Done.
-parsing GTF file: /tmp/nxf.2slL2KydIu/tih_rna_sample_00729_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.2slL2KydIu/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.2slL2KydIu/tih_rna_sample_00729_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.2slL2KydIu/tih_rna_sample_00729_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.2slL2KydIu/fi_workdir/tih_rna_sample_00729_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.2slL2KydIu/fi_workdir/tih_rna_sample_00729_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00729_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00729_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:25:38 : INFO : Done.
-parsing GTF file: /tmp/nxf.2slL2KydIu/fi_workdir/tih_rna_sample_00729_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.2slL2KydIu/fi_workdir/tih_rna_sample_00729_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[2210000]   -done parsing /tmp/nxf.2slL2KydIu/fi_workdir/tih_rna_sample_00729_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 300,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 1524,
          ' ** passed ** ' => 9257,
          'seq-similar region overlap' => 3,
          'low complexity anchor region' => 19,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 24,
          'exons hit < 2' => 1,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 348,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 6,
          'excessive soft clipping' => 25411,
          'per_id < 96' => 14579,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 3364,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 839,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 14,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 510,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 112,
          'num genes matched < 2' => 33,
          'small anchor length' => 430,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 1598,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 137
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.2slL2KydIu/fi_workdir/tih_rna_sample_00729_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[3000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[204000]   -fusion SPANNING read extraction for scaff: AUTS2--TFAP2A

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[1086000]   
[1087000]   
[1088000]   
[1089000]   
[1090000]   
[1091000]   -fusion SPANNING read extraction for scaff: IGH-@-ext--EPHA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[133000]   
[134000]   
[135000]   
[136000]   
[137000]   
[138000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
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[130000]   
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[140000]   
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[158000]   
[159000]   
[160000]   
[161000]   
[162000]   -fusion SPANNING read extraction for scaff: PRSS27--TPSB2

[1000]   
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[6000]   
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[8000]   
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[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

[1000]   
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[204000]   -fusion SPANNING read extraction for scaff: TFAP2A--AUTS2

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[31000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

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

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[14000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[154000]   -fusion SPANNING read extraction for scaff: ZSWIM8--PKD2L1
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 15881,
          'lacks exon overlap' => 2189
        };
EM: Starting log likelihood: -1940.125577
EM: Round [1] log likelihood: -1939.715704
EM: Round [2] log likelihood: -1939.696547
EM: Round [3] log likelihood: -1939.677860
EM: Round [4] log likelihood: -1939.659557
EM: Round [5] log likelihood: -1939.641623
EM: Round [6] log likelihood: -1939.624044
EM: Round [7] log likelihood: -1939.606807
EM: Round [8] log likelihood: -1939.589900
EM: Round [9] log likelihood: -1939.573311
EM: Round [10] log likelihood: -1939.557028
EM: Round [11] log likelihood: -1939.541042
EM: Round [12] log likelihood: -1939.525343
EM: Round [13] log likelihood: -1939.509920
EM: Round [14] log likelihood: -1939.494766
EM: Round [15] log likelihood: -1939.479871
EM: Round [16] log likelihood: -1939.465227
EM: Round [17] log likelihood: -1939.450826
EM: Round [18] log likelihood: -1939.436662
