Done.
-parsing GTF file: /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.jfar3XoMy6/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.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00569_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00569_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:39:40 : INFO : Done.
-parsing GTF file: /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[3500000]   -done parsing /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 38,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'exons hit < 2' => 11,
          'small anchor length' => 23,
          ' ** passed ** ' => 7261,
          'low complexity anchor region' => 1,
          'num genes matched < 2' => 22,
          'per_id < 96' => 10537,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 336,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 7,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 24,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 36,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 77,
          'seq-similar region overlap' => 133,
          'excessive soft clipping' => 16526
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[4000]   -fusion SPANNING read extraction for scaff: AC020550.2--APBA1
-fusion SPANNING read extraction for scaff: AC023866.2--ALB

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[14000]   -fusion SPANNING read extraction for scaff: AC090735.1--PRKCA

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

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[4000]   -fusion SPANNING read extraction for scaff: AC104041.1--APBA1

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[181000]   -fusion SPANNING read extraction for scaff: AFAP1--SMARCA2

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[30000]   -fusion SPANNING read extraction for scaff: ANXA8--VSTM4

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[74000]   -fusion SPANNING read extraction for scaff: EXOC4--CHCHD3

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[38000]   -fusion SPANNING read extraction for scaff: EXOC4--FP236383.3

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[7000]   -fusion SPANNING read extraction for scaff: GUCY1B2--NKAIN2

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[7000]   -fusion SPANNING read extraction for scaff: LINC00381--NKAIN2

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[21000]   -fusion SPANNING read extraction for scaff: MED12L--PRKCA

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[12000]   -fusion SPANNING read extraction for scaff: MRPL39--SLC4A4

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[10000]   -fusion SPANNING read extraction for scaff: MTRF1LP2--GSDMC

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[445000]   
[446000]   -fusion SPANNING read extraction for scaff: NOTCH2--SPAG17

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[8000]   
[9000]   
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[12000]   
[13000]   
[14000]   
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[16000]   -fusion SPANNING read extraction for scaff: NXPE3--AC107297.1

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[9000]   
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[15000]   
[16000]   -fusion SPANNING read extraction for scaff: NXPE3--AC078828.1

[1000]   
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[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   -fusion SPANNING read extraction for scaff: OR10Z1--CAPZB

[1000]   
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[6000]   
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[8000]   
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[30000]   
[31000]   
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[34000]   
[35000]   
[36000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
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[6000]   
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[8000]   
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[34000]   
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[36000]   
[37000]   
[38000]   
[39000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
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[6000]   
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[8000]   
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[34000]   
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[36000]   
[37000]   
[38000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
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[6000]   
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[8000]   
[9000]   
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[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHA9--PCDHAC2

[1000]   
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[6000]   
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[9000]   
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[11000]   
[12000]   
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[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHA9--PCDHAC1

[1000]   
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[6000]   
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[8000]   
[9000]   
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[11000]   
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[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHA9--PCDHA13

[1000]   
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[9000]   
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[12000]   
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[14000]   
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[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8

[1000]   
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[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
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[6000]   
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[8000]   
[9000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6

[1000]   
[2000]   
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[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[10000]   
[11000]   
[12000]   
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[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12

[1000]   
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[4000]   
[5000]   
[6000]   
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[8000]   
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[45000]   
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[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3

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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11

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[6000]   
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[8000]   
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[52000]   
[53000]   -fusion SPANNING read extraction for scaff: PLXNA4--CNTNAP2

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[23000]   
[24000]   -fusion SPANNING read extraction for scaff: ROR2--RABL3

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[207000]   
[208000]   -fusion SPANNING read extraction for scaff: SLC2A9--WDR1

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[6000]   
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[24000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[6000]   
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[8000]   
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[15000]   
[16000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[42000]   
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[46000]   
[47000]   
[48000]   -fusion SPANNING read extraction for scaff: TWSG1--PTPRM

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[100000]   
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[1821000]   -fusion SPANNING read extraction for scaff: WWTR1--KRT6A

