Done.
-parsing GTF file: /tmp/nxf.FiP3s1aXwE/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.FiP3s1aXwE/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.FiP3s1aXwE/659_bNS-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.FiP3s1aXwE/659_bNS-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.FiP3s1aXwE/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.FiP3s1aXwE/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
11:09:24 : INFO : Done.
-parsing GTF file: /tmp/nxf.FiP3s1aXwE/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.FiP3s1aXwE/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

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[1350000]   -done parsing /tmp/nxf.FiP3s1aXwE/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 9,
          'num genes matched < 2' => 4,
          'per_id < 96' => 4265,
          'low complexity anchor region' => 1,
          'seq-similar region overlap' => 202,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 4,
          'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 36,
          'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 2,
          ' ** passed ** ' => 24921,
          'excessive soft clipping' => 5754,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 2,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 30,
          'small anchor length' => 251
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.FiP3s1aXwE/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[10000]   -fusion SPANNING read extraction for scaff: AC091132.4--AC103810.6

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[25000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[254000]   
[255000]   -fusion SPANNING read extraction for scaff: EML4--ALK

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[15000]   -fusion SPANNING read extraction for scaff: FBXO25--AL669831.1

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[37000]   -fusion SPANNING read extraction for scaff: IGFL1P2--HIF3A

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

[1000]   
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[31000]   
[32000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[25000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

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[30000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[22000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10

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[7000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6

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[6000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4

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[21000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7

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[22000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9

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[65000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3

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[22000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

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[7000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

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[6000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

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[21000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

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[22000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

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[10000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

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[65000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

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[22000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10

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

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6

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

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[21000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7

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[22000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12

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[11000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9

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[64000]   
[65000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3

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[23000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
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[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[23000]   
[24000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
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[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[64000]   
[65000]   
[66000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[33000]   
[34000]   
[35000]   -fusion SPANNING read extraction for scaff: SNTB2--TANGO6

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[30000]   
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[34000]   
[35000]   
[36000]   -fusion SPANNING read extraction for scaff: TMEM120B--ORAI1

