
EM: Round [762] log likelihood: -8463.000981
EM: Round [763] log likelihood: -8463.000187
EM: Round [764] log likelihood: -8462.999395
EM: Round [765] log likelihood: -8462.998603
EM: Round [766] log likelihood: -8462.997812
EM: Round [767] log likelihood: -8462.997023
EM: Round [768] log likelihood: -8462.996234
EM: Round [769] log likelihood: -8462.995446
EM: Round [770] log likelihood: -8462.994659
EM: Round [771] log likelihood: -8462.993873
EM: Round [772] log likelihood: -8462.993089
EM: Round [773] log likelihood: -8462.992305
EM: Round [774] log likelihood: -8462.991522
EM: Round [775] log likelihood: -8462.990740
EM: Round [776] log likelihood: -8462.989959
EM: Round [777] log likelihood: -8462.989179
EM: Round [778] log likelihood: -8462.988399
EM: Round [779] log likelihood: -8462.987621
EM: Round [780] log likelihood: -8462.986844
EM: Round [781] log likelihood: -8462.986068
EM: Round [782] log likelihood: -8462.985292
EM: Round [783] log likelihood: -8462.984518
EM: Round [784] log likelihood: -8462.983745
EM: Round [785] log likelihood: -8462.982972
EM: Round [786] log likelihood: -8462.982201
EM: Round [787] log likelihood: -8462.981430
EM: Round [788] log likelihood: -8462.980660
EM: Round [789] log likelihood: -8462.979892
EM: Round [790] log likelihood: -8462.979124
EM: Round [791] log likelihood: -8462.978357
EM: Round [792] log likelihood: -8462.977591
EM: Round [793] log likelihood: -8462.976826
EM: Round [794] log likelihood: -8462.976062
EM: Round [795] log likelihood: -8462.975299
EM: Round [796] log likelihood: -8462.974536
EM: Round [797] log likelihood: -8462.973775
EM: Round [798] log likelihood: -8462.973015
EM: Round [799] log likelihood: -8462.972255
EM: Round [800] log likelihood: -8462.971496
EM: Round [801] log likelihood: -8462.970739
EM: Round [802] log likelihood: -8462.969982
EM: Round [803] log likelihood: -8462.969226
EM: Round [804] log likelihood: -8462.968471
EM: Round [805] log likelihood: -8462.967717
EM: Round [806] log likelihood: -8462.966964
EM: Round [807] log likelihood: -8462.966212
EM: Round [808] log likelihood: -8462.965460
EM: Round [809] log likelihood: -8462.964710
EM: Round [810] log likelihood: -8462.963960
EM: Round [811] log likelihood: -8462.963212
EM: Round [812] log likelihood: -8462.962464
EM: Round [813] log likelihood: -8462.961717
EM: Round [814] log likelihood: -8462.960971
EM: Round [815] log likelihood: -8462.960226
EM: Round [816] log likelihood: -8462.959482
EM: Round [817] log likelihood: -8462.958738
EM: Round [818] log likelihood: -8462.957996
EM: Round [819] log likelihood: -8462.957254
EM: Round [820] log likelihood: -8462.956514
EM: Round [821] log likelihood: -8462.955774
EM: Round [822] log likelihood: -8462.955035
EM: Round [823] log likelihood: -8462.954297
EM: Round [824] log likelihood: -8462.953560
EM: Round [825] log likelihood: -8462.952823
EM: Round [826] log likelihood: -8462.952088
EM: Round [827] log likelihood: -8462.951353
EM: Round [828] log likelihood: -8462.950619
EM: Round [829] log likelihood: -8462.949887
EM: Round [830] log likelihood: -8462.949155
EM: Round [831] log likelihood: -8462.948423
EM: Round [832] log likelihood: -8462.947693
EM: Round [833] log likelihood: -8462.946964
EM: Round [834] log likelihood: -8462.946235
EM: Round [835] log likelihood: -8462.945507
EM: Round [836] log likelihood: -8462.944781
EM: Round [837] log likelihood: -8462.944055
EM: Round [838] log likelihood: -8462.943329
EM: Round [839] log likelihood: -8462.942605
EM: Round [840] log likelihood: -8462.941882
EM: Round [841] log likelihood: -8462.941159
EM: Round [842] log likelihood: -8462.940437
EM: Round [843] log likelihood: -8462.939716
EM: Round [844] log likelihood: -8462.938996
EM: Round [845] log likelihood: -8462.938277
EM: Round [846] log likelihood: -8462.937559
EM: Round [847] log likelihood: -8462.936841
EM: Round [848] log likelihood: -8462.936124
EM: Round [849] log likelihood: -8462.935408
