Done.
-parsing GTF file: /tmp/nxf.vwGMaJYqtO/786-O_FFPE_RNA_0001_B23LG7FLT4_2.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.vwGMaJYqtO/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.vwGMaJYqtO/786-O_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz /tmp/nxf.vwGMaJYqtO/786-O_FFPE_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.vwGMaJYqtO/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.vwGMaJYqtO/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
23:54:21 : INFO : Done.
-parsing GTF file: /tmp/nxf.vwGMaJYqtO/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_2.gtf
-parsing /tmp/nxf.vwGMaJYqtO/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam

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[2280000]   -done parsing /tmp/nxf.vwGMaJYqtO/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          ' ** passed ** ' => 46807,
          'per_id < 96' => 12989,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 6,
          'small anchor length' => 242,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 344,
          'num genes matched < 2' => 5,
          'exons hit < 2' => 7,
          'low complexity anchor region' => 14,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 5,
          'excessive soft clipping' => 14858,
          'seq-similar region overlap' => 16
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.vwGMaJYqtO/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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[745000]   
[746000]   -fusion SPANNING read extraction for scaff: LMNA--MEX3A

[1000]   
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[195000]   
[196000]   -fusion SPANNING read extraction for scaff: LRP1B--AC078882.1

[1000]   
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[4000]   
[5000]   
[6000]   
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[8000]   
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[25000]   
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[28000]   
[29000]   
[30000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
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[8000]   
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[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
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[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
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[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
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[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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

[1000]   
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[6000]   
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[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
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[6000]   
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[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
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[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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

[1000]   
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[68000]   
[69000]   
[70000]   
[71000]   
[72000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
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[216000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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

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

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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 = {
          'seq similar region alignment' => 16316,
          'lacks exon overlap' => 28315
        };
EM: Starting log likelihood: -8961.089938
EM: Round [1] log likelihood: -8957.039755
EM: Round [2] log likelihood: -8957.015472
EM: Round [3] log likelihood: -8956.999221
EM: Round [4] log likelihood: -8956.983257
EM: Round [5] log likelihood: -8956.967393
EM: Round [6] log likelihood: -8956.951623
EM: Round [7] log likelihood: -8956.935943
EM: Round [8] log likelihood: -8956.920354
EM: Round [9] log likelihood: -8956.904854
EM: Round [10] log likelihood: -8956.889442
EM: Round [11] log likelihood: -8956.874118
EM: Round [12] log likelihood: -8956.858881
EM: Round [13] log likelihood: -8956.843730
EM: Round [14] log likelihood: -8956.828664
EM: Round [15] log likelihood: -8956.813682
EM: Round [16] log likelihood: -8956.798783
EM: Round [17] log likelihood: -8956.783967
EM: Round [18] log likelihood: -8956.769233
EM: Round [19] log likelihood: -8956.754580
EM: Round [20] log likelihood: -8956.740008
EM: Round [21] log likelihood: -8956.725514
EM: Round [22] log likelihood: -8956.711100
EM: Round [23] log likelihood: -8956.696764
EM: Round [24] log likelihood: -8956.682505