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[24000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 8130,
          'seq similar region alignment' => 47107
        };
EM: Starting log likelihood: -6358.314416
EM: Round [1] log likelihood: -6356.348898
EM: Round [2] log likelihood: -6355.206607
EM: Round [3] log likelihood: -6354.401147
EM: Round [4] log likelihood: -6353.807840
EM: Round [5] log likelihood: -6353.349878
EM: Round [6] log likelihood: -6352.979301
EM: Round [7] log likelihood: -6352.665924
EM: Round [8] log likelihood: -6352.390650
EM: Round [9] log likelihood: -6352.141360
EM: Round [10] log likelihood: -6351.910349
EM: Round [11] log likelihood: -6351.692716
EM: Round [12] log likelihood: -6351.485346
EM: Round [13] log likelihood: -6351.286263
EM: Round [14] log likelihood: -6351.094213
EM: Round [15] log likelihood: -6350.908406
EM: Round [16] log likelihood: -6350.728342
EM: Round [17] log likelihood: -6350.553705
EM: Round [18] log likelihood: -6350.384292
EM: Round [19] log likelihood: -6350.219969
EM: Round [20] log likelihood: -6350.060639
EM: Round [21] log likelihood: -6349.906229
EM: Round [22] log likelihood: -6349.756671
EM: Round [23] log likelihood: -6349.611901
EM: Round [24] log likelihood: -6349.471853
EM: Round [25] log likelihood: -6349.336453
EM: Round [26] log likelihood: -6349.205625
EM: Round [27] log likelihood: -6349.079282
EM: Round [28] log likelihood: -6348.957333
EM: Round [29] log likelihood: -6348.839680
EM: Round [30] log likelihood: -6348.726220
EM: Round [31] log likelihood: -6348.616845
EM: Round [32] log likelihood: -6348.511445
EM: Round [33] log likelihood: -6348.409904
EM: Round [34] log likelihood: -6348.312106
EM: Round [35] log likelihood: -6348.217933
EM: Round [36] log likelihood: -6348.127267
EM: Round [37] log likelihood: -6348.039988
EM: Round [38] log likelihood: -6347.955979
EM: Round [39] log likelihood: -6347.875122
EM: Round [40] log likelihood: -6347.797302
EM: Round [41] log likelihood: -6347.722405
EM: Round [42] log likelihood: -6347.650319
EM: Round [43] log likelihood: -6347.580934
EM: Round [44] log likelihood: -6347.514145
EM: Round [45] log likelihood: -6347.449846
EM: Round [46] log likelihood: -6347.387939
EM: Round [47] log likelihood: -6347.328324
EM: Round [48] log likelihood: -6347.270907
EM: Round [49] log likelihood: -6347.215598
EM: Round [50] log likelihood: -6347.162307
EM: Round [51] log likelihood: -6347.110950
EM: Round [52] log likelihood: -6347.061446
EM: Round [53] log likelihood: -6347.013715
EM: Round [54] log likelihood: -6346.967683
EM: Round [55] log likelihood: -6346.923277
EM: Round [56] log likelihood: -6346.880427
EM: Round [57] log likelihood: -6346.839069
EM: Round [58] log likelihood: -6346.799137
EM: Round [59] log likelihood: -6346.760572
EM: Round [60] log likelihood: -6346.723316
EM: Round [61] log likelihood: -6346.687312
EM: Round [62] log likelihood: -6346.652508
EM: Round [63] log likelihood: -6346.618853
EM: Round [64] log likelihood: -6346.586299
EM: Round [65] log likelihood: -6346.554801
EM: Round [66] log likelihood: -6346.524313
EM: Round [67] log likelihood: -6346.494794
EM: Round [68] log likelihood: -6346.466205
EM: Round [69] log likelihood: -6346.438507
EM: Round [70] log likelihood: -6346.411663
EM: Round [71] log likelihood: -6346.385640
EM: Round [72] log likelihood: -6346.360403
EM: Round [73] log likelihood: -6346.335922
EM: Round [74] log likelihood: -6346.312167
EM: Round [75] log likelihood: -6346.289109
EM: Round [76] log likelihood: -6346.266720
EM: Round [77] log likelihood: -6346.244975
EM: Round [78] log likelihood: -6346.223849
EM: Round [79] log likelihood: -6346.203317
EM: Round [80] log likelihood: -6346.183359
EM: Round [81] log likelihood: -6346.163951
EM: Round [82] log likelihood: -6346.145074
EM: Round [83] log likelihood: -6346.126707
EM: Round [84] log likelihood: -6346.108832
EM: Round [85] log likelihood: -6346.091431
EM: Round [86] log likelihood: -6346.074488
EM: Round [87] log likelihood: -6346.057984
EM: Round [88] log likelihood: -6346.041906
EM: Round [89] log likelihood: -6346.026237
EM: Round [90] log likelihood: -6346.010964
EM: Round [91] log likelihood: -6345.996072
EM: Round [92] log likelihood: -6345.981550
EM: Round [93] log likelihood: -6345.967383
EM: Round [94] log likelihood: -6345.953561
EM: Round [95] log likelihood: -6345.940071