EM: Round [850] log likelihood: -8462.934693
EM: Round [851] log likelihood: -8462.933979
EM: Round [852] log likelihood: -8462.933265
EM: Round [853] log likelihood: -8462.932553
EM: Round [854] log likelihood: -8462.931841
EM: Round [855] log likelihood: -8462.931130
EM: Round [856] log likelihood: -8462.930420
EM: Round [857] log likelihood: -8462.929711
EM: Round [858] log likelihood: -8462.929002
EM: Round [859] log likelihood: -8462.928294
EM: Round [860] log likelihood: -8462.927587
EM: Round [861] log likelihood: -8462.926881
EM: Round [862] log likelihood: -8462.926176
EM: Round [863] log likelihood: -8462.925472
EM: Round [864] log likelihood: -8462.924768
EM: Round [865] log likelihood: -8462.924065
EM: Round [866] log likelihood: -8462.923363
EM: Round [867] log likelihood: -8462.922662
EM: Round [868] log likelihood: -8462.921962
EM: Round [869] log likelihood: -8462.921262
EM: Round [870] log likelihood: -8462.920563
EM: Round [871] log likelihood: -8462.919865
EM: Round [872] log likelihood: -8462.919168
EM: Round [873] log likelihood: -8462.918471
EM: Round [874] log likelihood: -8462.917776
EM: Round [875] log likelihood: -8462.917081
EM: Round [876] log likelihood: -8462.916387
EM: Round [877] log likelihood: -8462.915694
EM: Round [878] log likelihood: -8462.915001
EM: Round [879] log likelihood: -8462.914310
EM: Round [880] log likelihood: -8462.913619
EM: Round [881] log likelihood: -8462.912928
EM: Round [882] log likelihood: -8462.912239
EM: Round [883] log likelihood: -8462.911551
EM: Round [884] log likelihood: -8462.910863
EM: Round [885] log likelihood: -8462.910176
EM: Round [886] log likelihood: -8462.909490
EM: Round [887] log likelihood: -8462.908804
EM: Round [888] log likelihood: -8462.908120
EM: Round [889] log likelihood: -8462.907436
EM: Round [890] log likelihood: -8462.906752
EM: Round [891] log likelihood: -8462.906070
EM: Round [892] log likelihood: -8462.905389
EM: Round [893] log likelihood: -8462.904708
EM: Round [894] log likelihood: -8462.904028
EM: Round [895] log likelihood: -8462.903348
EM: Round [896] log likelihood: -8462.902670
EM: Round [897] log likelihood: -8462.901992
EM: Round [898] log likelihood: -8462.901315
EM: Round [899] log likelihood: -8462.900639
EM: Round [900] log likelihood: -8462.899963
EM: Round [901] log likelihood: -8462.899289
EM: Round [902] log likelihood: -8462.898615
EM: Round [903] log likelihood: -8462.897941
EM: Round [904] log likelihood: -8462.897269
EM: Round [905] log likelihood: -8462.896597
EM: Round [906] log likelihood: -8462.895926
EM: Round [907] log likelihood: -8462.895256
EM: Round [908] log likelihood: -8462.894586
EM: Round [909] log likelihood: -8462.893918
EM: Round [910] log likelihood: -8462.893250
EM: Round [911] log likelihood: -8462.892582
EM: Round [912] log likelihood: -8462.891916
EM: Round [913] log likelihood: -8462.891250
EM: Round [914] log likelihood: -8462.890585
EM: Round [915] log likelihood: -8462.889921
EM: Round [916] log likelihood: -8462.889257
EM: Round [917] log likelihood: -8462.888595
EM: Round [918] log likelihood: -8462.887932
EM: Round [919] log likelihood: -8462.887271
EM: Round [920] log likelihood: -8462.886610
EM: Round [921] log likelihood: -8462.885951
EM: Round [922] log likelihood: -8462.885291
EM: Round [923] log likelihood: -8462.884633
EM: Round [924] log likelihood: -8462.883975
EM: Round [925] log likelihood: -8462.883318
EM: Round [926] log likelihood: -8462.882662
EM: Round [927] log likelihood: -8462.882006
EM: Round [928] log likelihood: -8462.881352
EM: Round [929] log likelihood: -8462.880697
EM: Round [930] log likelihood: -8462.880044
EM: Round [931] log likelihood: -8462.879391
EM: Round [932] log likelihood: -8462.878739
EM: Round [933] log likelihood: -8462.878088
EM: Round [934] log likelihood: -8462.877438
EM: Round [935] log likelihood: -8462.876788
EM: Round [936] log likelihood: -8462.876139
EM: Round [937] log likelihood: -8462.875490