EM: Round [19] log likelihood: -1939.422726
EM: Round [20] log likelihood: -1939.409012
EM: Round [21] log likelihood: -1939.395514
EM: Round [22] log likelihood: -1939.382225
EM: Round [23] log likelihood: -1939.369140
EM: Round [24] log likelihood: -1939.356253
EM: Round [25] log likelihood: -1939.343557
EM: Round [26] log likelihood: -1939.331049
EM: Round [27] log likelihood: -1939.318723
EM: Round [28] log likelihood: -1939.306574
EM: Round [29] log likelihood: -1939.294597
EM: Round [30] log likelihood: -1939.282789
EM: Round [31] log likelihood: -1939.271144
EM: Round [32] log likelihood: -1939.259659
EM: Round [33] log likelihood: -1939.248330
EM: Round [34] log likelihood: -1939.237152
EM: Round [35] log likelihood: -1939.226123
EM: Round [36] log likelihood: -1939.215238
EM: Round [37] log likelihood: -1939.204494
EM: Round [38] log likelihood: -1939.193888
EM: Round [39] log likelihood: -1939.183417
EM: Round [40] log likelihood: -1939.173078
EM: Round [41] log likelihood: -1939.162867
EM: Round [42] log likelihood: -1939.152781
EM: Round [43] log likelihood: -1939.142819
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EM: Round [45] log likelihood: -1939.123252
EM: Round [46] log likelihood: -1939.113643
EM: Round [47] log likelihood: -1939.104146
EM: Round [48] log likelihood: -1939.094760
EM: Round [49] log likelihood: -1939.085481
EM: Round [50] log likelihood: -1939.076309
EM: Round [51] log likelihood: -1939.067240
EM: Round [52] log likelihood: -1939.058272
EM: Round [53] log likelihood: -1939.049404
EM: Round [54] log likelihood: -1939.040634
EM: Round [55] log likelihood: -1939.031959
EM: Round [56] log likelihood: -1939.023378
EM: Round [57] log likelihood: -1939.014888
EM: Round [58] log likelihood: -1939.006489
EM: Round [59] log likelihood: -1938.998179
EM: Round [60] log likelihood: -1938.989955
EM: Round [61] log likelihood: -1938.981817
EM: Round [62] log likelihood: -1938.973762
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EM: Round [65] log likelihood: -1938.950086
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EM: Round [68] log likelihood: -1938.927110
EM: Round [69] log likelihood: -1938.919600
EM: Round [70] log likelihood: -1938.912164
EM: Round [71] log likelihood: -1938.904798
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EM: Round [74] log likelihood: -1938.883118
EM: Round [75] log likelihood: -1938.876027
EM: Round [76] log likelihood: -1938.869001
EM: Round [77] log likelihood: -1938.862039
EM: Round [78] log likelihood: -1938.855142
EM: Round [79] log likelihood: -1938.848306
EM: Round [80] log likelihood: -1938.841532
EM: Round [81] log likelihood: -1938.834819
EM: Round [82] log likelihood: -1938.828166
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EM: Round [85] log likelihood: -1938.808553
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EM: Round [87] log likelihood: -1938.795761
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EM: Round [90] log likelihood: -1938.776977
EM: Round [91] log likelihood: -1938.770822
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EM: Round [99] log likelihood: -1938.723362
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EM: Round [103] log likelihood: -1938.700753
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EM: Round [148] log likelihood: -1938.487123
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EM: Round [156] log likelihood: -1938.455419
EM: Round [157] log likelihood: -1938.451565
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EM: Round [159] log likelihood: -1938.443926
EM: Round [160] log likelihood: -1938.440141
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EM: Round [162] log likelihood: -1938.432639
EM: Round [163] log likelihood: -1938.428922
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EM: Round [165] log likelihood: -1938.421553
EM: Round [166] log likelihood: -1938.417901
EM: Round [167] log likelihood: -1938.414270
EM: Round [168] log likelihood: -1938.410661
EM: Round [169] log likelihood: -1938.407073
EM: Round [170] log likelihood: -1938.403505
EM: Round [171] log likelihood: -1938.399958
EM: Round [172] log likelihood: -1938.396432
EM: Round [173] log likelihood: -1938.392926
EM: Round [174] log likelihood: -1938.389440
EM: Round [175] log likelihood: -1938.385973
EM: Round [176] log likelihood: -1938.382527
EM: Round [177] log likelihood: -1938.379100
EM: Round [178] log likelihood: -1938.375692
EM: Round [179] log likelihood: -1938.372303
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EM: Round [181] log likelihood: -1938.365583
EM: Round [182] log likelihood: -1938.362251