EM: Round [96] log likelihood: -6345.926903
EM: Round [97] log likelihood: -6345.914046
EM: Round [98] log likelihood: -6345.901489
EM: Round [99] log likelihood: -6345.889224
EM: Round [100] log likelihood: -6345.877240
EM: Round [101] log likelihood: -6345.865528
EM: Round [102] log likelihood: -6345.854081
EM: Round [103] log likelihood: -6345.842890
EM: Round [104] log likelihood: -6345.831946
EM: Round [105] log likelihood: -6345.821242
EM: Round [106] log likelihood: -6345.810772
EM: Round [107] log likelihood: -6345.800526
EM: Round [108] log likelihood: -6345.790500
EM: Round [109] log likelihood: -6345.780685
EM: Round [110] log likelihood: -6345.771077
EM: Round [111] log likelihood: -6345.761668
EM: Round [112] log likelihood: -6345.752453
EM: Round [113] log likelihood: -6345.743427
EM: Round [114] log likelihood: -6345.734583
EM: Round [115] log likelihood: -6345.725916
EM: Round [116] log likelihood: -6345.717422
EM: Round [117] log likelihood: -6345.709095
EM: Round [118] log likelihood: -6345.700931
EM: Round [119] log likelihood: -6345.692926
EM: Round [120] log likelihood: -6345.685073
EM: Round [121] log likelihood: -6345.677371
EM: Round [122] log likelihood: -6345.669813
EM: Round [123] log likelihood: -6345.662397
EM: Round [124] log likelihood: -6345.655118
EM: Round [125] log likelihood: -6345.647973
EM: Round [126] log likelihood: -6345.640958
EM: Round [127] log likelihood: -6345.634069
EM: Round [128] log likelihood: -6345.627303
EM: Round [129] log likelihood: -6345.620658
EM: Round [130] log likelihood: -6345.614129
EM: Round [131] log likelihood: -6345.607713
EM: Round [132] log likelihood: -6345.601408
EM: Round [133] log likelihood: -6345.595211
EM: Round [134] log likelihood: -6345.589119
EM: Round [135] log likelihood: -6345.583129
EM: Round [136] log likelihood: -6345.577239
EM: Round [137] log likelihood: -6345.571445
EM: Round [138] log likelihood: -6345.565746
EM: Round [139] log likelihood: -6345.560139
EM: Round [140] log likelihood: -6345.554622
EM: Round [141] log likelihood: -6345.549192
EM: Round [142] log likelihood: -6345.543848
EM: Round [143] log likelihood: -6345.538587
EM: Round [144] log likelihood: -6345.533407
EM: Round [145] log likelihood: -6345.528306
EM: Round [146] log likelihood: -6345.523282
EM: Round [147] log likelihood: -6345.518333
EM: Round [148] log likelihood: -6345.513458
EM: Round [149] log likelihood: -6345.508654
EM: Round [150] log likelihood: -6345.503920
EM: Round [151] log likelihood: -6345.499254
EM: Round [152] log likelihood: -6345.494655
EM: Round [153] log likelihood: -6345.490121
EM: Round [154] log likelihood: -6345.485650
EM: Round [155] log likelihood: -6345.481240
EM: Round [156] log likelihood: -6345.476892
EM: Round [157] log likelihood: -6345.472602
EM: Round [158] log likelihood: -6345.468369
EM: Round [159] log likelihood: -6345.464193
EM: Round [160] log likelihood: -6345.460072
EM: Round [161] log likelihood: -6345.456004
EM: Round [162] log likelihood: -6345.451989
EM: Round [163] log likelihood: -6345.448025
EM: Round [164] log likelihood: -6345.444111
EM: Round [165] log likelihood: -6345.440245
EM: Round [166] log likelihood: -6345.436428
EM: Round [167] log likelihood: -6345.432656
EM: Round [168] log likelihood: -6345.428931
EM: Round [169] log likelihood: -6345.425250
EM: Round [170] log likelihood: -6345.421612
EM: Round [171] log likelihood: -6345.418017
EM: Round [172] log likelihood: -6345.414464
EM: Round [173] log likelihood: -6345.410951
EM: Round [174] log likelihood: -6345.407478
EM: Round [175] log likelihood: -6345.404044
EM: Round [176] log likelihood: -6345.400648
EM: Round [177] log likelihood: -6345.397290
EM: Round [178] log likelihood: -6345.393967
EM: Round [179] log likelihood: -6345.390680
EM: Round [180] log likelihood: -6345.387428
EM: Round [181] log likelihood: -6345.384210
EM: Round [182] log likelihood: -6345.381026
EM: Round [183] log likelihood: -6345.377874
EM: Round [184] log likelihood: -6345.374754
EM: Round [185] log likelihood: -6345.371665
EM: Round [186] log likelihood: -6345.368607
EM: Round [187] log likelihood: -6345.365579
EM: Round [188] log likelihood: -6345.362580
EM: Round [189] log likelihood: -6345.359610
EM: Round [190] log likelihood: -6345.356668
EM: Round [191] log likelihood: -6345.353754
EM: Round [192] log likelihood: -6345.350867