EM: Round [25] log likelihood: -8956.668323
EM: Round [26] log likelihood: -8956.654216
EM: Round [27] log likelihood: -8956.640185
EM: Round [28] log likelihood: -8956.626229
EM: Round [29] log likelihood: -8956.612346
EM: Round [30] log likelihood: -8956.598537
EM: Round [31] log likelihood: -8956.584800
EM: Round [32] log likelihood: -8956.571135
EM: Round [33] log likelihood: -8956.557541
EM: Round [34] log likelihood: -8956.544018
EM: Round [35] log likelihood: -8956.530565
EM: Round [36] log likelihood: -8956.517181
EM: Round [37] log likelihood: -8956.503866
EM: Round [38] log likelihood: -8956.490620
EM: Round [39] log likelihood: -8956.477441
EM: Round [40] log likelihood: -8956.464329
EM: Round [41] log likelihood: -8956.451283
EM: Round [42] log likelihood: -8956.438303
EM: Round [43] log likelihood: -8956.425389
EM: Round [44] log likelihood: -8956.412539
EM: Round [45] log likelihood: -8956.399754
EM: Round [46] log likelihood: -8956.387032
EM: Round [47] log likelihood: -8956.374374
EM: Round [48] log likelihood: -8956.361778
EM: Round [49] log likelihood: -8956.349244
EM: Round [50] log likelihood: -8956.336772
EM: Round [51] log likelihood: -8956.324361
EM: Round [52] log likelihood: -8956.312010
EM: Round [53] log likelihood: -8956.299719
EM: Round [54] log likelihood: -8956.287489
EM: Round [55] log likelihood: -8956.275317
EM: Round [56] log likelihood: -8956.263204
EM: Round [57] log likelihood: -8956.251149
EM: Round [58] log likelihood: -8956.239151
EM: Round [59] log likelihood: -8956.227211
EM: Round [60] log likelihood: -8956.215328
EM: Round [61] log likelihood: -8956.203501
EM: Round [62] log likelihood: -8956.191730
EM: Round [63] log likelihood: -8956.180014
EM: Round [64] log likelihood: -8956.168354
EM: Round [65] log likelihood: -8956.156748
EM: Round [66] log likelihood: -8956.145196
EM: Round [67] log likelihood: -8956.133698
EM: Round [68] log likelihood: -8956.122253
EM: Round [69] log likelihood: -8956.110862
EM: Round [70] log likelihood: -8956.099522
EM: Round [71] log likelihood: -8956.088235
EM: Round [72] log likelihood: -8956.077000
EM: Round [73] log likelihood: -8956.065816
EM: Round [74] log likelihood: -8956.054683
EM: Round [75] log likelihood: -8956.043600
EM: Round [76] log likelihood: -8956.032568
EM: Round [77] log likelihood: -8956.021585
EM: Round [78] log likelihood: -8956.010652
EM: Round [79] log likelihood: -8955.999768
EM: Round [80] log likelihood: -8955.988933
EM: Round [81] log likelihood: -8955.978146
EM: Round [82] log likelihood: -8955.967407
EM: Round [83] log likelihood: -8955.956716
EM: Round [84] log likelihood: -8955.946072
EM: Round [85] log likelihood: -8955.935475
EM: Round [86] log likelihood: -8955.924925
EM: Round [87] log likelihood: -8955.914421
EM: Round [88] log likelihood: -8955.903963
EM: Round [89] log likelihood: -8955.893550
EM: Round [90] log likelihood: -8955.883183
EM: Round [91] log likelihood: -8955.872861
EM: Round [92] log likelihood: -8955.862584
EM: Round [93] log likelihood: -8955.852351
EM: Round [94] log likelihood: -8955.842162
EM: Round [95] log likelihood: -8955.832016
EM: Round [96] log likelihood: -8955.821915
EM: Round [97] log likelihood: -8955.811856
EM: Round [98] log likelihood: -8955.801840
EM: Round [99] log likelihood: -8955.791867
EM: Round [100] log likelihood: -8955.781936
EM: Round [101] log likelihood: -8955.772047
EM: Round [102] log likelihood: -8955.762200
EM: Round [103] log likelihood: -8955.752394
EM: Round [104] log likelihood: -8955.742629
EM: Round [105] log likelihood: -8955.732905
EM: Round [106] log likelihood: -8955.723221
EM: Round [107] log likelihood: -8955.713578
EM: Round [108] log likelihood: -8955.703975
EM: Round [109] log likelihood: -8955.694412
EM: Round [110] log likelihood: -8955.684888
EM: Round [111] log likelihood: -8955.675403
EM: Round [112] log likelihood: -8955.665957
EM: Round [113] log likelihood: -8955.656550
EM: Round [114] log likelihood: -8955.647182
EM: Round [115] log likelihood: -8955.637851
EM: Round [116] log likelihood: -8955.628559
EM: Round [117] log likelihood: -8955.619304
EM: Round [118] log likelihood: -8955.610087
EM: Round [119] log likelihood: -8955.600907
EM: Round [120] log likelihood: -8955.591764
EM: Round [121] log likelihood: -8955.582658
EM: Round [122] log likelihood: -8955.573588
EM: Round [123] log likelihood: -8955.564555
EM: Round [124] log likelihood: -8955.555557
EM: Round [125] log likelihood: -8955.546596
EM: Round [126] log likelihood: -8955.537670
EM: Round [127] log likelihood: -8955.528779
EM: Round [128] log likelihood: -8955.519924
EM: Round [129] log likelihood: -8955.511103
EM: Round [130] log likelihood: -8955.502317
EM: Round [131] log likelihood: -8955.493566
EM: Round [132] log likelihood: -8955.484849
EM: Round [133] log likelihood: -8955.476166
