Done.
-parsing GTF file: /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.YfmKDMcENe/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.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00624_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00624_B23MVV7LT4_1.star.sortedByCoord.out.bam
10:41:33 : INFO : Done.
-parsing GTF file: /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[1290000]   -done parsing /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'seq-similar region overlap' => 409,
          'low complexity anchor region' => 6,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 28,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 13,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 103,
          'small anchor length' => 57,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 20,
          ' ** passed ** ' => 6476,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 177,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 198,
          'excessive soft clipping' => 6689,
          'exons hit < 2' => 3,
          'per_id < 96' => 4052
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[75000]   -fusion SPANNING read extraction for scaff: AC004980.3--UPK3BL1

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[419000]   -fusion SPANNING read extraction for scaff: ACTBP6--ACTB

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[8000]   -fusion SPANNING read extraction for scaff: C1QTNF3--AMACR

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[3000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

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[15000]   -fusion SPANNING read extraction for scaff: LPGAT1--CBX1P3

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[15000]   -fusion SPANNING read extraction for scaff: LPGAT1--AC096645.1

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[91000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

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[75000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[94000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

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[84000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

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[68000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

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[88000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

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[165000]   -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408

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[44000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[10000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[16000]   -fusion SPANNING read extraction for scaff: UFL1--AL355143.1