[1000]   
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[11000]   -fusion SPANNING read extraction for scaff: ZNF488--VSTM4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 17868,
          'seq similar region alignment' => 36861
        };
EM: Starting log likelihood: -5697.128655
EM: Round [1] log likelihood: -5688.420879
EM: Round [2] log likelihood: -5685.020401
EM: Round [3] log likelihood: -5683.135521
EM: Round [4] log likelihood: -5681.877949
EM: Round [5] log likelihood: -5680.967729
EM: Round [6] log likelihood: -5680.278430
EM: Round [7] log likelihood: -5679.737227
EM: Round [8] log likelihood: -5679.297987
EM: Round [9] log likelihood: -5678.930391
EM: Round [10] log likelihood: -5678.614131
EM: Round [11] log likelihood: -5678.335420
EM: Round [12] log likelihood: -5678.084795
EM: Round [13] log likelihood: -5677.855694
EM: Round [14] log likelihood: -5677.643521
EM: Round [15] log likelihood: -5677.445023
EM: Round [16] log likelihood: -5677.257865
EM: Round [17] log likelihood: -5677.080351
EM: Round [18] log likelihood: -5676.911227
EM: Round [19] log likelihood: -5676.749550
EM: Round [20] log likelihood: -5676.594594
EM: Round [21] log likelihood: -5676.445787
EM: Round [22] log likelihood: -5676.302671
EM: Round [23] log likelihood: -5676.164866
EM: Round [24] log likelihood: -5676.032052
EM: Round [25] log likelihood: -5675.903954
EM: Round [26] log likelihood: -5675.780327
EM: Round [27] log likelihood: -5675.660957
EM: Round [28] log likelihood: -5675.545646
EM: Round [29] log likelihood: -5675.434214
EM: Round [30] log likelihood: -5675.326496
EM: Round [31] log likelihood: -5675.222337
EM: Round [32] log likelihood: -5675.121590
EM: Round [33] log likelihood: -5675.024120
EM: Round [34] log likelihood: -5674.929799
EM: Round [35] log likelihood: -5674.838503
EM: Round [36] log likelihood: -5674.750117
EM: Round [37] log likelihood: -5674.664531
EM: Round [38] log likelihood: -5674.581639
EM: Round [39] log likelihood: -5674.501343
EM: Round [40] log likelihood: -5674.423546
EM: Round [41] log likelihood: -5674.348157
EM: Round [42] log likelihood: -5674.275089
EM: Round [43] log likelihood: -5674.204259
EM: Round [44] log likelihood: -5674.135587
EM: Round [45] log likelihood: -5674.068996
EM: Round [46] log likelihood: -5674.004413
EM: Round [47] log likelihood: -5673.941768
EM: Round [48] log likelihood: -5673.880993
EM: Round [49] log likelihood: -5673.822024
EM: Round [50] log likelihood: -5673.764798
EM: Round [51] log likelihood: -5673.709257
EM: Round [52] log likelihood: -5673.655343
EM: Round [53] log likelihood: -5673.603001
EM: Round [54] log likelihood: -5673.552178
EM: Round [55] log likelihood: -5673.502823
EM: Round [56] log likelihood: -5673.454888
EM: Round [57] log likelihood: -5673.408325
EM: Round [58] log likelihood: -5673.363090
EM: Round [59] log likelihood: -5673.319139
EM: Round [60] log likelihood: -5673.276430
EM: Round [61] log likelihood: -5673.234923
EM: Round [62] log likelihood: -5673.194578
EM: Round [63] log likelihood: -5673.155359
EM: Round [64] log likelihood: -5673.117230
EM: Round [65] log likelihood: -5673.080155
EM: Round [66] log likelihood: -5673.044102
EM: Round [67] log likelihood: -5673.009037
EM: Round [68] log likelihood: -5672.974931
EM: Round [69] log likelihood: -5672.941752
EM: Round [70] log likelihood: -5672.909473
EM: Round [71] log likelihood: -5672.878064
EM: Round [72] log likelihood: -5672.847500
EM: Round [73] log likelihood: -5672.817754
EM: Round [74] log likelihood: -5672.788800
EM: Round [75] log likelihood: -5672.760615
EM: Round [76] log likelihood: -5672.733176
EM: Round [77] log likelihood: -5672.706459
EM: Round [78] log likelihood: -5672.680443
EM: Round [79] log likelihood: -5672.655107
EM: Round [80] log likelihood: -5672.630430
EM: Round [81] log likelihood: -5672.606393
EM: Round [82] log likelihood: -5672.582976
EM: Round [83] log likelihood: -5672.560161
EM: Round [84] log likelihood: -5672.537930
EM: Round [85] log likelihood: -5672.516267
EM: Round [86] log likelihood: -5672.495154
EM: Round [87] log likelihood: -5672.474575
EM: Round [88] log likelihood: -5672.454515