EM: Round [193] log likelihood: -6345.348006
EM: Round [194] log likelihood: -6345.345171
EM: Round [195] log likelihood: -6345.342361
EM: Round [196] log likelihood: -6345.339576
EM: Round [197] log likelihood: -6345.336816
EM: Round [198] log likelihood: -6345.334079
EM: Round [199] log likelihood: -6345.331366
EM: Round [200] log likelihood: -6345.328676
EM: Round [201] log likelihood: -6345.326009
EM: Round [202] log likelihood: -6345.323363
EM: Round [203] log likelihood: -6345.320739
EM: Round [204] log likelihood: -6345.318136
EM: Round [205] log likelihood: -6345.315554
EM: Round [206] log likelihood: -6345.312993
EM: Round [207] log likelihood: -6345.310452
EM: Round [208] log likelihood: -6345.307930
EM: Round [209] log likelihood: -6345.305427
EM: Round [210] log likelihood: -6345.302944
EM: Round [211] log likelihood: -6345.300479
EM: Round [212] log likelihood: -6345.298032
EM: Round [213] log likelihood: -6345.295603
EM: Round [214] log likelihood: -6345.293192
EM: Round [215] log likelihood: -6345.290798
EM: Round [216] log likelihood: -6345.288421
EM: Round [217] log likelihood: -6345.286060
EM: Round [218] log likelihood: -6345.283716
EM: Round [219] log likelihood: -6345.281388
EM: Round [220] log likelihood: -6345.279076
EM: Round [221] log likelihood: -6345.276779
EM: Round [222] log likelihood: -6345.274497
EM: Round [223] log likelihood: -6345.272231
EM: Round [224] log likelihood: -6345.269979
EM: Round [225] log likelihood: -6345.267741
EM: Round [226] log likelihood: -6345.265518
EM: Round [227] log likelihood: -6345.263309
EM: Round [228] log likelihood: -6345.261113
EM: Round [229] log likelihood: -6345.258931
EM: Round [230] log likelihood: -6345.256763
EM: Round [231] log likelihood: -6345.254607
EM: Round [232] log likelihood: -6345.252464
EM: Round [233] log likelihood: -6345.250334
EM: Round [234] log likelihood: -6345.248216
EM: Round [235] log likelihood: -6345.246111
EM: Round [236] log likelihood: -6345.244018
EM: Round [237] log likelihood: -6345.241936
EM: Round [238] log likelihood: -6345.239866
EM: Round [239] log likelihood: -6345.237808
EM: Round [240] log likelihood: -6345.235761
EM: Round [241] log likelihood: -6345.233726
EM: Round [242] log likelihood: -6345.231701
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EM: Round [701] log likelihood: -6344.736062
EM: Round [702] log likelihood: -6344.735448
EM: Round [703] log likelihood: -6344.734835
EM: Round [704] log likelihood: -6344.734224
EM: Round [705] log likelihood: -6344.733614
EM: Round [706] log likelihood: -6344.733004
EM: Round [707] log likelihood: -6344.732397
EM: Round [708] log likelihood: -6344.731790
EM: Round [709] log likelihood: -6344.731184
EM: Round [710] log likelihood: -6344.730580
EM: Round [711] log likelihood: -6344.729976
EM: Round [712] log likelihood: -6344.729374
EM: Round [713] log likelihood: -6344.728773
EM: Round [714] log likelihood: -6344.728173
EM: Round [715] log likelihood: -6344.727575
EM: Round [716] log likelihood: -6344.726977
EM: Round [717] log likelihood: -6344.726381
EM: Round [718] log likelihood: -6344.725785
EM: Round [719] log likelihood: -6344.725191
EM: Round [720] log likelihood: -6344.724598
EM: Round [721] log likelihood: -6344.724006
EM: Round [722] log likelihood: -6344.723415
EM: Round [723] log likelihood: -6344.722826
EM: Round [724] log likelihood: -6344.722237
EM: Round [725] log likelihood: -6344.721650
EM: Round [726] log likelihood: -6344.721063
EM: Round [727] log likelihood: -6344.720478
EM: Round [728] log likelihood: -6344.719894
EM: Round [729] log likelihood: -6344.719311
EM: Round [730] log likelihood: -6344.718729
EM: Round [731] log likelihood: -6344.718148
EM: Round [732] log likelihood: -6344.717568
EM: Round [733] log likelihood: -6344.716990
EM: Round [734] log likelihood: -6344.716412
EM: Round [735] log likelihood: -6344.715835
EM: Round [736] log likelihood: -6344.715260
EM: Round [737] log likelihood: -6344.714686
EM: Round [738] log likelihood: -6344.714112
EM: Round [739] log likelihood: -6344.713540
EM: Round [740] log likelihood: -6344.712969
EM: Round [741] log likelihood: -6344.712399
EM: Round [742] log likelihood: -6344.711830
EM: Round [743] log likelihood: -6344.711262
EM: Round [744] log likelihood: -6344.710695
EM: Round [745] log likelihood: -6344.710130
EM: Round [746] log likelihood: -6344.709565