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[16000]   -fusion SPANNING read extraction for scaff: UFL1--EEF1GP6
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 81467,
          'lacks exon overlap' => 3141
        };
EM: Starting log likelihood: -3850.694002
EM: Round [1] log likelihood: -3848.044229
EM: Round [2] log likelihood: -3846.017350
EM: Round [3] log likelihood: -3844.305709
EM: Round [4] log likelihood: -3842.848975
EM: Round [5] log likelihood: -3841.602975
EM: Round [6] log likelihood: -3840.532780
EM: Round [7] log likelihood: -3839.610348
EM: Round [8] log likelihood: -3838.812897
EM: Round [9] log likelihood: -3838.121721
EM: Round [10] log likelihood: -3837.521334
EM: Round [11] log likelihood: -3836.998809
EM: Round [12] log likelihood: -3836.543291
EM: Round [13] log likelihood: -3836.145606
EM: Round [14] log likelihood: -3835.797964
EM: Round [15] log likelihood: -3835.493721
EM: Round [16] log likelihood: -3835.227187
EM: Round [17] log likelihood: -3834.993476
EM: Round [18] log likelihood: -3834.788373
EM: Round [19] log likelihood: -3834.608240
EM: Round [20] log likelihood: -3834.449925
EM: Round [21] log likelihood: -3834.310691
EM: Round [22] log likelihood: -3834.188162
EM: Round [23] log likelihood: -3834.080266
EM: Round [24] log likelihood: -3833.985199
EM: Round [25] log likelihood: -3833.901384
EM: Round [26] log likelihood: -3833.827444
EM: Round [27] log likelihood: -3833.762173
EM: Round [28] log likelihood: -3833.704519
EM: Round [29] log likelihood: -3833.653555
EM: Round [30] log likelihood: -3833.608473
EM: Round [31] log likelihood: -3833.568562
EM: Round [32] log likelihood: -3833.533197
EM: Round [33] log likelihood: -3833.501833
EM: Round [34] log likelihood: -3833.473987
EM: Round [35] log likelihood: -3833.449238
EM: Round [36] log likelihood: -3833.427214
EM: Round [37] log likelihood: -3833.407589
EM: Round [38] log likelihood: -3833.390076
EM: Round [39] log likelihood: -3833.374422
EM: Round [40] log likelihood: -3833.360406
EM: Round [41] log likelihood: -3833.347833
EM: Round [42] log likelihood: -3833.336530
EM: Round [43] log likelihood: -3833.326346
EM: Round [44] log likelihood: -3833.317149
EM: Round [45] log likelihood: -3833.308821
EM: Round [46] log likelihood: -3833.301259
EM: Round [47] log likelihood: -3833.294373
EM: Round [48] log likelihood: -3833.288083
EM: Round [49] log likelihood: -3833.282318
EM: Round [50] log likelihood: -3833.277017
EM: Round [51] log likelihood: -3833.272124
EM: Round [52] log likelihood: -3833.267593
EM: Round [53] log likelihood: -3833.263381
EM: Round [54] log likelihood: -3833.259451
EM: Round [55] log likelihood: -3833.255769
EM: Round [56] log likelihood: -3833.252308
EM: Round [57] log likelihood: -3833.249041
EM: Round [58] log likelihood: -3833.245947
EM: Round [59] log likelihood: -3833.243005
EM: Round [60] log likelihood: -3833.240199
EM: Round [61] log likelihood: -3833.237513
EM: Round [62] log likelihood: -3833.234933
EM: Round [63] log likelihood: -3833.232448
EM: Round [64] log likelihood: -3833.230048
EM: Round [65] log likelihood: -3833.227723
EM: Round [66] log likelihood: -3833.225464
EM: Round [67] log likelihood: -3833.223266
EM: Round [68] log likelihood: -3833.221121
EM: Round [69] log likelihood: -3833.219024
EM: Round [70] log likelihood: -3833.216971
EM: Round [71] log likelihood: -3833.214956
EM: Round [72] log likelihood: -3833.212977
EM: Round [73] log likelihood: -3833.211029
EM: Round [74] log likelihood: -3833.209110
EM: Round [75] log likelihood: -3833.207217
EM: Round [76] log likelihood: -3833.205348
EM: Round [77] log likelihood: -3833.203501
EM: Round [78] log likelihood: -3833.201674
EM: Round [79] log likelihood: -3833.199865
EM: Round [80] log likelihood: -3833.198074
EM: Round [81] log likelihood: -3833.196298
EM: Round [82] log likelihood: -3833.194537
EM: Round [83] log likelihood: -3833.192790
EM: Round [84] log likelihood: -3833.191056
EM: Round [85] log likelihood: -3833.189335
EM: Round [86] log likelihood: -3833.187624
EM: Round [87] log likelihood: -3833.185925