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EM: Round [184] log likelihood: -1938.355642
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EM: Round [186] log likelihood: -1938.349105
EM: Round [187] log likelihood: -1938.345864
EM: Round [188] log likelihood: -1938.342640
EM: Round [189] log likelihood: -1938.339434
EM: Round [190] log likelihood: -1938.336245
EM: Round [191] log likelihood: -1938.333074
EM: Round [192] log likelihood: -1938.329920
EM: Round [193] log likelihood: -1938.326782
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EM: Round [195] log likelihood: -1938.320557
EM: Round [196] log likelihood: -1938.317470
EM: Round [197] log likelihood: -1938.314399
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EM: Round [199] log likelihood: -1938.308305
EM: Round [200] log likelihood: -1938.305282
EM: Round [201] log likelihood: -1938.302276
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EM: Round [204] log likelihood: -1938.293348
EM: Round [205] log likelihood: -1938.290404
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EM: Round [207] log likelihood: -1938.284559
EM: Round [208] log likelihood: -1938.281660
EM: Round [209] log likelihood: -1938.278775
EM: Round [210] log likelihood: -1938.275905
EM: Round [211] log likelihood: -1938.273049
EM: Round [212] log likelihood: -1938.270209
EM: Round [213] log likelihood: -1938.267382
EM: Round [214] log likelihood: -1938.264570
EM: Round [215] log likelihood: -1938.261772
EM: Round [216] log likelihood: -1938.258987
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EM: Round [220] log likelihood: -1938.247989
EM: Round [221] log likelihood: -1938.245274
EM: Round [222] log likelihood: -1938.242572
EM: Round [223] log likelihood: -1938.239883
EM: Round [224] log likelihood: -1938.237207
EM: Round [225] log likelihood: -1938.234545
EM: Round [226] log likelihood: -1938.231895
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EM: Round [228] log likelihood: -1938.226635
EM: Round [229] log likelihood: -1938.224024
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EM: Round [231] log likelihood: -1938.218839
EM: Round [232] log likelihood: -1938.216266
EM: Round [233] log likelihood: -1938.213705
EM: Round [234] log likelihood: -1938.211156
EM: Round [235] log likelihood: -1938.208619
EM: Round [236] log likelihood: -1938.206094
EM: Round [237] log likelihood: -1938.203582
EM: Round [238] log likelihood: -1938.201081
EM: Round [239] log likelihood: -1938.198592
EM: Round [240] log likelihood: -1938.196115
EM: Round [241] log likelihood: -1938.193649
EM: Round [242] log likelihood: -1938.191195
EM: Round [243] log likelihood: -1938.188752
EM: Round [244] log likelihood: -1938.186321
EM: Round [245] log likelihood: -1938.183901
EM: Round [246] log likelihood: -1938.181493
EM: Round [247] log likelihood: -1938.179095
EM: Round [248] log likelihood: -1938.176709
EM: Round [249] log likelihood: -1938.174333
EM: Round [250] log likelihood: -1938.171969
EM: Round [251] log likelihood: -1938.169615
EM: Round [252] log likelihood: -1938.167272
EM: Round [253] log likelihood: -1938.164940
EM: Round [254] log likelihood: -1938.162619
EM: Round [255] log likelihood: -1938.160308
EM: Round [256] log likelihood: -1938.158007
EM: Round [257] log likelihood: -1938.155717
EM: Round [258] log likelihood: -1938.153438
EM: Round [259] log likelihood: -1938.151168
EM: Round [260] log likelihood: -1938.148909
EM: Round [261] log likelihood: -1938.146660
EM: Round [262] log likelihood: -1938.144421
EM: Round [263] log likelihood: -1938.142192
EM: Round [264] log likelihood: -1938.139972
EM: Round [265] log likelihood: -1938.137763
EM: Round [266] log likelihood: -1938.135564
EM: Round [267] log likelihood: -1938.133374
EM: Round [268] log likelihood: -1938.131194
EM: Round [269] log likelihood: -1938.129023
EM: Round [270] log likelihood: -1938.126862
EM: Round [271] log likelihood: -1938.124711
EM: Round [272] log likelihood: -1938.122569
EM: Round [273] log likelihood: -1938.120436
EM: Round [274] log likelihood: -1938.118313
EM: Round [275] log likelihood: -1938.116198
EM: Round [276] log likelihood: -1938.114093
EM: Round [277] log likelihood: -1938.111998
EM: Round [278] log likelihood: -1938.109911
EM: Round [279] log likelihood: -1938.107833
EM: Round [280] log likelihood: -1938.105764
EM: Round [281] log likelihood: -1938.103704
EM: Round [282] log likelihood: -1938.101653
EM: Round [283] log likelihood: -1938.099610
EM: Round [284] log likelihood: -1938.097577
EM: Round [285] log likelihood: -1938.095552
EM: Round [286] log likelihood: -1938.093535