EM: Round [134] log likelihood: -8955.467517
EM: Round [135] log likelihood: -8955.458901
EM: Round [136] log likelihood: -8955.450319
EM: Round [137] log likelihood: -8955.441771
EM: Round [138] log likelihood: -8955.433255
EM: Round [139] log likelihood: -8955.424772
EM: Round [140] log likelihood: -8955.416321
EM: Round [141] log likelihood: -8955.407904
EM: Round [142] log likelihood: -8955.399518
EM: Round [143] log likelihood: -8955.391164
EM: Round [144] log likelihood: -8955.382843
EM: Round [145] log likelihood: -8955.374552
EM: Round [146] log likelihood: -8955.366294
EM: Round [147] log likelihood: -8955.358067
EM: Round [148] log likelihood: -8955.349870
EM: Round [149] log likelihood: -8955.341705
EM: Round [150] log likelihood: -8955.333570
EM: Round [151] log likelihood: -8955.325466
EM: Round [152] log likelihood: -8955.317393
EM: Round [153] log likelihood: -8955.309349
EM: Round [154] log likelihood: -8955.301336
EM: Round [155] log likelihood: -8955.293352
EM: Round [156] log likelihood: -8955.285398
EM: Round [157] log likelihood: -8955.277474
EM: Round [158] log likelihood: -8955.269579
EM: Round [159] log likelihood: -8955.261713
EM: Round [160] log likelihood: -8955.253876
EM: Round [161] log likelihood: -8955.246068
EM: Round [162] log likelihood: -8955.238289
EM: Round [163] log likelihood: -8955.230538
EM: Round [164] log likelihood: -8955.222815
EM: Round [165] log likelihood: -8955.215121
EM: Round [166] log likelihood: -8955.207454
EM: Round [167] log likelihood: -8955.199816
EM: Round [168] log likelihood: -8955.192205
EM: Round [169] log likelihood: -8955.184622
EM: Round [170] log likelihood: -8955.177066
EM: Round [171] log likelihood: -8955.169537
EM: Round [172] log likelihood: -8955.162036
EM: Round [173] log likelihood: -8955.154561
EM: Round [174] log likelihood: -8955.147113
EM: Round [175] log likelihood: -8955.139692
EM: Round [176] log likelihood: -8955.132297
EM: Round [177] log likelihood: -8955.124929
EM: Round [178] log likelihood: -8955.117587
EM: Round [179] log likelihood: -8955.110271
EM: Round [180] log likelihood: -8955.102981
EM: Round [181] log likelihood: -8955.095717
EM: Round [182] log likelihood: -8955.088478
EM: Round [183] log likelihood: -8955.081265
EM: Round [184] log likelihood: -8955.074077
EM: Round [185] log likelihood: -8955.066914
EM: Round [186] log likelihood: -8955.059777
EM: Round [187] log likelihood: -8955.052664
EM: Round [188] log likelihood: -8955.045577
EM: Round [189] log likelihood: -8955.038514
EM: Round [190] log likelihood: -8955.031475
EM: Round [191] log likelihood: -8955.024461
EM: Round [192] log likelihood: -8955.017472
EM: Round [193] log likelihood: -8955.010506
EM: Round [194] log likelihood: -8955.003565
EM: Round [195] log likelihood: -8954.996647
EM: Round [196] log likelihood: -8954.989753
EM: Round [197] log likelihood: -8954.982883
EM: Round [198] log likelihood: -8954.976037
EM: Round [199] log likelihood: -8954.969214
EM: Round [200] log likelihood: -8954.962414
EM: Round [201] log likelihood: -8954.955637
EM: Round [202] log likelihood: -8954.948884
EM: Round [203] log likelihood: -8954.942153
EM: Round [204] log likelihood: -8954.935446
EM: Round [205] log likelihood: -8954.928761
EM: Round [206] log likelihood: -8954.922098
EM: Round [207] log likelihood: -8954.915458
EM: Round [208] log likelihood: -8954.908841
EM: Round [209] log likelihood: -8954.902245
EM: Round [210] log likelihood: -8954.895672
EM: Round [211] log likelihood: -8954.889121
EM: Round [212] log likelihood: -8954.882592
EM: Round [213] log likelihood: -8954.876084
EM: Round [214] log likelihood: -8954.869599
EM: Round [215] log likelihood: -8954.863134
EM: Round [216] log likelihood: -8954.856692
EM: Round [217] log likelihood: -8954.850270
EM: Round [218] log likelihood: -8954.843870
EM: Round [219] log likelihood: -8954.837492
EM: Round [220] log likelihood: -8954.831134
EM: Round [221] log likelihood: -8954.824797
EM: Round [222] log likelihood: -8954.818481
EM: Round [223] log likelihood: -8954.812186
EM: Round [224] log likelihood: -8954.805911
EM: Round [225] log likelihood: -8954.799657
EM: Round [226] log likelihood: -8954.793423
EM: Round [227] log likelihood: -8954.787210
EM: Round [228] log likelihood: -8954.781017
EM: Round [229] log likelihood: -8954.774844
EM: Round [230] log likelihood: -8954.768691
EM: Round [231] log likelihood: -8954.762559
EM: Round [232] log likelihood: -8954.756445
EM: Round [233] log likelihood: -8954.750352
EM: Round [234] log likelihood: -8954.744279
EM: Round [235] log likelihood: -8954.738225
EM: Round [236] log likelihood: -8954.732190
EM: Round [237] log likelihood: -8954.726175
EM: Round [238] log likelihood: -8954.720179
EM: Round [239] log likelihood: -8954.714202
EM: Round [240] log likelihood: -8954.708245
EM: Round [241] log likelihood: -8954.702306