EM: Round [88] log likelihood: -3833.184236
EM: Round [89] log likelihood: -3833.182557
EM: Round [90] log likelihood: -3833.180888
EM: Round [91] log likelihood: -3833.179228
EM: Round [92] log likelihood: -3833.177576
EM: Round [93] log likelihood: -3833.175933
EM: Round [94] log likelihood: -3833.174299
EM: Round [95] log likelihood: -3833.172672
EM: Round [96] log likelihood: -3833.171053
EM: Round [97] log likelihood: -3833.169442
EM: Round [98] log likelihood: -3833.167838
EM: Round [99] log likelihood: -3833.166242
EM: Round [100] log likelihood: -3833.164653
EM: Round [101] log likelihood: -3833.163071
EM: Round [102] log likelihood: -3833.161495
EM: Round [103] log likelihood: -3833.159927
EM: Round [104] log likelihood: -3833.158365
EM: Round [105] log likelihood: -3833.156810
EM: Round [106] log likelihood: -3833.155261
EM: Round [107] log likelihood: -3833.153719
EM: Round [108] log likelihood: -3833.152183
EM: Round [109] log likelihood: -3833.150654
EM: Round [110] log likelihood: -3833.149130
EM: Round [111] log likelihood: -3833.147613
EM: Round [112] log likelihood: -3833.146103
EM: Round [113] log likelihood: -3833.144598
EM: Round [114] log likelihood: -3833.143099
EM: Round [115] log likelihood: -3833.141606
EM: Round [116] log likelihood: -3833.140119
EM: Round [117] log likelihood: -3833.138638
EM: Round [118] log likelihood: -3833.137163
EM: Round [119] log likelihood: -3833.135694
EM: Round [120] log likelihood: -3833.134231
EM: Round [121] log likelihood: -3833.132773
EM: Round [122] log likelihood: -3833.131321
EM: Round [123] log likelihood: -3833.129875
EM: Round [124] log likelihood: -3833.128434
EM: Round [125] log likelihood: -3833.126999
EM: Round [126] log likelihood: -3833.125569
EM: Round [127] log likelihood: -3833.124145
EM: Round [128] log likelihood: -3833.122727
EM: Round [129] log likelihood: -3833.121314
EM: Round [130] log likelihood: -3833.119906
EM: Round [131] log likelihood: -3833.118504
EM: Round [132] log likelihood: -3833.117107
EM: Round [133] log likelihood: -3833.115716
EM: Round [134] log likelihood: -3833.114329
EM: Round [135] log likelihood: -3833.112949
EM: Round [136] log likelihood: -3833.111573
EM: Round [137] log likelihood: -3833.110203
EM: Round [138] log likelihood: -3833.108837
EM: Round [139] log likelihood: -3833.107477
EM: Round [140] log likelihood: -3833.106123
EM: Round [141] log likelihood: -3833.104773
EM: Round [142] log likelihood: -3833.103428
EM: Round [143] log likelihood: -3833.102089
EM: Round [144] log likelihood: -3833.100754
EM: Round [145] log likelihood: -3833.099425
EM: Round [146] log likelihood: -3833.098101
EM: Round [147] log likelihood: -3833.096781
EM: Round [148] log likelihood: -3833.095467
EM: Round [149] log likelihood: -3833.094157
EM: Round [150] log likelihood: -3833.092852
EM: Round [151] log likelihood: -3833.091552
EM: Round [152] log likelihood: -3833.090257
EM: Round [153] log likelihood: -3833.088967
EM: Round [154] log likelihood: -3833.087682
EM: Round [155] log likelihood: -3833.086401
EM: Round [156] log likelihood: -3833.085125
EM: Round [157] log likelihood: -3833.083854
EM: Round [158] log likelihood: -3833.082588
EM: Round [159] log likelihood: -3833.081326
EM: Round [160] log likelihood: -3833.080069
EM: Round [161] log likelihood: -3833.078817
EM: Round [162] log likelihood: -3833.077569
EM: Round [163] log likelihood: -3833.076325
EM: Round [164] log likelihood: -3833.075087
EM: Round [165] log likelihood: -3833.073853
EM: Round [166] log likelihood: -3833.072623
EM: Round [167] log likelihood: -3833.071398
EM: Round [168] log likelihood: -3833.070177
EM: Round [169] log likelihood: -3833.068961
EM: Round [170] log likelihood: -3833.067749
EM: Round [171] log likelihood: -3833.066542
EM: Round [172] log likelihood: -3833.065339
EM: Round [173] log likelihood: -3833.064140
EM: Round [174] log likelihood: -3833.062946
EM: Round [175] log likelihood: -3833.061756
EM: Round [176] log likelihood: -3833.060570
EM: Round [177] log likelihood: -3833.059389
EM: Round [178] log likelihood: -3833.058212