EM: Round [747] log likelihood: -6344.709001
EM: Round [748] log likelihood: -6344.708439
EM: Round [749] log likelihood: -6344.707877
EM: Round [750] log likelihood: -6344.707317
EM: Round [751] log likelihood: -6344.706757
EM: Round [752] log likelihood: -6344.706199
EM: Round [753] log likelihood: -6344.705641
EM: Round [754] log likelihood: -6344.705085
EM: Round [755] log likelihood: -6344.704530
EM: Round [756] log likelihood: -6344.703975
EM: Round [757] log likelihood: -6344.703422
EM: Round [758] log likelihood: -6344.702870
EM: Round [759] log likelihood: -6344.702319
EM: Round [760] log likelihood: -6344.701769
EM: Round [761] log likelihood: -6344.701219
EM: Round [762] log likelihood: -6344.700671
EM: Round [763] log likelihood: -6344.700124
EM: Round [764] log likelihood: -6344.699578
EM: Round [765] log likelihood: -6344.699033
EM: Round [766] log likelihood: -6344.698489
EM: Round [767] log likelihood: -6344.697946
EM: Round [768] log likelihood: -6344.697404
EM: Round [769] log likelihood: -6344.696862
EM: Round [770] log likelihood: -6344.696322
EM: Round [771] log likelihood: -6344.695783
EM: Round [772] log likelihood: -6344.695245
EM: Round [773] log likelihood: -6344.694708
EM: Round [774] log likelihood: -6344.694172
EM: Round [775] log likelihood: -6344.693637
EM: Round [776] log likelihood: -6344.693103
EM: Round [777] log likelihood: -6344.692569
EM: Round [778] log likelihood: -6344.692037
EM: Round [779] log likelihood: -6344.691506
EM: Round [780] log likelihood: -6344.690976
EM: Round [781] log likelihood: -6344.690446
EM: Round [782] log likelihood: -6344.689918
EM: Round [783] log likelihood: -6344.689391
EM: Round [784] log likelihood: -6344.688864
EM: Round [785] log likelihood: -6344.688339
EM: Round [786] log likelihood: -6344.687814
EM: Round [787] log likelihood: -6344.687291
EM: Round [788] log likelihood: -6344.686768
EM: Round [789] log likelihood: -6344.686247
EM: Round [790] log likelihood: -6344.685726
EM: Round [791] log likelihood: -6344.685207
EM: Round [792] log likelihood: -6344.684688
EM: Round [793] log likelihood: -6344.684170
EM: Round [794] log likelihood: -6344.683653
EM: Round [795] log likelihood: -6344.683137
EM: Round [796] log likelihood: -6344.682622
EM: Round [797] log likelihood: -6344.682108
EM: Round [798] log likelihood: -6344.681595
EM: Round [799] log likelihood: -6344.681083
EM: Round [800] log likelihood: -6344.680572
EM: Round [801] log likelihood: -6344.680061
EM: Round [802] log likelihood: -6344.679552
EM: Round [803] log likelihood: -6344.679044
EM: Round [804] log likelihood: -6344.678536
EM: Round [805] log likelihood: -6344.678029
EM: Round [806] log likelihood: -6344.677524
EM: Round [807] log likelihood: -6344.677019
EM: Round [808] log likelihood: -6344.676515
EM: Round [809] log likelihood: -6344.676012
EM: Round [810] log likelihood: -6344.675510
EM: Round [811] log likelihood: -6344.675009
EM: Round [812] log likelihood: -6344.674508
EM: Round [813] log likelihood: -6344.674009
EM: Round [814] log likelihood: -6344.673511
EM: Round [815] log likelihood: -6344.673013
EM: Round [816] log likelihood: -6344.672516
EM: Round [817] log likelihood: -6344.672021
EM: Round [818] log likelihood: -6344.671526
EM: Round [819] log likelihood: -6344.671032
EM: Round [820] log likelihood: -6344.670539
EM: Round [821] log likelihood: -6344.670047
EM: Round [822] log likelihood: -6344.669555
EM: Round [823] log likelihood: -6344.669065
EM: Round [824] log likelihood: -6344.668575
EM: Round [825] log likelihood: -6344.668086
EM: Round [826] log likelihood: -6344.667599
EM: Round [827] log likelihood: -6344.667112
EM: Round [828] log likelihood: -6344.666626
EM: Round [829] log likelihood: -6344.666140
EM: Round [830] log likelihood: -6344.665656
EM: Round [831] log likelihood: -6344.665173
EM: Round [832] log likelihood: -6344.664690
EM: Round [833] log likelihood: -6344.664208
EM: Round [834] log likelihood: -6344.663727
EM: Round [835] log likelihood: -6344.663247
EM: Round [836] log likelihood: -6344.662768
EM: Round [837] log likelihood: -6344.662290
EM: Round [838] log likelihood: -6344.661812
EM: Round [839] log likelihood: -6344.661336
EM: Round [840] log likelihood: -6344.660860
EM: Round [841] log likelihood: -6344.660385
EM: Round [842] log likelihood: -6344.659911
EM: Round [843] log likelihood: -6344.659438