EM: Round [89] log likelihood: -5672.434959
EM: Round [90] log likelihood: -5672.415891
EM: Round [91] log likelihood: -5672.397299
EM: Round [92] log likelihood: -5672.379168
EM: Round [93] log likelihood: -5672.361484
EM: Round [94] log likelihood: -5672.344236
EM: Round [95] log likelihood: -5672.327411
EM: Round [96] log likelihood: -5672.310996
EM: Round [97] log likelihood: -5672.294980
EM: Round [98] log likelihood: -5672.279352
EM: Round [99] log likelihood: -5672.264102
EM: Round [100] log likelihood: -5672.249217
EM: Round [101] log likelihood: -5672.234688
EM: Round [102] log likelihood: -5672.220506
EM: Round [103] log likelihood: -5672.206660
EM: Round [104] log likelihood: -5672.193141
EM: Round [105] log likelihood: -5672.179940
EM: Round [106] log likelihood: -5672.167048
EM: Round [107] log likelihood: -5672.154458
EM: Round [108] log likelihood: -5672.142159
EM: Round [109] log likelihood: -5672.130146
EM: Round [110] log likelihood: -5672.118409
EM: Round [111] log likelihood: -5672.106941
EM: Round [112] log likelihood: -5672.095735
EM: Round [113] log likelihood: -5672.084785
EM: Round [114] log likelihood: -5672.074082
EM: Round [115] log likelihood: -5672.063620
EM: Round [116] log likelihood: -5672.053394
EM: Round [117] log likelihood: -5672.043395
EM: Round [118] log likelihood: -5672.033620
EM: Round [119] log likelihood: -5672.024060
EM: Round [120] log likelihood: -5672.014712
EM: Round [121] log likelihood: -5672.005569
EM: Round [122] log likelihood: -5671.996626
EM: Round [123] log likelihood: -5671.987877
EM: Round [124] log likelihood: -5671.979317
EM: Round [125] log likelihood: -5671.970942
EM: Round [126] log likelihood: -5671.962747
EM: Round [127] log likelihood: -5671.954727
EM: Round [128] log likelihood: -5671.946877
EM: Round [129] log likelihood: -5671.939193
EM: Round [130] log likelihood: -5671.931670
EM: Round [131] log likelihood: -5671.924305
EM: Round [132] log likelihood: -5671.917094
EM: Round [133] log likelihood: -5671.910032
EM: Round [134] log likelihood: -5671.903116
EM: Round [135] log likelihood: -5671.896342
EM: Round [136] log likelihood: -5671.889706
EM: Round [137] log likelihood: -5671.883205
EM: Round [138] log likelihood: -5671.876836
EM: Round [139] log likelihood: -5671.870594
EM: Round [140] log likelihood: -5671.864478
EM: Round [141] log likelihood: -5671.858483
EM: Round [142] log likelihood: -5671.852607
EM: Round [143] log likelihood: -5671.846847
EM: Round [144] log likelihood: -5671.841199
EM: Round [145] log likelihood: -5671.835661
EM: Round [146] log likelihood: -5671.830231
EM: Round [147] log likelihood: -5671.824905
EM: Round [148] log likelihood: -5671.819682
EM: Round [149] log likelihood: -5671.814557
EM: Round [150] log likelihood: -5671.809530
EM: Round [151] log likelihood: -5671.804598
EM: Round [152] log likelihood: -5671.799758
EM: Round [153] log likelihood: -5671.795008
EM: Round [154] log likelihood: -5671.790345
EM: Round [155] log likelihood: -5671.785769
EM: Round [156] log likelihood: -5671.781276
EM: Round [157] log likelihood: -5671.776865
EM: Round [158] log likelihood: -5671.772534
EM: Round [159] log likelihood: -5671.768281
EM: Round [160] log likelihood: -5671.764103
EM: Round [161] log likelihood: -5671.759999
EM: Round [162] log likelihood: -5671.755968
EM: Round [163] log likelihood: -5671.752008
EM: Round [164] log likelihood: -5671.748116
EM: Round [165] log likelihood: -5671.744291
EM: Round [166] log likelihood: -5671.740533
EM: Round [167] log likelihood: -5671.736838
EM: Round [168] log likelihood: -5671.733206
EM: Round [169] log likelihood: -5671.729635
EM: Round [170] log likelihood: -5671.726124
EM: Round [171] log likelihood: -5671.722672
EM: Round [172] log likelihood: -5671.719276
EM: Round [173] log likelihood: -5671.715936
EM: Round [174] log likelihood: -5671.712650
EM: Round [175] log likelihood: -5671.709418
EM: Round [176] log likelihood: -5671.706237
EM: Round [177] log likelihood: -5671.703107
EM: Round [178] log likelihood: -5671.700027
EM: Round [179] log likelihood: -5671.696995
EM: Round [180] log likelihood: -5671.694010