EM: Round [242] log likelihood: -8954.696387
EM: Round [243] log likelihood: -8954.690486
EM: Round [244] log likelihood: -8954.684604
EM: Round [245] log likelihood: -8954.678741
EM: Round [246] log likelihood: -8954.672896
EM: Round [247] log likelihood: -8954.667070
EM: Round [248] log likelihood: -8954.661262
EM: Round [249] log likelihood: -8954.655472
EM: Round [250] log likelihood: -8954.649701
EM: Round [251] log likelihood: -8954.643948
EM: Round [252] log likelihood: -8954.638213
EM: Round [253] log likelihood: -8954.632495
EM: Round [254] log likelihood: -8954.626796
EM: Round [255] log likelihood: -8954.621115
EM: Round [256] log likelihood: -8954.615451
EM: Round [257] log likelihood: -8954.609805
EM: Round [258] log likelihood: -8954.604177
EM: Round [259] log likelihood: -8954.598566
EM: Round [260] log likelihood: -8954.592972
EM: Round [261] log likelihood: -8954.587396
EM: Round [262] log likelihood: -8954.581837
EM: Round [263] log likelihood: -8954.576295
EM: Round [264] log likelihood: -8954.570771
EM: Round [265] log likelihood: -8954.565263
EM: Round [266] log likelihood: -8954.559772
EM: Round [267] log likelihood: -8954.554298
EM: Round [268] log likelihood: -8954.548841
EM: Round [269] log likelihood: -8954.543401
EM: Round [270] log likelihood: -8954.537977
EM: Round [271] log likelihood: -8954.532570
EM: Round [272] log likelihood: -8954.527180
EM: Round [273] log likelihood: -8954.521806
EM: Round [274] log likelihood: -8954.516448
EM: Round [275] log likelihood: -8954.511106
EM: Round [276] log likelihood: -8954.505781
EM: Round [277] log likelihood: -8954.500472
EM: Round [278] log likelihood: -8954.495178
EM: Round [279] log likelihood: -8954.489901
EM: Round [280] log likelihood: -8954.484640
EM: Round [281] log likelihood: -8954.479395
EM: Round [282] log likelihood: -8954.474165
EM: Round [283] log likelihood: -8954.468951
EM: Round [284] log likelihood: -8954.463753
EM: Round [285] log likelihood: -8954.458571
EM: Round [286] log likelihood: -8954.453403
EM: Round [287] log likelihood: -8954.448252
EM: Round [288] log likelihood: -8954.443115
EM: Round [289] log likelihood: -8954.437994
EM: Round [290] log likelihood: -8954.432889
EM: Round [291] log likelihood: -8954.427798
EM: Round [292] log likelihood: -8954.422723
EM: Round [293] log likelihood: -8954.417662
EM: Round [294] log likelihood: -8954.412617
EM: Round [295] log likelihood: -8954.407587
EM: Round [296] log likelihood: -8954.402571
EM: Round [297] log likelihood: -8954.397570
EM: Round [298] log likelihood: -8954.392584
EM: Round [299] log likelihood: -8954.387613
EM: Round [300] log likelihood: -8954.382656
EM: Round [301] log likelihood: -8954.377714
EM: Round [302] log likelihood: -8954.372786
EM: Round [303] log likelihood: -8954.367873
EM: Round [304] log likelihood: -8954.362974
EM: Round [305] log likelihood: -8954.358089
EM: Round [306] log likelihood: -8954.353219
EM: Round [307] log likelihood: -8954.348363
EM: Round [308] log likelihood: -8954.343521
EM: Round [309] log likelihood: -8954.338693
EM: Round [310] log likelihood: -8954.333879
EM: Round [311] log likelihood: -8954.329079
EM: Round [312] log likelihood: -8954.324293
EM: Round [313] log likelihood: -8954.319520
EM: Round [314] log likelihood: -8954.314762
EM: Round [315] log likelihood: -8954.310017
EM: Round [316] log likelihood: -8954.305286
EM: Round [317] log likelihood: -8954.300569
EM: Round [318] log likelihood: -8954.295865
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EM: Round [778] log likelihood: -8953.021192
EM: Round [779] log likelihood: -8953.019624
EM: Round [780] log likelihood: -8953.018059
EM: Round [781] log likelihood: -8953.016497
EM: Round [782] log likelihood: -8953.014938
EM: Round [783] log likelihood: -8953.013383
EM: Round [784] log likelihood: -8953.011831
EM: Round [785] log likelihood: -8953.010282
EM: Round [786] log likelihood: -8953.008737
EM: Round [787] log likelihood: -8953.007194
EM: Round [788] log likelihood: -8953.005655
EM: Round [789] log likelihood: -8953.004119
EM: Round [790] log likelihood: -8953.002586
EM: Round [791] log likelihood: -8953.001057
EM: Round [792] log likelihood: -8952.999530
EM: Round [793] log likelihood: -8952.998007
EM: Round [794] log likelihood: -8952.996486
EM: Round [795] log likelihood: -8952.994969
EM: Round [796] log likelihood: -8952.993455
EM: Round [797] log likelihood: -8952.991944
EM: Round [798] log likelihood: -8952.990437
EM: Round [799] log likelihood: -8952.988932
EM: Round [800] log likelihood: -8952.987430
EM: Round [801] log likelihood: -8952.985932
EM: Round [802] log likelihood: -8952.984437
EM: Round [803] log likelihood: -8952.982944
EM: Round [804] log likelihood: -8952.981455
EM: Round [805] log likelihood: -8952.979969
EM: Round [806] log likelihood: -8952.978486
EM: Round [807] log likelihood: -8952.977006