EM: Round [844] log likelihood: -6344.658965
EM: Round [845] log likelihood: -6344.658494
EM: Round [846] log likelihood: -6344.658023
EM: Round [847] log likelihood: -6344.657553
EM: Round [848] log likelihood: -6344.657084
EM: Round [849] log likelihood: -6344.656616
EM: Round [850] log likelihood: -6344.656149
EM: Round [851] log likelihood: -6344.655682
EM: Round [852] log likelihood: -6344.655216
EM: Round [853] log likelihood: -6344.654751
EM: Round [854] log likelihood: -6344.654287
EM: Round [855] log likelihood: -6344.653824
EM: Round [856] log likelihood: -6344.653362
EM: Round [857] log likelihood: -6344.652900
EM: Round [858] log likelihood: -6344.652439
EM: Round [859] log likelihood: -6344.651979
EM: Round [860] log likelihood: -6344.651520
EM: Round [861] log likelihood: -6344.651062
EM: Round [862] log likelihood: -6344.650604
EM: Round [863] log likelihood: -6344.650147
EM: Round [864] log likelihood: -6344.649691
EM: Round [865] log likelihood: -6344.649236
EM: Round [866] log likelihood: -6344.648782
EM: Round [867] log likelihood: -6344.648328
EM: Round [868] log likelihood: -6344.647875
EM: Round [869] log likelihood: -6344.647423
EM: Round [870] log likelihood: -6344.646972
EM: Round [871] log likelihood: -6344.646522
EM: Round [872] log likelihood: -6344.646072
EM: Round [873] log likelihood: -6344.645623
EM: Round [874] log likelihood: -6344.645175
EM: Round [875] log likelihood: -6344.644728
EM: Round [876] log likelihood: -6344.644282
EM: Round [877] log likelihood: -6344.643836
EM: Round [878] log likelihood: -6344.643391
EM: Round [879] log likelihood: -6344.642947
EM: Round [880] log likelihood: -6344.642504
EM: Round [881] log likelihood: -6344.642061
EM: Round [882] log likelihood: -6344.641619
EM: Round [883] log likelihood: -6344.641178
EM: Round [884] log likelihood: -6344.640738
EM: Round [885] log likelihood: -6344.640298
EM: Round [886] log likelihood: -6344.639860
EM: Round [887] log likelihood: -6344.639422
EM: Round [888] log likelihood: -6344.638984
EM: Round [889] log likelihood: -6344.638548
EM: Round [890] log likelihood: -6344.638112
EM: Round [891] log likelihood: -6344.637677
EM: Round [892] log likelihood: -6344.637243
EM: Round [893] log likelihood: -6344.636810
EM: Round [894] log likelihood: -6344.636377
EM: Round [895] log likelihood: -6344.635945
EM: Round [896] log likelihood: -6344.635514
EM: Round [897] log likelihood: -6344.635084
EM: Round [898] log likelihood: -6344.634654
EM: Round [899] log likelihood: -6344.634225
EM: Round [900] log likelihood: -6344.633797
EM: Round [901] log likelihood: -6344.633369
EM: Round [902] log likelihood: -6344.632943
EM: Round [903] log likelihood: -6344.632517
EM: Round [904] log likelihood: -6344.632091
EM: Round [905] log likelihood: -6344.631667
EM: Round [906] log likelihood: -6344.631243
EM: Round [907] log likelihood: -6344.630820
EM: Round [908] log likelihood: -6344.630398
EM: Round [909] log likelihood: -6344.629976
EM: Round [910] log likelihood: -6344.629555
EM: Round [911] log likelihood: -6344.629135
EM: Round [912] log likelihood: -6344.628716
EM: Round [913] log likelihood: -6344.628297
EM: Round [914] log likelihood: -6344.627879
EM: Round [915] log likelihood: -6344.627462
EM: Round [916] log likelihood: -6344.627046
EM: Round [917] log likelihood: -6344.626630
EM: Round [918] log likelihood: -6344.626215
EM: Round [919] log likelihood: -6344.625800
EM: Round [920] log likelihood: -6344.625387
EM: Round [921] log likelihood: -6344.624974
EM: Round [922] log likelihood: -6344.624561
EM: Round [923] log likelihood: -6344.624150
EM: Round [924] log likelihood: -6344.623739
EM: Round [925] log likelihood: -6344.623329
EM: Round [926] log likelihood: -6344.622920
EM: Round [927] log likelihood: -6344.622511
EM: Round [928] log likelihood: -6344.622103
EM: Round [929] log likelihood: -6344.621696
EM: Round [930] log likelihood: -6344.621289
EM: Round [931] log likelihood: -6344.620883
EM: Round [932] log likelihood: -6344.620478
EM: Round [933] log likelihood: -6344.620073
EM: Round [934] log likelihood: -6344.619669
EM: Round [935] log likelihood: -6344.619266
EM: Round [936] log likelihood: -6344.618864
EM: Round [937] log likelihood: -6344.618462
EM: Round [938] log likelihood: -6344.618061
EM: Round [939] log likelihood: -6344.617660
EM: Round [940] log likelihood: -6344.617261