EM: Round [181] log likelihood: -5671.691072
EM: Round [182] log likelihood: -5671.688178
EM: Round [183] log likelihood: -5671.685329
EM: Round [184] log likelihood: -5671.682523
EM: Round [185] log likelihood: -5671.679759
EM: Round [186] log likelihood: -5671.677037
EM: Round [187] log likelihood: -5671.674355
EM: Round [188] log likelihood: -5671.671712
EM: Round [189] log likelihood: -5671.669108
EM: Round [190] log likelihood: -5671.666541
EM: Round [191] log likelihood: -5671.664012
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EM: Round [654] log likelihood: -5671.320465
EM: Round [655] log likelihood: -5671.320158
EM: Round [656] log likelihood: -5671.319853
EM: Round [657] log likelihood: -5671.319547
EM: Round [658] log likelihood: -5671.319243
EM: Round [659] log likelihood: -5671.318939
EM: Round [660] log likelihood: -5671.318636
EM: Round [661] log likelihood: -5671.318334
EM: Round [662] log likelihood: -5671.318033
EM: Round [663] log likelihood: -5671.317732
EM: Round [664] log likelihood: -5671.317432
EM: Round [665] log likelihood: -5671.317133
EM: Round [666] log likelihood: -5671.316834
EM: Round [667] log likelihood: -5671.316537
EM: Round [668] log likelihood: -5671.316240
EM: Round [669] log likelihood: -5671.315943
EM: Round [670] log likelihood: -5671.315648
EM: Round [671] log likelihood: -5671.315353
EM: Round [672] log likelihood: -5671.315059
EM: Round [673] log likelihood: -5671.314765
EM: Round [674] log likelihood: -5671.314473
EM: Round [675] log likelihood: -5671.314181
EM: Round [676] log likelihood: -5671.313889
EM: Round [677] log likelihood: -5671.313599
EM: Round [678] log likelihood: -5671.313309
EM: Round [679] log likelihood: -5671.313020
EM: Round [680] log likelihood: -5671.312731
EM: Round [681] log likelihood: -5671.312444
EM: Round [682] log likelihood: -5671.312157
EM: Round [683] log likelihood: -5671.311870
EM: Round [684] log likelihood: -5671.311585
EM: Round [685] log likelihood: -5671.311300
EM: Round [686] log likelihood: -5671.311015
EM: Round [687] log likelihood: -5671.310732
EM: Round [688] log likelihood: -5671.310449
EM: Round [689] log likelihood: -5671.310167
EM: Round [690] log likelihood: -5671.309885
EM: Round [691] log likelihood: -5671.309605
EM: Round [692] log likelihood: -5671.309325
EM: Round [693] log likelihood: -5671.309045
EM: Round [694] log likelihood: -5671.308766
EM: Round [695] log likelihood: -5671.308488
EM: Round [696] log likelihood: -5671.308211
EM: Round [697] log likelihood: -5671.307934
EM: Round [698] log likelihood: -5671.307658
EM: Round [699] log likelihood: -5671.307383
EM: Round [700] log likelihood: -5671.307108
EM: Round [701] log likelihood: -5671.306834
EM: Round [702] log likelihood: -5671.306561
EM: Round [703] log likelihood: -5671.306288
EM: Round [704] log likelihood: -5671.306016
EM: Round [705] log likelihood: -5671.305744
EM: Round [706] log likelihood: -5671.305474
EM: Round [707] log likelihood: -5671.305204
EM: Round [708] log likelihood: -5671.304934
EM: Round [709] log likelihood: -5671.304665
EM: Round [710] log likelihood: -5671.304397
EM: Round [711] log likelihood: -5671.304130
EM: Round [712] log likelihood: -5671.303863
EM: Round [713] log likelihood: -5671.303597
EM: Round [714] log likelihood: -5671.303331
EM: Round [715] log likelihood: -5671.303066
EM: Round [716] log likelihood: -5671.302802
EM: Round [717] log likelihood: -5671.302538
EM: Round [718] log likelihood: -5671.302275
EM: Round [719] log likelihood: -5671.302013
EM: Round [720] log likelihood: -5671.301751
EM: Round [721] log likelihood: -5671.301490
EM: Round [722] log likelihood: -5671.301230
EM: Round [723] log likelihood: -5671.300970
EM: Round [724] log likelihood: -5671.300711
EM: Round [725] log likelihood: -5671.300452
EM: Round [726] log likelihood: -5671.300194
EM: Round [727] log likelihood: -5671.299937
EM: Round [728] log likelihood: -5671.299680
EM: Round [729] log likelihood: -5671.299424
EM: Round [730] log likelihood: -5671.299168
EM: Round [731] log likelihood: -5671.298914
EM: Round [732] log likelihood: -5671.298659
EM: Round [733] log likelihood: -5671.298406