EM: Round [287] log likelihood: -1938.091528
EM: Round [288] log likelihood: -1938.089528
EM: Round [289] log likelihood: -1938.087537
EM: Round [290] log likelihood: -1938.085555
EM: Round [291] log likelihood: -1938.083581
EM: Round [292] log likelihood: -1938.081615
EM: Round [293] log likelihood: -1938.079657
EM: Round [294] log likelihood: -1938.077708
EM: Round [295] log likelihood: -1938.075766
EM: Round [296] log likelihood: -1938.073833
EM: Round [297] log likelihood: -1938.071908
EM: Round [298] log likelihood: -1938.069991
EM: Round [299] log likelihood: -1938.068082
EM: Round [300] log likelihood: -1938.066180
EM: Round [301] log likelihood: -1938.064287
EM: Round [302] log likelihood: -1938.062401
EM: Round [303] log likelihood: -1938.060523
EM: Round [304] log likelihood: -1938.058653
EM: Round [305] log likelihood: -1938.056791
EM: Round [306] log likelihood: -1938.054936
EM: Round [307] log likelihood: -1938.053088
EM: Round [308] log likelihood: -1938.051249
EM: Round [309] log likelihood: -1938.049416
EM: Round [310] log likelihood: -1938.047591
EM: Round [311] log likelihood: -1938.045774
EM: Round [312] log likelihood: -1938.043964
EM: Round [313] log likelihood: -1938.042161
EM: Round [314] log likelihood: -1938.040365
EM: Round [315] log likelihood: -1938.038577
EM: Round [316] log likelihood: -1938.036796
EM: Round [317] log likelihood: -1938.035022
EM: Round [318] log likelihood: -1938.033255
EM: Round [319] log likelihood: -1938.031495
EM: Round [320] log likelihood: -1938.029742
EM: Round [321] log likelihood: -1938.027996
EM: Round [322] log likelihood: -1938.026257
EM: Round [323] log likelihood: -1938.024525
EM: Round [324] log likelihood: -1938.022800
EM: Round [325] log likelihood: -1938.021082
EM: Round [326] log likelihood: -1938.019370
EM: Round [327] log likelihood: -1938.017665
EM: Round [328] log likelihood: -1938.015967
EM: Round [329] log likelihood: -1938.014276
EM: Round [330] log likelihood: -1938.012591
EM: Round [331] log likelihood: -1938.010913
EM: Round [332] log likelihood: -1938.009241
EM: Round [333] log likelihood: -1938.007576
EM: Round [334] log likelihood: -1938.005917
EM: Round [335] log likelihood: -1938.004265
EM: Round [336] log likelihood: -1938.002619
EM: Round [337] log likelihood: -1938.000980
EM: Round [338] log likelihood: -1937.999347
EM: Round [339] log likelihood: -1937.997720
EM: Round [340] log likelihood: -1937.996099
EM: Round [341] log likelihood: -1937.994485
EM: Round [342] log likelihood: -1937.992877
EM: Round [343] log likelihood: -1937.991275
EM: Round [344] log likelihood: -1937.989679
EM: Round [345] log likelihood: -1937.988090
EM: Round [346] log likelihood: -1937.986506
EM: Round [347] log likelihood: -1937.984929
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EM: Round [832] log likelihood: -1937.602554
EM: Round [833] log likelihood: -1937.602192
EM: Round [834] log likelihood: -1937.601831
EM: Round [835] log likelihood: -1937.601470
EM: Round [836] log likelihood: -1937.601111
EM: Round [837] log likelihood: -1937.600753
EM: Round [838] log likelihood: -1937.600395
EM: Round [839] log likelihood: -1937.600039
EM: Round [840] log likelihood: -1937.599683
EM: Round [841] log likelihood: -1937.599329
EM: Round [842] log likelihood: -1937.598975
EM: Round [843] log likelihood: -1937.598622
EM: Round [844] log likelihood: -1937.598271
EM: Round [845] log likelihood: -1937.597920
EM: Round [846] log likelihood: -1937.597570
EM: Round [847] log likelihood: -1937.597220
EM: Round [848] log likelihood: -1937.596872
EM: Round [849] log likelihood: -1937.596525
EM: Round [850] log likelihood: -1937.596178
EM: Round [851] log likelihood: -1937.595833
EM: Round [852] log likelihood: -1937.595488
EM: Round [853] log likelihood: -1937.595144
EM: Round [854] log likelihood: -1937.594802
EM: Round [855] log likelihood: -1937.594460
EM: Round [856] log likelihood: -1937.594118
EM: Round [857] log likelihood: -1937.593778
EM: Round [858] log likelihood: -1937.593439
EM: Round [859] log likelihood: -1937.593100
EM: Round [860] log likelihood: -1937.592763
EM: Round [861] log likelihood: -1937.592426
EM: Round [862] log likelihood: -1937.592090
EM: Round [863] log likelihood: -1937.591755
EM: Round [864] log likelihood: -1937.591421
EM: Round [865] log likelihood: -1937.591088
EM: Round [866] log likelihood: -1937.590755
EM: Round [867] log likelihood: -1937.590424
EM: Round [868] log likelihood: -1937.590093
EM: Round [869] log likelihood: -1937.589763
EM: Round [870] log likelihood: -1937.589434
EM: Round [871] log likelihood: -1937.589106