EM: Round [808] log likelihood: -8952.975529
EM: Round [809] log likelihood: -8952.974054
EM: Round [810] log likelihood: -8952.972583
EM: Round [811] log likelihood: -8952.971116
EM: Round [812] log likelihood: -8952.969651
EM: Round [813] log likelihood: -8952.968189
EM: Round [814] log likelihood: -8952.966730
EM: Round [815] log likelihood: -8952.965274
EM: Round [816] log likelihood: -8952.963821
EM: Round [817] log likelihood: -8952.962370
EM: Round [818] log likelihood: -8952.960923
EM: Round [819] log likelihood: -8952.959479
EM: Round [820] log likelihood: -8952.958038
EM: Round [821] log likelihood: -8952.956600
EM: Round [822] log likelihood: -8952.955165
EM: Round [823] log likelihood: -8952.953732
EM: Round [824] log likelihood: -8952.952303
EM: Round [825] log likelihood: -8952.950876
EM: Round [826] log likelihood: -8952.949453
EM: Round [827] log likelihood: -8952.948032
EM: Round [828] log likelihood: -8952.946614
EM: Round [829] log likelihood: -8952.945199
EM: Round [830] log likelihood: -8952.943787
EM: Round [831] log likelihood: -8952.942378
EM: Round [832] log likelihood: -8952.940971
EM: Round [833] log likelihood: -8952.939568
EM: Round [834] log likelihood: -8952.938167
EM: Round [835] log likelihood: -8952.936770
EM: Round [836] log likelihood: -8952.935375
EM: Round [837] log likelihood: -8952.933983
EM: Round [838] log likelihood: -8952.932593
EM: Round [839] log likelihood: -8952.931207
EM: Round [840] log likelihood: -8952.929823
EM: Round [841] log likelihood: -8952.928442
EM: Round [842] log likelihood: -8952.927064
EM: Round [843] log likelihood: -8952.925689
EM: Round [844] log likelihood: -8952.924317
EM: Round [845] log likelihood: -8952.922947
EM: Round [846] log likelihood: -8952.921580
EM: Round [847] log likelihood: -8952.920216
EM: Round [848] log likelihood: -8952.918854
EM: Round [849] log likelihood: -8952.917496
EM: Round [850] log likelihood: -8952.916140
EM: Round [851] log likelihood: -8952.914787
EM: Round [852] log likelihood: -8952.913436
EM: Round [853] log likelihood: -8952.912089
EM: Round [854] log likelihood: -8952.910744
EM: Round [855] log likelihood: -8952.909402
EM: Round [856] log likelihood: -8952.908062
EM: Round [857] log likelihood: -8952.906725
EM: Round [858] log likelihood: -8952.905391
EM: Round [859] log likelihood: -8952.904059
EM: Round [860] log likelihood: -8952.902731
EM: Round [861] log likelihood: -8952.901405
EM: Round [862] log likelihood: -8952.900081
EM: Round [863] log likelihood: -8952.898760
EM: Round [864] log likelihood: -8952.897442
EM: Round [865] log likelihood: -8952.896127
EM: Round [866] log likelihood: -8952.894814
EM: Round [867] log likelihood: -8952.893504
EM: Round [868] log likelihood: -8952.892196
EM: Round [869] log likelihood: -8952.890891
EM: Round [870] log likelihood: -8952.889589
EM: Round [871] log likelihood: -8952.888289
EM: Round [872] log likelihood: -8952.886992
EM: Round [873] log likelihood: -8952.885698
EM: Round [874] log likelihood: -8952.884406
EM: Round [875] log likelihood: -8952.883117
EM: Round [876] log likelihood: -8952.881830
EM: Round [877] log likelihood: -8952.880546
EM: Round [878] log likelihood: -8952.879264
EM: Round [879] log likelihood: -8952.877985
EM: Round [880] log likelihood: -8952.876709
EM: Round [881] log likelihood: -8952.875435
EM: Round [882] log likelihood: -8952.874164
EM: Round [883] log likelihood: -8952.872895
EM: Round [884] log likelihood: -8952.871628
EM: Round [885] log likelihood: -8952.870365
EM: Round [886] log likelihood: -8952.869104
EM: Round [887] log likelihood: -8952.867845
EM: Round [888] log likelihood: -8952.866589
EM: Round [889] log likelihood: -8952.865335
EM: Round [890] log likelihood: -8952.864084
EM: Round [891] log likelihood: -8952.862835
EM: Round [892] log likelihood: -8952.861589
EM: Round [893] log likelihood: -8952.860345
EM: Round [894] log likelihood: -8952.859104
EM: Round [895] log likelihood: -8952.857865
EM: Round [896] log likelihood: -8952.856629
EM: Round [897] log likelihood: -8952.855395
EM: Round [898] log likelihood: -8952.854164
EM: Round [899] log likelihood: -8952.852935
EM: Round [900] log likelihood: -8952.851708
EM: Round [901] log likelihood: -8952.850484
EM: Round [902] log likelihood: -8952.849263
EM: Round [903] log likelihood: -8952.848044
EM: Round [904] log likelihood: -8952.846827
EM: Round [905] log likelihood: -8952.845612
EM: Round [906] log likelihood: -8952.844401
EM: Round [907] log likelihood: -8952.843191
EM: Round [908] log likelihood: -8952.841984
EM: Round [909] log likelihood: -8952.840779
EM: Round [910] log likelihood: -8952.839577
EM: Round [911] log likelihood: -8952.838377
EM: Round [912] log likelihood: -8952.837179
EM: Round [913] log likelihood: -8952.835984
EM: Round [914] log likelihood: -8952.834791
EM: Round [915] log likelihood: -8952.833601