EM: Round [734] log likelihood: -5671.298153
EM: Round [735] log likelihood: -5671.297900
EM: Round [736] log likelihood: -5671.297648
EM: Round [737] log likelihood: -5671.297397
EM: Round [738] log likelihood: -5671.297146
EM: Round [739] log likelihood: -5671.296896
EM: Round [740] log likelihood: -5671.296647
EM: Round [741] log likelihood: -5671.296398
EM: Round [742] log likelihood: -5671.296150
EM: Round [743] log likelihood: -5671.295902
EM: Round [744] log likelihood: -5671.295655
EM: Round [745] log likelihood: -5671.295409
EM: Round [746] log likelihood: -5671.295163
EM: Round [747] log likelihood: -5671.294918
EM: Round [748] log likelihood: -5671.294673
EM: Round [749] log likelihood: -5671.294429
EM: Round [750] log likelihood: -5671.294186
EM: Round [751] log likelihood: -5671.293943
EM: Round [752] log likelihood: -5671.293700
EM: Round [753] log likelihood: -5671.293458
EM: Round [754] log likelihood: -5671.293217
EM: Round [755] log likelihood: -5671.292977
EM: Round [756] log likelihood: -5671.292737
EM: Round [757] log likelihood: -5671.292497
EM: Round [758] log likelihood: -5671.292258
EM: Round [759] log likelihood: -5671.292020
EM: Round [760] log likelihood: -5671.291782
EM: Round [761] log likelihood: -5671.291545
EM: Round [762] log likelihood: -5671.291308
EM: Round [763] log likelihood: -5671.291072
EM: Round [764] log likelihood: -5671.290837
EM: Round [765] log likelihood: -5671.290602
EM: Round [766] log likelihood: -5671.290368
EM: Round [767] log likelihood: -5671.290134
EM: Round [768] log likelihood: -5671.289901
EM: Round [769] log likelihood: -5671.289668
EM: Round [770] log likelihood: -5671.289436
EM: Round [771] log likelihood: -5671.289204
EM: Round [772] log likelihood: -5671.288973
EM: Round [773] log likelihood: -5671.288743
EM: Round [774] log likelihood: -5671.288513
EM: Round [775] log likelihood: -5671.288283
EM: Round [776] log likelihood: -5671.288054
EM: Round [777] log likelihood: -5671.287826
EM: Round [778] log likelihood: -5671.287598
EM: Round [779] log likelihood: -5671.287371
EM: Round [780] log likelihood: -5671.287144
EM: Round [781] log likelihood: -5671.286918
EM: Round [782] log likelihood: -5671.286693
EM: Round [783] log likelihood: -5671.286468
EM: Round [784] log likelihood: -5671.286243
EM: Round [785] log likelihood: -5671.286019
EM: Round [786] log likelihood: -5671.285796
EM: Round [787] log likelihood: -5671.285573
EM: Round [788] log likelihood: -5671.285350
EM: Round [789] log likelihood: -5671.285128
EM: Round [790] log likelihood: -5671.284907
EM: Round [791] log likelihood: -5671.284686
EM: Round [792] log likelihood: -5671.284466
EM: Round [793] log likelihood: -5671.284246
EM: Round [794] log likelihood: -5671.284027
EM: Round [795] log likelihood: -5671.283808
EM: Round [796] log likelihood: -5671.283590
EM: Round [797] log likelihood: -5671.283372
EM: Round [798] log likelihood: -5671.283155
EM: Round [799] log likelihood: -5671.282938
EM: Round [800] log likelihood: -5671.282722
EM: Round [801] log likelihood: -5671.282507
EM: Round [802] log likelihood: -5671.282291
EM: Round [803] log likelihood: -5671.282077
EM: Round [804] log likelihood: -5671.281863
EM: Round [805] log likelihood: -5671.281649
EM: Round [806] log likelihood: -5671.281436
EM: Round [807] log likelihood: -5671.281223
EM: Round [808] log likelihood: -5671.281011
EM: Round [809] log likelihood: -5671.280799
EM: Round [810] log likelihood: -5671.280588
EM: Round [811] log likelihood: -5671.280378
EM: Round [812] log likelihood: -5671.280168
EM: Round [813] log likelihood: -5671.279958
EM: Round [814] log likelihood: -5671.279749
EM: Round [815] log likelihood: -5671.279540
EM: Round [816] log likelihood: -5671.279332
EM: Round [817] log likelihood: -5671.279124
EM: Round [818] log likelihood: -5671.278917
EM: Round [819] log likelihood: -5671.278711
EM: Round [820] log likelihood: -5671.278504
EM: Round [821] log likelihood: -5671.278299
EM: Round [822] log likelihood: -5671.278093
EM: Round [823] log likelihood: -5671.277889
EM: Round [824] log likelihood: -5671.277684
EM: Round [825] log likelihood: -5671.277481