EM: Round [179] log likelihood: -3833.057039
EM: Round [180] log likelihood: -3833.055870
EM: Round [181] log likelihood: -3833.054706
EM: Round [182] log likelihood: -3833.053545
EM: Round [183] log likelihood: -3833.052389
EM: Round [184] log likelihood: -3833.051237
EM: Round [185] log likelihood: -3833.050090
EM: Round [186] log likelihood: -3833.048946
EM: Round [187] log likelihood: -3833.047806
EM: Round [188] log likelihood: -3833.046671
EM: Round [189] log likelihood: -3833.045539
EM: Round [190] log likelihood: -3833.044412
EM: Round [191] log likelihood: -3833.043288
EM: Round [192] log likelihood: -3833.042169
EM: Round [193] log likelihood: -3833.041053
EM: Round [194] log likelihood: -3833.039941
EM: Round [195] log likelihood: -3833.038834
EM: Round [196] log likelihood: -3833.037730
EM: Round [197] log likelihood: -3833.036630
EM: Round [198] log likelihood: -3833.035534
EM: Round [199] log likelihood: -3833.034442
EM: Round [200] log likelihood: -3833.033354
EM: Round [201] log likelihood: -3833.032270
EM: Round [202] log likelihood: -3833.031189
EM: Round [203] log likelihood: -3833.030112
EM: Round [204] log likelihood: -3833.029039
EM: Round [205] log likelihood: -3833.027970
EM: Round [206] log likelihood: -3833.026904
EM: Round [207] log likelihood: -3833.025842
EM: Round [208] log likelihood: -3833.024784
EM: Round [209] log likelihood: -3833.023730
EM: Round [210] log likelihood: -3833.022679
EM: Round [211] log likelihood: -3833.021632
EM: Round [212] log likelihood: -3833.020589
EM: Round [213] log likelihood: -3833.019549
EM: Round [214] log likelihood: -3833.018512
EM: Round [215] log likelihood: -3833.017480
EM: Round [216] log likelihood: -3833.016451
EM: Round [217] log likelihood: -3833.015425
EM: Round [218] log likelihood: -3833.014403
EM: Round [219] log likelihood: -3833.013385
EM: Round [220] log likelihood: -3833.012370
EM: Round [221] log likelihood: -3833.011358
EM: Round [222] log likelihood: -3833.010350
EM: Round [223] log likelihood: -3833.009346
EM: Round [224] log likelihood: -3833.008345
EM: Round [225] log likelihood: -3833.007347
EM: Round [226] log likelihood: -3833.006353
EM: Round [227] log likelihood: -3833.005362
EM: Round [228] log likelihood: -3833.004375
EM: Round [229] log likelihood: -3833.003391
EM: Round [230] log likelihood: -3833.002410
EM: Round [231] log likelihood: -3833.001433
EM: Round [232] log likelihood: -3833.000459
EM: Round [233] log likelihood: -3832.999488
EM: Round [234] log likelihood: -3832.998521
EM: Round [235] log likelihood: -3832.997557
EM: Round [236] log likelihood: -3832.996596
EM: Round [237] log likelihood: -3832.995638
EM: Round [238] log likelihood: -3832.994684
EM: Round [239] log likelihood: -3832.993733
EM: Round [240] log likelihood: -3832.992785
EM: Round [241] log likelihood: -3832.991840
EM: Round [242] log likelihood: -3832.990899
EM: Round [243] log likelihood: -3832.989960
EM: Round [244] log likelihood: -3832.989025
EM: Round [245] log likelihood: -3832.988093
EM: Round [246] log likelihood: -3832.987164
EM: Round [247] log likelihood: -3832.986239
EM: Round [248] log likelihood: -3832.985316
EM: Round [249] log likelihood: -3832.984396
EM: Round [250] log likelihood: -3832.983480
EM: Round [251] log likelihood: -3832.982566
EM: Round [252] log likelihood: -3832.981656
EM: Round [253] log likelihood: -3832.980749
EM: Round [254] log likelihood: -3832.979844
EM: Round [255] log likelihood: -3832.978943
EM: Round [256] log likelihood: -3832.978045
EM: Round [257] log likelihood: -3832.977149
EM: Round [258] log likelihood: -3832.976257
EM: Round [259] log likelihood: -3832.975368
EM: Round [260] log likelihood: -3832.974481
EM: Round [261] log likelihood: -3832.973598
EM: Round [262] log likelihood: -3832.972717
EM: Round [263] log likelihood: -3832.971840
EM: Round [264] log likelihood: -3832.970965
EM: Round [265] log likelihood: -3832.970093
EM: Round [266] log likelihood: -3832.969224
EM: Round [267] log likelihood: -3832.968358
EM: Round [268] log likelihood: -3832.967495
EM: Round [269] log likelihood: -3832.966634