EM: Round [916] log likelihood: -8952.832413
EM: Round [917] log likelihood: -8952.831227
EM: Round [918] log likelihood: -8952.830043
EM: Round [919] log likelihood: -8952.828862
EM: Round [920] log likelihood: -8952.827683
EM: Round [921] log likelihood: -8952.826507
EM: Round [922] log likelihood: -8952.825333
EM: Round [923] log likelihood: -8952.824161
EM: Round [924] log likelihood: -8952.822992
EM: Round [925] log likelihood: -8952.821824
EM: Round [926] log likelihood: -8952.820660
EM: Round [927] log likelihood: -8952.819497
EM: Round [928] log likelihood: -8952.818337
EM: Round [929] log likelihood: -8952.817179
EM: Round [930] log likelihood: -8952.816023
EM: Round [931] log likelihood: -8952.814870
EM: Round [932] log likelihood: -8952.813718
EM: Round [933] log likelihood: -8952.812570
EM: Round [934] log likelihood: -8952.811423
EM: Round [935] log likelihood: -8952.810279
EM: Round [936] log likelihood: -8952.809136
EM: Round [937] log likelihood: -8952.807997
EM: Round [938] log likelihood: -8952.806859
EM: Round [939] log likelihood: -8952.805724
EM: Round [940] log likelihood: -8952.804590
EM: Round [941] log likelihood: -8952.803459
EM: Round [942] log likelihood: -8952.802331
EM: Round [943] log likelihood: -8952.801204
EM: Round [944] log likelihood: -8952.800080
EM: Round [945] log likelihood: -8952.798958
EM: Round [946] log likelihood: -8952.797838
EM: Round [947] log likelihood: -8952.796720
EM: Round [948] log likelihood: -8952.795605
EM: Round [949] log likelihood: -8952.794491
EM: Round [950] log likelihood: -8952.793380
EM: Round [951] log likelihood: -8952.792271
EM: Round [952] log likelihood: -8952.791165
EM: Round [953] log likelihood: -8952.790060
EM: Round [954] log likelihood: -8952.788957
EM: Round [955] log likelihood: -8952.787857
EM: Round [956] log likelihood: -8952.786759
EM: Round [957] log likelihood: -8952.785663
EM: Round [958] log likelihood: -8952.784569
EM: Round [959] log likelihood: -8952.783477
EM: Round [960] log likelihood: -8952.782388
EM: Round [961] log likelihood: -8952.781300
EM: Round [962] log likelihood: -8952.780215
EM: Round [963] log likelihood: -8952.779132
EM: Round [964] log likelihood: -8952.778051
EM: Round [965] log likelihood: -8952.776972
EM: Round [966] log likelihood: -8952.775895
EM: Round [967] log likelihood: -8952.774820
EM: Round [968] log likelihood: -8952.773747
EM: Round [969] log likelihood: -8952.772677
EM: Round [970] log likelihood: -8952.771608
EM: Round [971] log likelihood: -8952.770542
EM: Round [972] log likelihood: -8952.769477
EM: Round [973] log likelihood: -8952.768415
EM: Round [974] log likelihood: -8952.767355
EM: Round [975] log likelihood: -8952.766297
EM: Round [976] log likelihood: -8952.765241
EM: Round [977] log likelihood: -8952.764187
EM: Round [978] log likelihood: -8952.763135
EM: Round [979] log likelihood: -8952.762085
EM: Round [980] log likelihood: -8952.761037
EM: Round [981] log likelihood: -8952.759991
EM: Round [982] log likelihood: -8952.758947
EM: Round [983] log likelihood: -8952.757905
EM: Round [984] log likelihood: -8952.756865
EM: Round [985] log likelihood: -8952.755828
EM: Round [986] log likelihood: -8952.754792
EM: Round [987] log likelihood: -8952.753758
EM: Round [988] log likelihood: -8952.752726
EM: Round [989] log likelihood: -8952.751697
EM: Round [990] log likelihood: -8952.750669
EM: Round [991] log likelihood: -8952.749643
EM: Round [992] log likelihood: -8952.748619
EM: Round [993] log likelihood: -8952.747598
EM: Round [994] log likelihood: -8952.746578
EM: Round [995] log likelihood: -8952.745560
EM: Round [996] log likelihood: -8952.744544
EM: Round [997] log likelihood: -8952.743530
EM: Round [998] log likelihood: -8952.742518
EM: Round [999] log likelihood: -8952.741508
EM: Round [1000] log likelihood: -8952.740500
EM: Round [1001] log likelihood: -8952.739494
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.vwGMaJYqtO/786-O_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam into /tmp/nxf.vwGMaJYqtO/786-O_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.vwGMaJYqtO/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.vwGMaJYqtO/786-O_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.read_coords > /tmp/nxf.vwGMaJYqtO/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.vwGMaJYqtO/786-O_FFPE_RNA_0001_B23LG7FLT4_2.consolidated.bam.frag_coords > /tmp/nxf.vwGMaJYqtO/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.vwGMaJYqtO/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.vwGMaJYqtO/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.vwGMaJYqtO/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.vwGMaJYqtO/786-O_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.vwGMaJYqtO/786-O_FFPE_RNA_0001_B23LG7FLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -8479.222760