EM: Round [826] log likelihood: -5671.277277
EM: Round [827] log likelihood: -5671.277075
EM: Round [828] log likelihood: -5671.276872
EM: Round [829] log likelihood: -5671.276670
EM: Round [830] log likelihood: -5671.276469
EM: Round [831] log likelihood: -5671.276268
EM: Round [832] log likelihood: -5671.276068
EM: Round [833] log likelihood: -5671.275868
EM: Round [834] log likelihood: -5671.275668
EM: Round [835] log likelihood: -5671.275469
EM: Round [836] log likelihood: -5671.275271
EM: Round [837] log likelihood: -5671.275072
EM: Round [838] log likelihood: -5671.274875
EM: Round [839] log likelihood: -5671.274678
EM: Round [840] log likelihood: -5671.274481
EM: Round [841] log likelihood: -5671.274285
EM: Round [842] log likelihood: -5671.274089
EM: Round [843] log likelihood: -5671.273893
EM: Round [844] log likelihood: -5671.273699
EM: Round [845] log likelihood: -5671.273504
EM: Round [846] log likelihood: -5671.273310
EM: Round [847] log likelihood: -5671.273117
EM: Round [848] log likelihood: -5671.272924
EM: Round [849] log likelihood: -5671.272731
EM: Round [850] log likelihood: -5671.272539
EM: Round [851] log likelihood: -5671.272347
EM: Round [852] log likelihood: -5671.272156
EM: Round [853] log likelihood: -5671.271965
EM: Round [854] log likelihood: -5671.271775
EM: Round [855] log likelihood: -5671.271585
EM: Round [856] log likelihood: -5671.271395
EM: Round [857] log likelihood: -5671.271206
EM: Round [858] log likelihood: -5671.271018
EM: Round [859] log likelihood: -5671.270830
EM: Round [860] log likelihood: -5671.270642
EM: Round [861] log likelihood: -5671.270455
EM: Round [862] log likelihood: -5671.270268
EM: Round [863] log likelihood: -5671.270081
EM: Round [864] log likelihood: -5671.269895
EM: Round [865] log likelihood: -5671.269710
EM: Round [866] log likelihood: -5671.269525
EM: Round [867] log likelihood: -5671.269340
EM: Round [868] log likelihood: -5671.269156
EM: Round [869] log likelihood: -5671.268972
EM: Round [870] log likelihood: -5671.268789
EM: Round [871] log likelihood: -5671.268606
EM: Round [872] log likelihood: -5671.268423
EM: Round [873] log likelihood: -5671.268241
EM: Round [874] log likelihood: -5671.268060
EM: Round [875] log likelihood: -5671.267878
EM: Round [876] log likelihood: -5671.267698
EM: Round [877] log likelihood: -5671.267517
EM: Round [878] log likelihood: -5671.267337
EM: Round [879] log likelihood: -5671.267158
EM: Round [880] log likelihood: -5671.266978
EM: Round [881] log likelihood: -5671.266800
EM: Round [882] log likelihood: -5671.266621
EM: Round [883] log likelihood: -5671.266444
EM: Round [884] log likelihood: -5671.266266
EM: Round [885] log likelihood: -5671.266089
EM: Round [886] log likelihood: -5671.265912
EM: Round [887] log likelihood: -5671.265736
EM: Round [888] log likelihood: -5671.265560
EM: Round [889] log likelihood: -5671.265385
EM: Round [890] log likelihood: -5671.265210
EM: Round [891] log likelihood: -5671.265035
EM: Round [892] log likelihood: -5671.264861
EM: Round [893] log likelihood: -5671.264687
EM: Round [894] log likelihood: -5671.264514
EM: Round [895] log likelihood: -5671.264341
EM: Round [896] log likelihood: -5671.264168
EM: Round [897] log likelihood: -5671.263996
EM: Round [898] log likelihood: -5671.263824
EM: Round [899] log likelihood: -5671.263653
EM: Round [900] log likelihood: -5671.263482
EM: Round [901] log likelihood: -5671.263311
EM: Round [902] log likelihood: -5671.263141
EM: Round [903] log likelihood: -5671.262971
EM: Round [904] log likelihood: -5671.262802
EM: Round [905] log likelihood: -5671.262633
EM: Round [906] log likelihood: -5671.262464
EM: Round [907] log likelihood: -5671.262296
EM: Round [908] log likelihood: -5671.262128
EM: Round [909] log likelihood: -5671.261961
EM: Round [910] log likelihood: -5671.261793
EM: Round [911] log likelihood: -5671.261627
EM: Round [912] log likelihood: -5671.261461
EM: Round [913] log likelihood: -5671.261295
EM: Round [914] log likelihood: -5671.261129
EM: Round [915] log likelihood: -5671.260964
EM: Round [916] log likelihood: -5671.260799
EM: Round [917] log likelihood: -5671.260635