EM: Round [938] log likelihood: -8462.874843
EM: Round [939] log likelihood: -8462.874196
EM: Round [940] log likelihood: -8462.873549
EM: Round [941] log likelihood: -8462.872904
EM: Round [942] log likelihood: -8462.872259
EM: Round [943] log likelihood: -8462.871615
EM: Round [944] log likelihood: -8462.870971
EM: Round [945] log likelihood: -8462.870329
EM: Round [946] log likelihood: -8462.869686
EM: Round [947] log likelihood: -8462.869045
EM: Round [948] log likelihood: -8462.868404
EM: Round [949] log likelihood: -8462.867764
EM: Round [950] log likelihood: -8462.867125
EM: Round [951] log likelihood: -8462.866487
EM: Round [952] log likelihood: -8462.865849
EM: Round [953] log likelihood: -8462.865211
EM: Round [954] log likelihood: -8462.864575
EM: Round [955] log likelihood: -8462.863939
EM: Round [956] log likelihood: -8462.863304
EM: Round [957] log likelihood: -8462.862669
EM: Round [958] log likelihood: -8462.862036
EM: Round [959] log likelihood: -8462.861403
EM: Round [960] log likelihood: -8462.860770
EM: Round [961] log likelihood: -8462.860138
EM: Round [962] log likelihood: -8462.859507
EM: Round [963] log likelihood: -8462.858877
EM: Round [964] log likelihood: -8462.858247
EM: Round [965] log likelihood: -8462.857618
EM: Round [966] log likelihood: -8462.856990
EM: Round [967] log likelihood: -8462.856362
EM: Round [968] log likelihood: -8462.855735
EM: Round [969] log likelihood: -8462.855109
EM: Round [970] log likelihood: -8462.854483
EM: Round [971] log likelihood: -8462.853858
EM: Round [972] log likelihood: -8462.853234
EM: Round [973] log likelihood: -8462.852610
EM: Round [974] log likelihood: -8462.851987
EM: Round [975] log likelihood: -8462.851365
EM: Round [976] log likelihood: -8462.850743
EM: Round [977] log likelihood: -8462.850122
EM: Round [978] log likelihood: -8462.849502
EM: Round [979] log likelihood: -8462.848882
EM: Round [980] log likelihood: -8462.848263
EM: Round [981] log likelihood: -8462.847645
EM: Round [982] log likelihood: -8462.847027
EM: Round [983] log likelihood: -8462.846410
EM: Round [984] log likelihood: -8462.845794
EM: Round [985] log likelihood: -8462.845178
EM: Round [986] log likelihood: -8462.844563
EM: Round [987] log likelihood: -8462.843948
EM: Round [988] log likelihood: -8462.843334
EM: Round [989] log likelihood: -8462.842721
EM: Round [990] log likelihood: -8462.842109
EM: Round [991] log likelihood: -8462.841497
EM: Round [992] log likelihood: -8462.840886
EM: Round [993] log likelihood: -8462.840275
EM: Round [994] log likelihood: -8462.839665
EM: Round [995] log likelihood: -8462.839056
EM: Round [996] log likelihood: -8462.838447
EM: Round [997] log likelihood: -8462.837839
EM: Round [998] log likelihood: -8462.837232
EM: Round [999] log likelihood: -8462.836625
EM: Round [1000] log likelihood: -8462.836019
EM: Round [1001] log likelihood: -8462.835414
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.cfy5G5uomt/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam into /tmp/nxf.cfy5G5uomt/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.cfy5G5uomt/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.cfy5G5uomt/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords > /tmp/nxf.cfy5G5uomt/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.cfy5G5uomt/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.cfy5G5uomt/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.cfy5G5uomt/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.cfy5G5uomt/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.cfy5G5uomt/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.cfy5G5uomt/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.cfy5G5uomt/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -8004.660077
EM: Round [1] log likelihood: -8004.184587
EM: Round [2] log likelihood: -8004.181395
EM: Round [3] log likelihood: -8004.178321
EM: Round [4] log likelihood: -8004.175258
EM: Round [5] log likelihood: -8004.172206