EM: Round [1] log likelihood: -8478.968794
EM: Round [2] log likelihood: -8478.940605
EM: Round [3] log likelihood: -8478.914555
EM: Round [4] log likelihood: -8478.888787
EM: Round [5] log likelihood: -8478.863257
EM: Round [6] log likelihood: -8478.837961
EM: Round [7] log likelihood: -8478.812895
EM: Round [8] log likelihood: -8478.788054
EM: Round [9] log likelihood: -8478.763436
EM: Round [10] log likelihood: -8478.739036
EM: Round [11] log likelihood: -8478.714851
EM: Round [12] log likelihood: -8478.690877
EM: Round [13] log likelihood: -8478.667110
EM: Round [14] log likelihood: -8478.643549
EM: Round [15] log likelihood: -8478.620189
EM: Round [16] log likelihood: -8478.597027
EM: Round [17] log likelihood: -8478.574060
EM: Round [18] log likelihood: -8478.551284
EM: Round [19] log likelihood: -8478.528698
EM: Round [20] log likelihood: -8478.506299
EM: Round [21] log likelihood: -8478.484082
EM: Round [22] log likelihood: -8478.462046
EM: Round [23] log likelihood: -8478.440188
EM: Round [24] log likelihood: -8478.418505
EM: Round [25] log likelihood: -8478.396995
EM: Round [26] log likelihood: -8478.375655
EM: Round [27] log likelihood: -8478.354483
EM: Round [28] log likelihood: -8478.333476
EM: Round [29] log likelihood: -8478.312632
EM: Round [30] log likelihood: -8478.291948
EM: Round [31] log likelihood: -8478.271423
EM: Round [32] log likelihood: -8478.251054
EM: Round [33] log likelihood: -8478.230839
EM: Round [34] log likelihood: -8478.210776
EM: Round [35] log likelihood: -8478.190863
EM: Round [36] log likelihood: -8478.171097
EM: Round [37] log likelihood: -8478.151477
EM: Round [38] log likelihood: -8478.132001
EM: Round [39] log likelihood: -8478.112667
EM: Round [40] log likelihood: -8478.093473
EM: Round [41] log likelihood: -8478.074417
EM: Round [42] log likelihood: -8478.055498
EM: Round [43] log likelihood: -8478.036713
EM: Round [44] log likelihood: -8478.018061
EM: Round [45] log likelihood: -8477.999540
EM: Round [46] log likelihood: -8477.981149
EM: Round [47] log likelihood: -8477.962886
EM: Round [48] log likelihood: -8477.944749
EM: Round [49] log likelihood: -8477.926736
EM: Round [50] log likelihood: -8477.908847
EM: Round [51] log likelihood: -8477.891080
EM: Round [52] log likelihood: -8477.873433
EM: Round [53] log likelihood: -8477.855904
EM: Round [54] log likelihood: -8477.838493
EM: Round [55] log likelihood: -8477.821198
EM: Round [56] log likelihood: -8477.804017
EM: Round [57] log likelihood: -8477.786949
EM: Round [58] log likelihood: -8477.769994
EM: Round [59] log likelihood: -8477.753148
EM: Round [60] log likelihood: -8477.736412
EM: Round [61] log likelihood: -8477.719784
EM: Round [62] log likelihood: -8477.703263
EM: Round [63] log likelihood: -8477.686847
EM: Round [64] log likelihood: -8477.670536
EM: Round [65] log likelihood: -8477.654328
EM: Round [66] log likelihood: -8477.638221
EM: Round [67] log likelihood: -8477.622216
EM: Round [68] log likelihood: -8477.606310
EM: Round [69] log likelihood: -8477.590503
EM: Round [70] log likelihood: -8477.574793
EM: Round [71] log likelihood: -8477.559180
EM: Round [72] log likelihood: -8477.543662
EM: Round [73] log likelihood: -8477.528239
EM: Round [74] log likelihood: -8477.512909
EM: Round [75] log likelihood: -8477.497672
EM: Round [76] log likelihood: -8477.482526
EM: Round [77] log likelihood: -8477.467470
EM: Round [78] log likelihood: -8477.452504
EM: Round [79] log likelihood: -8477.437626
EM: Round [80] log likelihood: -8477.422836
EM: Round [81] log likelihood: -8477.408133
EM: Round [82] log likelihood: -8477.393516
EM: Round [83] log likelihood: -8477.378983
EM: Round [84] log likelihood: -8477.364535
EM: Round [85] log likelihood: -8477.350170
EM: Round [86] log likelihood: -8477.335887
EM: Round [87] log likelihood: -8477.321686
EM: Round [88] log likelihood: -8477.307566
EM: Round [89] log likelihood: -8477.293526
EM: Round [90] log likelihood: -8477.279565
EM: Round [91] log likelihood: -8477.265682
EM: Round [92] log likelihood: -8477.251877
EM: Round [93] log likelihood: -8477.238149
EM: Round [94] log likelihood: -8477.224497
EM: Round [95] log likelihood: -8477.210920
EM: Round [96] log likelihood: -8477.197418
EM: Round [97] log likelihood: -8477.183990
EM: Round [98] log likelihood: -8477.170636
EM: Round [99] log likelihood: -8477.157353
EM: Round [100] log likelihood: -8477.144143
EM: Round [101] log likelihood: -8477.131004
EM: Round [102] log likelihood: -8477.117936
EM: Round [103] log likelihood: -8477.104937
EM: Round [104] log likelihood: -8477.092008
EM: Round [105] log likelihood: -8477.079148
EM: Round [106] log likelihood: -8477.066355
EM: Round [107] log likelihood: -8477.053630
EM: Round [108] log likelihood: -8477.040972
EM: Round [109] log likelihood: -8477.028379
EM: Round [110] log likelihood: -8477.015853