EM: Round [872] log likelihood: -1937.588779
EM: Round [873] log likelihood: -1937.588452
EM: Round [874] log likelihood: -1937.588126
EM: Round [875] log likelihood: -1937.587802
EM: Round [876] log likelihood: -1937.587478
EM: Round [877] log likelihood: -1937.587154
EM: Round [878] log likelihood: -1937.586832
EM: Round [879] log likelihood: -1937.586511
EM: Round [880] log likelihood: -1937.586190
EM: Round [881] log likelihood: -1937.585870
EM: Round [882] log likelihood: -1937.585551
EM: Round [883] log likelihood: -1937.585233
EM: Round [884] log likelihood: -1937.584915
EM: Round [885] log likelihood: -1937.584599
EM: Round [886] log likelihood: -1937.584283
EM: Round [887] log likelihood: -1937.583968
EM: Round [888] log likelihood: -1937.583654
EM: Round [889] log likelihood: -1937.583340
EM: Round [890] log likelihood: -1937.583028
EM: Round [891] log likelihood: -1937.582716
EM: Round [892] log likelihood: -1937.582405
EM: Round [893] log likelihood: -1937.582095
EM: Round [894] log likelihood: -1937.581785
EM: Round [895] log likelihood: -1937.581476
EM: Round [896] log likelihood: -1937.581169
EM: Round [897] log likelihood: -1937.580862
EM: Round [898] log likelihood: -1937.580555
EM: Round [899] log likelihood: -1937.580250
EM: Round [900] log likelihood: -1937.579945
EM: Round [901] log likelihood: -1937.579641
EM: Round [902] log likelihood: -1937.579338
EM: Round [903] log likelihood: -1937.579035
EM: Round [904] log likelihood: -1937.578734
EM: Round [905] log likelihood: -1937.578433
EM: Round [906] log likelihood: -1937.578133
EM: Round [907] log likelihood: -1937.577833
EM: Round [908] log likelihood: -1937.577535
EM: Round [909] log likelihood: -1937.577237
EM: Round [910] log likelihood: -1937.576940
EM: Round [911] log likelihood: -1937.576643
EM: Round [912] log likelihood: -1937.576348
EM: Round [913] log likelihood: -1937.576053
EM: Round [914] log likelihood: -1937.575759
EM: Round [915] log likelihood: -1937.575466
EM: Round [916] log likelihood: -1937.575173
EM: Round [917] log likelihood: -1937.574881
EM: Round [918] log likelihood: -1937.574590
EM: Round [919] log likelihood: -1937.574300
EM: Round [920] log likelihood: -1937.574010
EM: Round [921] log likelihood: -1937.573721
EM: Round [922] log likelihood: -1937.573433
EM: Round [923] log likelihood: -1937.573145
EM: Round [924] log likelihood: -1937.572859
EM: Round [925] log likelihood: -1937.572573
EM: Round [926] log likelihood: -1937.572287
EM: Round [927] log likelihood: -1937.572003
EM: Round [928] log likelihood: -1937.571719
EM: Round [929] log likelihood: -1937.571436
EM: Round [930] log likelihood: -1937.571153
EM: Round [931] log likelihood: -1937.570871
EM: Round [932] log likelihood: -1937.570590
EM: Round [933] log likelihood: -1937.570310
EM: Round [934] log likelihood: -1937.570030
EM: Round [935] log likelihood: -1937.569752
EM: Round [936] log likelihood: -1937.569473
EM: Round [937] log likelihood: -1937.569196
EM: Round [938] log likelihood: -1937.568919
EM: Round [939] log likelihood: -1937.568643
EM: Round [940] log likelihood: -1937.568368
EM: Round [941] log likelihood: -1937.568093
EM: Round [942] log likelihood: -1937.567819
EM: Round [943] log likelihood: -1937.567545
EM: Round [944] log likelihood: -1937.567273
EM: Round [945] log likelihood: -1937.567001
EM: Round [946] log likelihood: -1937.566730
EM: Round [947] log likelihood: -1937.566459
EM: Round [948] log likelihood: -1937.566189
EM: Round [949] log likelihood: -1937.565920
EM: Round [950] log likelihood: -1937.565651
EM: Round [951] log likelihood: -1937.565383
EM: Round [952] log likelihood: -1937.565116
EM: Round [953] log likelihood: -1937.564849
EM: Round [954] log likelihood: -1937.564584
EM: Round [955] log likelihood: -1937.564318
EM: Round [956] log likelihood: -1937.564054
EM: Round [957] log likelihood: -1937.563790
EM: Round [958] log likelihood: -1937.563527
EM: Round [959] log likelihood: -1937.563264
EM: Round [960] log likelihood: -1937.563002
EM: Round [961] log likelihood: -1937.562741
EM: Round [962] log likelihood: -1937.562480
EM: Round [963] log likelihood: -1937.562220
EM: Round [964] log likelihood: -1937.561961
EM: Round [965] log likelihood: -1937.561702
EM: Round [966] log likelihood: -1937.561444
EM: Round [967] log likelihood: -1937.561187
EM: Round [968] log likelihood: -1937.560930
EM: Round [969] log likelihood: -1937.560674
EM: Round [970] log likelihood: -1937.560418
EM: Round [971] log likelihood: -1937.560163
EM: Round [972] log likelihood: -1937.559909
EM: Round [973] log likelihood: -1937.559656
EM: Round [974] log likelihood: -1937.559403