EM: Round [6] log likelihood: -8004.169165
EM: Round [7] log likelihood: -8004.166134
EM: Round [8] log likelihood: -8004.163114
EM: Round [9] log likelihood: -8004.160104
EM: Round [10] log likelihood: -8004.157104
EM: Round [11] log likelihood: -8004.154115
EM: Round [12] log likelihood: -8004.151136
EM: Round [13] log likelihood: -8004.148167
EM: Round [14] log likelihood: -8004.145208
EM: Round [15] log likelihood: -8004.142259
EM: Round [16] log likelihood: -8004.139321
EM: Round [17] log likelihood: -8004.136392
EM: Round [18] log likelihood: -8004.133473
EM: Round [19] log likelihood: -8004.130564
EM: Round [20] log likelihood: -8004.127664
EM: Round [21] log likelihood: -8004.124774
EM: Round [22] log likelihood: -8004.121894
EM: Round [23] log likelihood: -8004.119024
EM: Round [24] log likelihood: -8004.116162
EM: Round [25] log likelihood: -8004.113311
EM: Round [26] log likelihood: -8004.110468
EM: Round [27] log likelihood: -8004.107635
EM: Round [28] log likelihood: -8004.104811
EM: Round [29] log likelihood: -8004.101997
EM: Round [30] log likelihood: -8004.099191
EM: Round [31] log likelihood: -8004.096395
EM: Round [32] log likelihood: -8004.093608
EM: Round [33] log likelihood: -8004.090829
EM: Round [34] log likelihood: -8004.088060
EM: Round [35] log likelihood: -8004.085299
EM: Round [36] log likelihood: -8004.082548
EM: Round [37] log likelihood: -8004.079805
EM: Round [38] log likelihood: -8004.077071
EM: Round [39] log likelihood: -8004.074345
EM: Round [40] log likelihood: -8004.071628
EM: Round [41] log likelihood: -8004.068920
EM: Round [42] log likelihood: -8004.066220
EM: Round [43] log likelihood: -8004.063528
EM: Round [44] log likelihood: -8004.060845
EM: Round [45] log likelihood: -8004.058171
EM: Round [46] log likelihood: -8004.055504
EM: Round [47] log likelihood: -8004.052846
EM: Round [48] log likelihood: -8004.050197
EM: Round [49] log likelihood: -8004.047555
EM: Round [50] log likelihood: -8004.044921
EM: Round [51] log likelihood: -8004.042296
EM: Round [52] log likelihood: -8004.039679
EM: Round [53] log likelihood: -8004.037069
EM: Round [54] log likelihood: -8004.034468
EM: Round [55] log likelihood: -8004.031874
EM: Round [56] log likelihood: -8004.029289
EM: Round [57] log likelihood: -8004.026711
EM: Round [58] log likelihood: -8004.024141
EM: Round [59] log likelihood: -8004.021578
EM: Round [60] log likelihood: -8004.019024
EM: Round [61] log likelihood: -8004.016476
EM: Round [62] log likelihood: -8004.013937
EM: Round [63] log likelihood: -8004.011405
EM: Round [64] log likelihood: -8004.008881
EM: Round [65] log likelihood: -8004.006364
EM: Round [66] log likelihood: -8004.003854
EM: Round [67] log likelihood: -8004.001352
EM: Round [68] log likelihood: -8003.998858
EM: Round [69] log likelihood: -8003.996370
EM: Round [70] log likelihood: -8003.993890
EM: Round [71] log likelihood: -8003.991417
EM: Round [72] log likelihood: -8003.988951
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EM: Round [988] log likelihood: -8002.940724
EM: Round [989] log likelihood: -8002.940149
EM: Round [990] log likelihood: -8002.939576
EM: Round [991] log likelihood: -8002.939003
EM: Round [992] log likelihood: -8002.938431
EM: Round [993] log likelihood: -8002.937859
EM: Round [994] log likelihood: -8002.937288
EM: Round [995] log likelihood: -8002.936717
EM: Round [996] log likelihood: -8002.936147
EM: Round [997] log likelihood: -8002.935577
EM: Round [998] log likelihood: -8002.935009
EM: Round [999] log likelihood: -8002.934440
EM: Round [1000] log likelihood: -8002.933872
EM: Round [1001] log likelihood: -8002.933305
-total frags in /tmp/nxf.cfy5G5uomt/786-O_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz: 294468379
Warning - not locating file: /tmp/nxf.cfy5G5uomt/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 [ENSG00000176593.8]
WARNING, no entry stored in dbm for [ENSG00000176593.8]
ls: cannot access 'IGV_inputs': No such file or directory