EM: Round [111] log likelihood: -8477.003391
EM: Round [112] log likelihood: -8476.990994
EM: Round [113] log likelihood: -8476.978660
EM: Round [114] log likelihood: -8476.966390
EM: Round [115] log likelihood: -8476.954183
EM: Round [116] log likelihood: -8476.942038
EM: Round [117] log likelihood: -8476.929954
EM: Round [118] log likelihood: -8476.917932
EM: Round [119] log likelihood: -8476.905970
EM: Round [120] log likelihood: -8476.894069
EM: Round [121] log likelihood: -8476.882226
EM: Round [122] log likelihood: -8476.870443
EM: Round [123] log likelihood: -8476.858719
EM: Round [124] log likelihood: -8476.847052
EM: Round [125] log likelihood: -8476.835443
EM: Round [126] log likelihood: -8476.823891
EM: Round [127] log likelihood: -8476.812396
EM: Round [128] log likelihood: -8476.800957
EM: Round [129] log likelihood: -8476.789574
EM: Round [130] log likelihood: -8476.778245
EM: Round [131] log likelihood: -8476.766972
EM: Round [132] log likelihood: -8476.755753
EM: Round [133] log likelihood: -8476.744588
EM: Round [134] log likelihood: -8476.733476
EM: Round [135] log likelihood: -8476.722417
EM: Round [136] log likelihood: -8476.711411
EM: Round [137] log likelihood: -8476.700457
EM: Round [138] log likelihood: -8476.689555
EM: Round [139] log likelihood: -8476.678704
EM: Round [140] log likelihood: -8476.667904
EM: Round [141] log likelihood: -8476.657154
EM: Round [142] log likelihood: -8476.646455
EM: Round [143] log likelihood: -8476.635806
EM: Round [144] log likelihood: -8476.625205
EM: Round [145] log likelihood: -8476.614654
EM: Round [146] log likelihood: -8476.604152
EM: Round [147] log likelihood: -8476.593697
EM: Round [148] log likelihood: -8476.583291
EM: Round [149] log likelihood: -8476.572932
EM: Round [150] log likelihood: -8476.562620
EM: Round [151] log likelihood: -8476.552355
EM: Round [152] log likelihood: -8476.542136
EM: Round [153] log likelihood: -8476.531964
EM: Round [154] log likelihood: -8476.521837
EM: Round [155] log likelihood: -8476.511756
EM: Round [156] log likelihood: -8476.501719
EM: Round [157] log likelihood: -8476.491728
EM: Round [158] log likelihood: -8476.481780
EM: Round [159] log likelihood: -8476.471877
EM: Round [160] log likelihood: -8476.462018
EM: Round [161] log likelihood: -8476.452202
EM: Round [162] log likelihood: -8476.442429
EM: Round [163] log likelihood: -8476.432699
EM: Round [164] log likelihood: -8476.423011
EM: Round [165] log likelihood: -8476.413366
EM: Round [166] log likelihood: -8476.403762
EM: Round [167] log likelihood: -8476.394200
EM: Round [168] log likelihood: -8476.384680
EM: Round [169] log likelihood: -8476.375200
EM: Round [170] log likelihood: -8476.365761
EM: Round [171] log likelihood: -8476.356363
EM: Round [172] log likelihood: -8476.347004
EM: Round [173] log likelihood: -8476.337686
EM: Round [174] log likelihood: -8476.328407
EM: Round [175] log likelihood: -8476.319167
EM: Round [176] log likelihood: -8476.309967
EM: Round [177] log likelihood: -8476.300805
EM: Round [178] log likelihood: -8476.291682
EM: Round [179] log likelihood: -8476.282597
EM: Round [180] log likelihood: -8476.273549
EM: Round [181] log likelihood: -8476.264540
EM: Round [182] log likelihood: -8476.255568
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EM: Round [662] log likelihood: -8474.089257
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EM: Round [773] log likelihood: -8473.870137
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EM: Round [784] log likelihood: -8473.851167
EM: Round [785] log likelihood: -8473.849465
EM: Round [786] log likelihood: -8473.847766
EM: Round [787] log likelihood: -8473.846070
EM: Round [788] log likelihood: -8473.844379
EM: Round [789] log likelihood: -8473.842690
EM: Round [790] log likelihood: -8473.841006
EM: Round [791] log likelihood: -8473.839325
EM: Round [792] log likelihood: -8473.837648
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EM: Round [802] log likelihood: -8473.821067
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EM: Round [804] log likelihood: -8473.817793
EM: Round [805] log likelihood: -8473.816161
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EM: Round [816] log likelihood: -8473.798435
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EM: Round [819] log likelihood: -8473.793671
EM: Round [820] log likelihood: -8473.792090
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EM: Round [835] log likelihood: -8473.768764
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EM: Round [1001] log likelihood: -8473.553214
-total frags in /tmp/nxf.vwGMaJYqtO/786-O_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz: 294873575
Warning - not locating file: /tmp/nxf.vwGMaJYqtO/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 [ENSG00000176593.8]
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