EM: Round [975] log likelihood: -1937.559150
EM: Round [976] log likelihood: -1937.558899
EM: Round [977] log likelihood: -1937.558648
EM: Round [978] log likelihood: -1937.558397
EM: Round [979] log likelihood: -1937.558147
EM: Round [980] log likelihood: -1937.557898
EM: Round [981] log likelihood: -1937.557650
EM: Round [982] log likelihood: -1937.557402
EM: Round [983] log likelihood: -1937.557154
EM: Round [984] log likelihood: -1937.556908
EM: Round [985] log likelihood: -1937.556662
EM: Round [986] log likelihood: -1937.556416
EM: Round [987] log likelihood: -1937.556171
EM: Round [988] log likelihood: -1937.555927
EM: Round [989] log likelihood: -1937.555683
EM: Round [990] log likelihood: -1937.555440
EM: Round [991] log likelihood: -1937.555198
EM: Round [992] log likelihood: -1937.554956
EM: Round [993] log likelihood: -1937.554715
EM: Round [994] log likelihood: -1937.554474
EM: Round [995] log likelihood: -1937.554234
EM: Round [996] log likelihood: -1937.553994
EM: Round [997] log likelihood: -1937.553755
EM: Round [998] log likelihood: -1937.553517
EM: Round [999] log likelihood: -1937.553279
EM: Round [1000] log likelihood: -1937.553042
EM: Round [1001] log likelihood: -1937.552806
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.2slL2KydIu/tih_rna_sample_00729_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.2slL2KydIu/tih_rna_sample_00729_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.2slL2KydIu/tih_rna_sample_00729_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.2slL2KydIu/tih_rna_sample_00729_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.2slL2KydIu/tih_rna_sample_00729_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.2slL2KydIu/tih_rna_sample_00729_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.2slL2KydIu/tih_rna_sample_00729_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.2slL2KydIu/fi_workdir/tih_rna_sample_00729_B23MVV7LT4_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.2slL2KydIu/fi_workdir/tih_rna_sample_00729_B23MVV7LT4_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.2slL2KydIu/fi_workdir/tih_rna_sample_00729_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.2slL2KydIu/tih_rna_sample_00729_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.2slL2KydIu/tih_rna_sample_00729_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1672.247484
EM: Round [1] log likelihood: -1672.216206
EM: Round [2] log likelihood: -1672.201154
EM: Round [3] log likelihood: -1672.186405
EM: Round [4] log likelihood: -1672.171902
EM: Round [5] log likelihood: -1672.157639
EM: Round [6] log likelihood: -1672.143607
EM: Round [7] log likelihood: -1672.129800
EM: Round [8] log likelihood: -1672.116212
EM: Round [9] log likelihood: -1672.102835
EM: Round [10] log likelihood: -1672.089664
EM: Round [11] log likelihood: -1672.076694
EM: Round [12] log likelihood: -1672.063918
EM: Round [13] log likelihood: -1672.051331
EM: Round [14] log likelihood: -1672.038929
EM: Round [15] log likelihood: -1672.026705
EM: Round [16] log likelihood: -1672.014656
EM: Round [17] log likelihood: -1672.002777
EM: Round [18] log likelihood: -1671.991063
EM: Round [19] log likelihood: -1671.979511
EM: Round [20] log likelihood: -1671.968116
EM: Round [21] log likelihood: -1671.956875
EM: Round [22] log likelihood: -1671.945783
EM: Round [23] log likelihood: -1671.934838
EM: Round [24] log likelihood: -1671.924035
EM: Round [25] log likelihood: -1671.913371
EM: Round [26] log likelihood: -1671.902843
EM: Round [27] log likelihood: -1671.892448
EM: Round [28] log likelihood: -1671.882183
EM: Round [29] log likelihood: -1671.872045
EM: Round [30] log likelihood: -1671.862031
EM: Round [31] log likelihood: -1671.852138
EM: Round [32] log likelihood: -1671.842365
EM: Round [33] log likelihood: -1671.832707
EM: Round [34] log likelihood: -1671.823163
EM: Round [35] log likelihood: -1671.813730
EM: Round [36] log likelihood: -1671.804406
EM: Round [37] log likelihood: -1671.795189
EM: Round [38] log likelihood: -1671.786076
EM: Round [39] log likelihood: -1671.777066
EM: Round [40] log likelihood: -1671.768156
EM: Round [41] log likelihood: -1671.759344
EM: Round [42] log likelihood: -1671.750629
EM: Round [43] log likelihood: -1671.742009
EM: Round [44] log likelihood: -1671.733481
EM: Round [45] log likelihood: -1671.725044
EM: Round [46] log likelihood: -1671.716696
EM: Round [47] log likelihood: -1671.708436
EM: Round [48] log likelihood: -1671.700262
EM: Round [49] log likelihood: -1671.692172
EM: Round [50] log likelihood: -1671.684165
EM: Round [51] log likelihood: -1671.676239