EM: Round [270] log likelihood: -3832.965777
EM: Round [271] log likelihood: -3832.964922
EM: Round [272] log likelihood: -3832.964070
EM: Round [273] log likelihood: -3832.963221
EM: Round [274] log likelihood: -3832.962375
EM: Round [275] log likelihood: -3832.961531
EM: Round [276] log likelihood: -3832.960690
EM: Round [277] log likelihood: -3832.959852
EM: Round [278] log likelihood: -3832.959017
EM: Round [279] log likelihood: -3832.958184
EM: Round [280] log likelihood: -3832.957354
EM: Round [281] log likelihood: -3832.956527
EM: Round [282] log likelihood: -3832.955703
EM: Round [283] log likelihood: -3832.954881
EM: Round [284] log likelihood: -3832.954062
EM: Round [285] log likelihood: -3832.953245
EM: Round [286] log likelihood: -3832.952431
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EM: Round [743] log likelihood: -3832.750326
EM: Round [744] log likelihood: -3832.750108
EM: Round [745] log likelihood: -3832.749891
EM: Round [746] log likelihood: -3832.749674
EM: Round [747] log likelihood: -3832.749458
EM: Round [748] log likelihood: -3832.749243
EM: Round [749] log likelihood: -3832.749028
EM: Round [750] log likelihood: -3832.748814
EM: Round [751] log likelihood: -3832.748600
EM: Round [752] log likelihood: -3832.748387
EM: Round [753] log likelihood: -3832.748174
EM: Round [754] log likelihood: -3832.747962
EM: Round [755] log likelihood: -3832.747751
EM: Round [756] log likelihood: -3832.747540
EM: Round [757] log likelihood: -3832.747329
EM: Round [758] log likelihood: -3832.747119
EM: Round [759] log likelihood: -3832.746910
EM: Round [760] log likelihood: -3832.746701
EM: Round [761] log likelihood: -3832.746493
EM: Round [762] log likelihood: -3832.746286
EM: Round [763] log likelihood: -3832.746078
EM: Round [764] log likelihood: -3832.745872
EM: Round [765] log likelihood: -3832.745666
EM: Round [766] log likelihood: -3832.745461
EM: Round [767] log likelihood: -3832.745256
EM: Round [768] log likelihood: -3832.745051
EM: Round [769] log likelihood: -3832.744847
EM: Round [770] log likelihood: -3832.744644
EM: Round [771] log likelihood: -3832.744441
EM: Round [772] log likelihood: -3832.744239
EM: Round [773] log likelihood: -3832.744037
EM: Round [774] log likelihood: -3832.743836
EM: Round [775] log likelihood: -3832.743636
EM: Round [776] log likelihood: -3832.743436
EM: Round [777] log likelihood: -3832.743236
EM: Round [778] log likelihood: -3832.743037
EM: Round [779] log likelihood: -3832.742838
EM: Round [780] log likelihood: -3832.742640
EM: Round [781] log likelihood: -3832.742443
EM: Round [782] log likelihood: -3832.742246
EM: Round [783] log likelihood: -3832.742050
EM: Round [784] log likelihood: -3832.741854
EM: Round [785] log likelihood: -3832.741658
EM: Round [786] log likelihood: -3832.741463
EM: Round [787] log likelihood: -3832.741269
EM: Round [788] log likelihood: -3832.741075
EM: Round [789] log likelihood: -3832.740882
EM: Round [790] log likelihood: -3832.740689
EM: Round [791] log likelihood: -3832.740497
EM: Round [792] log likelihood: -3832.740305
EM: Round [793] log likelihood: -3832.740113
EM: Round [794] log likelihood: -3832.739923
EM: Round [795] log likelihood: -3832.739732
EM: Round [796] log likelihood: -3832.739542
EM: Round [797] log likelihood: -3832.739353
EM: Round [798] log likelihood: -3832.739164
EM: Round [799] log likelihood: -3832.738976
EM: Round [800] log likelihood: -3832.738788
EM: Round [801] log likelihood: -3832.738601
EM: Round [802] log likelihood: -3832.738414
EM: Round [803] log likelihood: -3832.738227
EM: Round [804] log likelihood: -3832.738041
EM: Round [805] log likelihood: -3832.737856
EM: Round [806] log likelihood: -3832.737671
EM: Round [807] log likelihood: -3832.737487
EM: Round [808] log likelihood: -3832.737303
EM: Round [809] log likelihood: -3832.737119
EM: Round [810] log likelihood: -3832.736936
EM: Round [811] log likelihood: -3832.736754
EM: Round [812] log likelihood: -3832.736572
EM: Round [813] log likelihood: -3832.736390
EM: Round [814] log likelihood: -3832.736209
EM: Round [815] log likelihood: -3832.736028