EM: Round [918] log likelihood: -5671.260471
EM: Round [919] log likelihood: -5671.260307
EM: Round [920] log likelihood: -5671.260144
EM: Round [921] log likelihood: -5671.259981
EM: Round [922] log likelihood: -5671.259819
EM: Round [923] log likelihood: -5671.259656
EM: Round [924] log likelihood: -5671.259495
EM: Round [925] log likelihood: -5671.259333
EM: Round [926] log likelihood: -5671.259172
EM: Round [927] log likelihood: -5671.259012
EM: Round [928] log likelihood: -5671.258851
EM: Round [929] log likelihood: -5671.258692
EM: Round [930] log likelihood: -5671.258532
EM: Round [931] log likelihood: -5671.258373
EM: Round [932] log likelihood: -5671.258214
EM: Round [933] log likelihood: -5671.258056
EM: Round [934] log likelihood: -5671.257898
EM: Round [935] log likelihood: -5671.257740
EM: Round [936] log likelihood: -5671.257583
EM: Round [937] log likelihood: -5671.257426
EM: Round [938] log likelihood: -5671.257269
EM: Round [939] log likelihood: -5671.257113
EM: Round [940] log likelihood: -5671.256957
EM: Round [941] log likelihood: -5671.256801
EM: Round [942] log likelihood: -5671.256646
EM: Round [943] log likelihood: -5671.256491
EM: Round [944] log likelihood: -5671.256337
EM: Round [945] log likelihood: -5671.256183
EM: Round [946] log likelihood: -5671.256029
EM: Round [947] log likelihood: -5671.255876
EM: Round [948] log likelihood: -5671.255723
EM: Round [949] log likelihood: -5671.255570
EM: Round [950] log likelihood: -5671.255418
EM: Round [951] log likelihood: -5671.255266
EM: Round [952] log likelihood: -5671.255114
EM: Round [953] log likelihood: -5671.254963
EM: Round [954] log likelihood: -5671.254812
EM: Round [955] log likelihood: -5671.254661
EM: Round [956] log likelihood: -5671.254511
EM: Round [957] log likelihood: -5671.254361
EM: Round [958] log likelihood: -5671.254212
EM: Round [959] log likelihood: -5671.254063
EM: Round [960] log likelihood: -5671.253914
EM: Round [961] log likelihood: -5671.253765
EM: Round [962] log likelihood: -5671.253617
EM: Round [963] log likelihood: -5671.253469
EM: Round [964] log likelihood: -5671.253322
EM: Round [965] log likelihood: -5671.253175
EM: Round [966] log likelihood: -5671.253028
EM: Round [967] log likelihood: -5671.252881
EM: Round [968] log likelihood: -5671.252735
EM: Round [969] log likelihood: -5671.252589
EM: Round [970] log likelihood: -5671.252444
EM: Round [971] log likelihood: -5671.252299
EM: Round [972] log likelihood: -5671.252154
EM: Round [973] log likelihood: -5671.252009
EM: Round [974] log likelihood: -5671.251865
EM: Round [975] log likelihood: -5671.251721
EM: Round [976] log likelihood: -5671.251578
EM: Round [977] log likelihood: -5671.251435
EM: Round [978] log likelihood: -5671.251292
EM: Round [979] log likelihood: -5671.251149
EM: Round [980] log likelihood: -5671.251007
EM: Round [981] log likelihood: -5671.250865
EM: Round [982] log likelihood: -5671.250724
EM: Round [983] log likelihood: -5671.250583
EM: Round [984] log likelihood: -5671.250442
EM: Round [985] log likelihood: -5671.250301
EM: Round [986] log likelihood: -5671.250161
EM: Round [987] log likelihood: -5671.250021
EM: Round [988] log likelihood: -5671.249882
EM: Round [989] log likelihood: -5671.249742
EM: Round [990] log likelihood: -5671.249603
EM: Round [991] log likelihood: -5671.249465
EM: Round [992] log likelihood: -5671.249326
EM: Round [993] log likelihood: -5671.249188
EM: Round [994] log likelihood: -5671.249051
EM: Round [995] log likelihood: -5671.248913
EM: Round [996] log likelihood: -5671.248776
EM: Round [997] log likelihood: -5671.248640
EM: Round [998] log likelihood: -5671.248503
EM: Round [999] log likelihood: -5671.248367
EM: Round [1000] log likelihood: -5671.248231
EM: Round [1001] log likelihood: -5671.248096
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_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.jfar3XoMy6/fi_workdir/tih_rna_sample_00569_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -4341.386119
EM: Round [1] log likelihood: -4338.384354
EM: Round [2] log likelihood: -4337.804658
EM: Round [3] log likelihood: -4337.710865