EM: Round [52] log likelihood: -1671.668393
EM: Round [53] log likelihood: -1671.660625
EM: Round [54] log likelihood: -1671.652935
EM: Round [55] log likelihood: -1671.645320
EM: Round [56] log likelihood: -1671.637780
EM: Round [57] log likelihood: -1671.630313
EM: Round [58] log likelihood: -1671.622917
EM: Round [59] log likelihood: -1671.615592
EM: Round [60] log likelihood: -1671.608337
EM: Round [61] log likelihood: -1671.601150
EM: Round [62] log likelihood: -1671.594030
EM: Round [63] log likelihood: -1671.586977
EM: Round [64] log likelihood: -1671.579988
EM: Round [65] log likelihood: -1671.573064
EM: Round [66] log likelihood: -1671.566202
EM: Round [67] log likelihood: -1671.559402
EM: Round [68] log likelihood: -1671.552663
EM: Round [69] log likelihood: -1671.545985
EM: Round [70] log likelihood: -1671.539365
EM: Round [71] log likelihood: -1671.532803
EM: Round [72] log likelihood: -1671.526299
EM: Round [73] log likelihood: -1671.519852
EM: Round [74] log likelihood: -1671.513459
EM: Round [75] log likelihood: -1671.507122
EM: Round [76] log likelihood: -1671.500839
EM: Round [77] log likelihood: -1671.494609
EM: Round [78] log likelihood: -1671.488431
EM: Round [79] log likelihood: -1671.482304
EM: Round [80] log likelihood: -1671.476229
EM: Round [81] log likelihood: -1671.470204
EM: Round [82] log likelihood: -1671.464228
EM: Round [83] log likelihood: -1671.458301
EM: Round [84] log likelihood: -1671.452422
EM: Round [85] log likelihood: -1671.446591
EM: Round [86] log likelihood: -1671.440806
EM: Round [87] log likelihood: -1671.435067
EM: Round [88] log likelihood: -1671.429374
EM: Round [89] log likelihood: -1671.423726
EM: Round [90] log likelihood: -1671.418122
EM: Round [91] log likelihood: -1671.412561
EM: Round [92] log likelihood: -1671.407044
EM: Round [93] log likelihood: -1671.401569
EM: Round [94] log likelihood: -1671.396136
EM: Round [95] log likelihood: -1671.390745
EM: Round [96] log likelihood: -1671.385394
EM: Round [97] log likelihood: -1671.380084
EM: Round [98] log likelihood: -1671.374813
EM: Round [99] log likelihood: -1671.369582
EM: Round [100] log likelihood: -1671.364390
EM: Round [101] log likelihood: -1671.359236
EM: Round [102] log likelihood: -1671.354120
EM: Round [103] log likelihood: -1671.349042
EM: Round [104] log likelihood: -1671.344000
EM: Round [105] log likelihood: -1671.338995
EM: Round [106] log likelihood: -1671.334026
EM: Round [107] log likelihood: -1671.329092
EM: Round [108] log likelihood: -1671.324194
EM: Round [109] log likelihood: -1671.319330
EM: Round [110] log likelihood: -1671.314501
EM: Round [111] log likelihood: -1671.309705
EM: Round [112] log likelihood: -1671.304944
EM: Round [113] log likelihood: -1671.300215
EM: Round [114] log likelihood: -1671.295519
EM: Round [115] log likelihood: -1671.290856
EM: Round [116] log likelihood: -1671.286224
EM: Round [117] log likelihood: -1671.281624
EM: Round [118] log likelihood: -1671.277056
EM: Round [119] log likelihood: -1671.272518
EM: Round [120] log likelihood: -1671.268011
EM: Round [121] log likelihood: -1671.263534
EM: Round [122] log likelihood: -1671.259087
EM: Round [123] log likelihood: -1671.254670
EM: Round [124] log likelihood: -1671.250282
EM: Round [125] log likelihood: -1671.245922
EM: Round [126] log likelihood: -1671.241592
EM: Round [127] log likelihood: -1671.237289
EM: Round [128] log likelihood: -1671.233015
EM: Round [129] log likelihood: -1671.228769
EM: Round [130] log likelihood: -1671.224549
EM: Round [131] log likelihood: -1671.220357
EM: Round [132] log likelihood: -1671.216192
EM: Round [133] log likelihood: -1671.212053
EM: Round [134] log likelihood: -1671.207941
EM: Round [135] log likelihood: -1671.203854
EM: Round [136] log likelihood: -1671.199793
EM: Round [137] log likelihood: -1671.195758
EM: Round [138] log likelihood: -1671.191748
EM: Round [139] log likelihood: -1671.187763
EM: Round [140] log likelihood: -1671.183802
EM: Round [141] log likelihood: -1671.179866
EM: Round [142] log likelihood: -1671.175954
EM: Round [143] log likelihood: -1671.172066
EM: Round [144] log likelihood: -1671.168202
EM: Round [145] log likelihood: -1671.164361
EM: Round [146] log likelihood: -1671.160544
EM: Round [147] log likelihood: -1671.156749
EM: Round [148] log likelihood: -1671.152977
EM: Round [149] log likelihood: -1671.149228
EM: Round [150] log likelihood: -1671.145501
EM: Round [151] log likelihood: -1671.141797
EM: Round [152] log likelihood: -1671.138114
EM: Round [153] log likelihood: -1671.134453
EM: Round [154] log likelihood: -1671.130813
EM: Round [155] log likelihood: -1671.127195