EM: Round [941] log likelihood: -6344.616862
EM: Round [942] log likelihood: -6344.616463
EM: Round [943] log likelihood: -6344.616065
EM: Round [944] log likelihood: -6344.615668
EM: Round [945] log likelihood: -6344.615272
EM: Round [946] log likelihood: -6344.614876
EM: Round [947] log likelihood: -6344.614481
EM: Round [948] log likelihood: -6344.614087
EM: Round [949] log likelihood: -6344.613693
EM: Round [950] log likelihood: -6344.613300
EM: Round [951] log likelihood: -6344.612908
EM: Round [952] log likelihood: -6344.612516
EM: Round [953] log likelihood: -6344.612125
EM: Round [954] log likelihood: -6344.611735
EM: Round [955] log likelihood: -6344.611345
EM: Round [956] log likelihood: -6344.610956
EM: Round [957] log likelihood: -6344.610568
EM: Round [958] log likelihood: -6344.610180
EM: Round [959] log likelihood: -6344.609793
EM: Round [960] log likelihood: -6344.609407
EM: Round [961] log likelihood: -6344.609021
EM: Round [962] log likelihood: -6344.608636
EM: Round [963] log likelihood: -6344.608252
EM: Round [964] log likelihood: -6344.607868
EM: Round [965] log likelihood: -6344.607485
EM: Round [966] log likelihood: -6344.607102
EM: Round [967] log likelihood: -6344.606720
EM: Round [968] log likelihood: -6344.606339
EM: Round [969] log likelihood: -6344.605959
EM: Round [970] log likelihood: -6344.605579
EM: Round [971] log likelihood: -6344.605199
EM: Round [972] log likelihood: -6344.604821
EM: Round [973] log likelihood: -6344.604443
EM: Round [974] log likelihood: -6344.604065
EM: Round [975] log likelihood: -6344.603688
EM: Round [976] log likelihood: -6344.603312
EM: Round [977] log likelihood: -6344.602937
EM: Round [978] log likelihood: -6344.602562
EM: Round [979] log likelihood: -6344.602188
EM: Round [980] log likelihood: -6344.601814
EM: Round [981] log likelihood: -6344.601441
EM: Round [982] log likelihood: -6344.601069
EM: Round [983] log likelihood: -6344.600697
EM: Round [984] log likelihood: -6344.600326
EM: Round [985] log likelihood: -6344.599956
EM: Round [986] log likelihood: -6344.599586
EM: Round [987] log likelihood: -6344.599217
EM: Round [988] log likelihood: -6344.598848
EM: Round [989] log likelihood: -6344.598480
EM: Round [990] log likelihood: -6344.598113
EM: Round [991] log likelihood: -6344.597746
EM: Round [992] log likelihood: -6344.597380
EM: Round [993] log likelihood: -6344.597014
EM: Round [994] log likelihood: -6344.596649
EM: Round [995] log likelihood: -6344.596285
EM: Round [996] log likelihood: -6344.595921
EM: Round [997] log likelihood: -6344.595558
EM: Round [998] log likelihood: -6344.595195
EM: Round [999] log likelihood: -6344.594834
EM: Round [1000] log likelihood: -6344.594472
EM: Round [1001] log likelihood: -6344.594112
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.FiP3s1aXwE/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.FiP3s1aXwE/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.FiP3s1aXwE/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.FiP3s1aXwE/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.FiP3s1aXwE/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.FiP3s1aXwE/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.FiP3s1aXwE/659_bNS-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.FiP3s1aXwE/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_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.FiP3s1aXwE/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_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.FiP3s1aXwE/fi_workdir/659_bNS-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.FiP3s1aXwE/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.FiP3s1aXwE/659_bNS-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -4717.726968
EM: Round [1] log likelihood: -4717.542288
EM: Round [2] log likelihood: -4717.533270
EM: Round [3] log likelihood: -4717.524460
EM: Round [4] log likelihood: -4717.515738
EM: Round [5] log likelihood: -4717.507103
EM: Round [6] log likelihood: -4717.498553
EM: Round [7] log likelihood: -4717.490087
EM: Round [8] log likelihood: -4717.481702
EM: Round [9] log likelihood: -4717.473398
EM: Round [10] log likelihood: -4717.465173
EM: Round [11] log likelihood: -4717.457026
EM: Round [12] log likelihood: -4717.448955
EM: Round [13] log likelihood: -4717.440959
EM: Round [14] log likelihood: -4717.433037
EM: Round [15] log likelihood: -4717.425187