EM: Round [4] log likelihood: -4337.696333
EM: Round [5] log likelihood: -4337.692677
EM: Round [6] log likelihood: -4337.690395
EM: Round [7] log likelihood: -4337.688287
EM: Round [8] log likelihood: -4337.686209
EM: Round [9] log likelihood: -4337.684141
EM: Round [10] log likelihood: -4337.682082
EM: Round [11] log likelihood: -4337.680032
EM: Round [12] log likelihood: -4337.677990
EM: Round [13] log likelihood: -4337.675958
EM: Round [14] log likelihood: -4337.673933
EM: Round [15] log likelihood: -4337.671917
EM: Round [16] log likelihood: -4337.669909
EM: Round [17] log likelihood: -4337.667910
EM: Round [18] log likelihood: -4337.665919
EM: Round [19] log likelihood: -4337.663936
EM: Round [20] log likelihood: -4337.661961
EM: Round [21] log likelihood: -4337.659995
EM: Round [22] log likelihood: -4337.658037
EM: Round [23] log likelihood: -4337.656086
EM: Round [24] log likelihood: -4337.654144
EM: Round [25] log likelihood: -4337.652209
EM: Round [26] log likelihood: -4337.650282
EM: Round [27] log likelihood: -4337.648364
EM: Round [28] log likelihood: -4337.646453
EM: Round [29] log likelihood: -4337.644549
EM: Round [30] log likelihood: -4337.642654
EM: Round [31] log likelihood: -4337.640766
EM: Round [32] log likelihood: -4337.638886
EM: Round [33] log likelihood: -4337.637013
EM: Round [34] log likelihood: -4337.635148
EM: Round [35] log likelihood: -4337.633290
EM: Round [36] log likelihood: -4337.631440
EM: Round [37] log likelihood: -4337.629597
EM: Round [38] log likelihood: -4337.627761
EM: Round [39] log likelihood: -4337.625933
EM: Round [40] log likelihood: -4337.624112
EM: Round [41] log likelihood: -4337.622298
EM: Round [42] log likelihood: -4337.620491
EM: Round [43] log likelihood: -4337.618692
EM: Round [44] log likelihood: -4337.616899
EM: Round [45] log likelihood: -4337.615114
EM: Round [46] log likelihood: -4337.613335
EM: Round [47] log likelihood: -4337.611564
EM: Round [48] log likelihood: -4337.609800
EM: Round [49] log likelihood: -4337.608042
EM: Round [50] log likelihood: -4337.606291
EM: Round [51] log likelihood: -4337.604547
EM: Round [52] log likelihood: -4337.602810
EM: Round [53] log likelihood: -4337.601080
EM: Round [54] log likelihood: -4337.599356
EM: Round [55] log likelihood: -4337.597639
EM: Round [56] log likelihood: -4337.595929
EM: Round [57] log likelihood: -4337.594225
EM: Round [58] log likelihood: -4337.592528
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EM: Round [978] log likelihood: -4337.074755
EM: Round [979] log likelihood: -4337.074616
EM: Round [980] log likelihood: -4337.074477
EM: Round [981] log likelihood: -4337.074338
EM: Round [982] log likelihood: -4337.074200
EM: Round [983] log likelihood: -4337.074062
EM: Round [984] log likelihood: -4337.073925
EM: Round [985] log likelihood: -4337.073788
EM: Round [986] log likelihood: -4337.073651
EM: Round [987] log likelihood: -4337.073514
EM: Round [988] log likelihood: -4337.073378
EM: Round [989] log likelihood: -4337.073242
EM: Round [990] log likelihood: -4337.073106
EM: Round [991] log likelihood: -4337.072971
EM: Round [992] log likelihood: -4337.072836
EM: Round [993] log likelihood: -4337.072701
EM: Round [994] log likelihood: -4337.072567
EM: Round [995] log likelihood: -4337.072433
EM: Round [996] log likelihood: -4337.072299
EM: Round [997] log likelihood: -4337.072165
EM: Round [998] log likelihood: -4337.072032
EM: Round [999] log likelihood: -4337.071899
EM: Round [1000] log likelihood: -4337.071767
EM: Round [1001] log likelihood: -4337.071634
-total frags in /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1_1.fastp.fastq.gz: 296330273
Warning - not locating file: /tmp/nxf.jfar3XoMy6/tih_rna_sample_00569_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000259692.6]
WARNING, no entry stored in dbm for [ENSG00000226240.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000253784.1]
WARNING, no entry stored in dbm for [ENSG00000254222.1]
WARNING, no entry stored in dbm for [ENSG00000280441.3]
WARNING, no entry stored in dbm for [ENSG00000280441.3]
ls: cannot access 'IGV_inputs': No such file or directory