EM: Round [156] log likelihood: -1671.123598
EM: Round [157] log likelihood: -1671.120021
EM: Round [158] log likelihood: -1671.116466
EM: Round [159] log likelihood: -1671.112931
EM: Round [160] log likelihood: -1671.109416
EM: Round [161] log likelihood: -1671.105921
EM: Round [162] log likelihood: -1671.102447
EM: Round [163] log likelihood: -1671.098992
EM: Round [164] log likelihood: -1671.095556
EM: Round [165] log likelihood: -1671.092140
EM: Round [166] log likelihood: -1671.088744
EM: Round [167] log likelihood: -1671.085366
EM: Round [168] log likelihood: -1671.082007
EM: Round [169] log likelihood: -1671.078667
EM: Round [170] log likelihood: -1671.075346
EM: Round [171] log likelihood: -1671.072043
EM: Round [172] log likelihood: -1671.068758
EM: Round [173] log likelihood: -1671.065491
EM: Round [174] log likelihood: -1671.062242
EM: Round [175] log likelihood: -1671.059011
EM: Round [176] log likelihood: -1671.055798
EM: Round [177] log likelihood: -1671.052601
EM: Round [178] log likelihood: -1671.049423
EM: Round [179] log likelihood: -1671.046261
EM: Round [180] log likelihood: -1671.043116
EM: Round [181] log likelihood: -1671.039989
EM: Round [182] log likelihood: -1671.036878
EM: Round [183] log likelihood: -1671.033783
EM: Round [184] log likelihood: -1671.030705
EM: Round [185] log likelihood: -1671.027643
EM: Round [186] log likelihood: -1671.024598
EM: Round [187] log likelihood: -1671.021568
EM: Round [188] log likelihood: -1671.018555
EM: Round [189] log likelihood: -1671.015557
EM: Round [190] log likelihood: -1671.012574
EM: Round [191] log likelihood: -1671.009608
EM: Round [192] log likelihood: -1671.006656
EM: Round [193] log likelihood: -1671.003720
EM: Round [194] log likelihood: -1671.000799
EM: Round [195] log likelihood: -1670.997893
EM: Round [196] log likelihood: -1670.995002
EM: Round [197] log likelihood: -1670.992126
EM: Round [198] log likelihood: -1670.989264
EM: Round [199] log likelihood: -1670.986417
EM: Round [200] log likelihood: -1670.983585
EM: Round [201] log likelihood: -1670.980766
EM: Round [202] log likelihood: -1670.977962
EM: Round [203] log likelihood: -1670.975172
EM: Round [204] log likelihood: -1670.972396
EM: Round [205] log likelihood: -1670.969634
EM: Round [206] log likelihood: -1670.966885
EM: Round [207] log likelihood: -1670.964151
EM: Round [208] log likelihood: -1670.961429
EM: Round [209] log likelihood: -1670.958722
EM: Round [210] log likelihood: -1670.956027
EM: Round [211] log likelihood: -1670.953346
EM: Round [212] log likelihood: -1670.950678
EM: Round [213] log likelihood: -1670.948023
EM: Round [214] log likelihood: -1670.945381
EM: Round [215] log likelihood: -1670.942752
EM: Round [216] log likelihood: -1670.940135
EM: Round [217] log likelihood: -1670.937531
EM: Round [218] log likelihood: -1670.934940
EM: Round [219] log likelihood: -1670.932361
EM: Round [220] log likelihood: -1670.929795
EM: Round [221] log likelihood: -1670.927241
EM: Round [222] log likelihood: -1670.924699
EM: Round [223] log likelihood: -1670.922169
EM: Round [224] log likelihood: -1670.919651
EM: Round [225] log likelihood: -1670.917146
EM: Round [226] log likelihood: -1670.914652
EM: Round [227] log likelihood: -1670.912169
EM: Round [228] log likelihood: -1670.909699
EM: Round [229] log likelihood: -1670.907240
EM: Round [230] log likelihood: -1670.904792
EM: Round [231] log likelihood: -1670.902356
EM: Round [232] log likelihood: -1670.899932
EM: Round [233] log likelihood: -1670.897518
EM: Round [234] log likelihood: -1670.895116
EM: Round [235] log likelihood: -1670.892725
EM: Round [236] log likelihood: -1670.890345
EM: Round [237] log likelihood: -1670.887976
EM: Round [238] log likelihood: -1670.885618
EM: Round [239] log likelihood: -1670.883270
EM: Round [240] log likelihood: -1670.880934
EM: Round [241] log likelihood: -1670.878608
EM: Round [242] log likelihood: -1670.876292
EM: Round [243] log likelihood: -1670.873987
EM: Round [244] log likelihood: -1670.871693
EM: Round [245] log likelihood: -1670.869409
EM: Round [246] log likelihood: -1670.867135
EM: Round [247] log likelihood: -1670.864871
EM: Round [248] log likelihood: -1670.862618
EM: Round [249] log likelihood: -1670.860374
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-total frags in /tmp/nxf.2slL2KydIu/tih_rna_sample_00729_B23MVV7LT4_1_1.fastp.fastq.gz: 296563078
Warning - not locating file: /tmp/nxf.2slL2KydIu/tih_rna_sample_00729_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000226049.3]
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ls: cannot access 'IGV_inputs': No such file or directory