EM: Round [16] log likelihood: -4717.417409
EM: Round [17] log likelihood: -4717.409701
EM: Round [18] log likelihood: -4717.402061
EM: Round [19] log likelihood: -4717.394489
EM: Round [20] log likelihood: -4717.386984
EM: Round [21] log likelihood: -4717.379545
EM: Round [22] log likelihood: -4717.372170
EM: Round [23] log likelihood: -4717.364859
EM: Round [24] log likelihood: -4717.357610
EM: Round [25] log likelihood: -4717.350422
EM: Round [26] log likelihood: -4717.343295
EM: Round [27] log likelihood: -4717.336228
EM: Round [28] log likelihood: -4717.329220
EM: Round [29] log likelihood: -4717.322269
EM: Round [30] log likelihood: -4717.315375
EM: Round [31] log likelihood: -4717.308538
EM: Round [32] log likelihood: -4717.301755
EM: Round [33] log likelihood: -4717.295027
EM: Round [34] log likelihood: -4717.288353
EM: Round [35] log likelihood: -4717.281732
EM: Round [36] log likelihood: -4717.275162
EM: Round [37] log likelihood: -4717.268644
EM: Round [38] log likelihood: -4717.262177
EM: Round [39] log likelihood: -4717.255759
EM: Round [40] log likelihood: -4717.249391
EM: Round [41] log likelihood: -4717.243072
EM: Round [42] log likelihood: -4717.236800
EM: Round [43] log likelihood: -4717.230575
EM: Round [44] log likelihood: -4717.224397
EM: Round [45] log likelihood: -4717.218265
EM: Round [46] log likelihood: -4717.212178
EM: Round [47] log likelihood: -4717.206136
EM: Round [48] log likelihood: -4717.200137
EM: Round [49] log likelihood: -4717.194183
EM: Round [50] log likelihood: -4717.188271
EM: Round [51] log likelihood: -4717.182402
EM: Round [52] log likelihood: -4717.176574
EM: Round [53] log likelihood: -4717.170788
EM: Round [54] log likelihood: -4717.165043
EM: Round [55] log likelihood: -4717.159338
EM: Round [56] log likelihood: -4717.153672
EM: Round [57] log likelihood: -4717.148046
EM: Round [58] log likelihood: -4717.142459
EM: Round [59] log likelihood: -4717.136910
EM: Round [60] log likelihood: -4717.131398
EM: Round [61] log likelihood: -4717.125924
EM: Round [62] log likelihood: -4717.120487
EM: Round [63] log likelihood: -4717.115087
EM: Round [64] log likelihood: -4717.109722
EM: Round [65] log likelihood: -4717.104393
EM: Round [66] log likelihood: -4717.099099
EM: Round [67] log likelihood: -4717.093840
EM: Round [68] log likelihood: -4717.088615
EM: Round [69] log likelihood: -4717.083424
EM: Round [70] log likelihood: -4717.078266
EM: Round [71] log likelihood: -4717.073142
EM: Round [72] log likelihood: -4717.068050
EM: Round [73] log likelihood: -4717.062991
EM: Round [74] log likelihood: -4717.057964
EM: Round [75] log likelihood: -4717.052968
EM: Round [76] log likelihood: -4717.048004
EM: Round [77] log likelihood: -4717.043071
EM: Round [78] log likelihood: -4717.038168
EM: Round [79] log likelihood: -4717.033295
EM: Round [80] log likelihood: -4717.028453
EM: Round [81] log likelihood: -4717.023640
EM: Round [82] log likelihood: -4717.018856
EM: Round [83] log likelihood: -4717.014102
EM: Round [84] log likelihood: -4717.009376
EM: Round [85] log likelihood: -4717.004678
EM: Round [86] log likelihood: -4717.000008
EM: Round [87] log likelihood: -4716.995366
EM: Round [88] log likelihood: -4716.990752
EM: Round [89] log likelihood: -4716.986165
EM: Round [90] log likelihood: -4716.981604
EM: Round [91] log likelihood: -4716.977071
EM: Round [92] log likelihood: -4716.972563
EM: Round [93] log likelihood: -4716.968082
EM: Round [94] log likelihood: -4716.963626
EM: Round [95] log likelihood: -4716.959196
EM: Round [96] log likelihood: -4716.954792
EM: Round [97] log likelihood: -4716.950412
EM: Round [98] log likelihood: -4716.946057
EM: Round [99] log likelihood: -4716.941727
EM: Round [100] log likelihood: -4716.937420
EM: Round [101] log likelihood: -4716.933138
EM: Round [102] log likelihood: -4716.928880
EM: Round [103] log likelihood: -4716.924645
EM: Round [104] log likelihood: -4716.920434
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-total frags in /tmp/nxf.FiP3s1aXwE/659_bNS-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295466443
Warning - not locating file: /tmp/nxf.FiP3s1aXwE/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000228327.3]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
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ls: cannot access 'IGV_inputs': No such file or directory