EM: Round [816] log likelihood: -3832.735848
EM: Round [817] log likelihood: -3832.735669
EM: Round [818] log likelihood: -3832.735489
EM: Round [819] log likelihood: -3832.735311
EM: Round [820] log likelihood: -3832.735132
EM: Round [821] log likelihood: -3832.734955
EM: Round [822] log likelihood: -3832.734777
EM: Round [823] log likelihood: -3832.734600
EM: Round [824] log likelihood: -3832.734424
EM: Round [825] log likelihood: -3832.734248
EM: Round [826] log likelihood: -3832.734073
EM: Round [827] log likelihood: -3832.733898
EM: Round [828] log likelihood: -3832.733723
EM: Round [829] log likelihood: -3832.733549
EM: Round [830] log likelihood: -3832.733375
EM: Round [831] log likelihood: -3832.733202
EM: Round [832] log likelihood: -3832.733029
EM: Round [833] log likelihood: -3832.732857
EM: Round [834] log likelihood: -3832.732685
EM: Round [835] log likelihood: -3832.732514
EM: Round [836] log likelihood: -3832.732343
EM: Round [837] log likelihood: -3832.732172
EM: Round [838] log likelihood: -3832.732002
EM: Round [839] log likelihood: -3832.731832
EM: Round [840] log likelihood: -3832.731663
EM: Round [841] log likelihood: -3832.731494
EM: Round [842] log likelihood: -3832.731326
EM: Round [843] log likelihood: -3832.731158
EM: Round [844] log likelihood: -3832.730991
EM: Round [845] log likelihood: -3832.730824
EM: Round [846] log likelihood: -3832.730657
EM: Round [847] log likelihood: -3832.730491
EM: Round [848] log likelihood: -3832.730325
EM: Round [849] log likelihood: -3832.730160
EM: Round [850] log likelihood: -3832.729995
EM: Round [851] log likelihood: -3832.729831
EM: Round [852] log likelihood: -3832.729667
EM: Round [853] log likelihood: -3832.729503
EM: Round [854] log likelihood: -3832.729340
EM: Round [855] log likelihood: -3832.729177
EM: Round [856] log likelihood: -3832.729015
EM: Round [857] log likelihood: -3832.728853
EM: Round [858] log likelihood: -3832.728692
EM: Round [859] log likelihood: -3832.728531
EM: Round [860] log likelihood: -3832.728370
EM: Round [861] log likelihood: -3832.728210
EM: Round [862] log likelihood: -3832.728050
EM: Round [863] log likelihood: -3832.727891
EM: Round [864] log likelihood: -3832.727732
EM: Round [865] log likelihood: -3832.727573
EM: Round [866] log likelihood: -3832.727415
EM: Round [867] log likelihood: -3832.727257
EM: Round [868] log likelihood: -3832.727100
EM: Round [869] log likelihood: -3832.726943
EM: Round [870] log likelihood: -3832.726786
EM: Round [871] log likelihood: -3832.726630
EM: Round [872] log likelihood: -3832.726475
EM: Round [873] log likelihood: -3832.726319
EM: Round [874] log likelihood: -3832.726164
EM: Round [875] log likelihood: -3832.726010
EM: Round [876] log likelihood: -3832.725856
EM: Round [877] log likelihood: -3832.725702
EM: Round [878] log likelihood: -3832.725549
EM: Round [879] log likelihood: -3832.725396
EM: Round [880] log likelihood: -3832.725243
EM: Round [881] log likelihood: -3832.725091
EM: Round [882] log likelihood: -3832.724940
EM: Round [883] log likelihood: -3832.724788
EM: Round [884] log likelihood: -3832.724637
EM: Round [885] log likelihood: -3832.724487
EM: Round [886] log likelihood: -3832.724337
EM: Round [887] log likelihood: -3832.724187
EM: Round [888] log likelihood: -3832.724037
EM: Round [889] log likelihood: -3832.723888
EM: Round [890] log likelihood: -3832.723740
EM: Round [891] log likelihood: -3832.723592
EM: Round [892] log likelihood: -3832.723444
EM: Round [893] log likelihood: -3832.723296
EM: Round [894] log likelihood: -3832.723149
EM: Round [895] log likelihood: -3832.723002
EM: Round [896] log likelihood: -3832.722856
EM: Round [897] log likelihood: -3832.722710
EM: Round [898] log likelihood: -3832.722565
EM: Round [899] log likelihood: -3832.722419
EM: Round [900] log likelihood: -3832.722275
EM: Round [901] log likelihood: -3832.722130
EM: Round [902] log likelihood: -3832.721986
EM: Round [903] log likelihood: -3832.721842
EM: Round [904] log likelihood: -3832.721699
EM: Round [905] log likelihood: -3832.721556
EM: Round [906] log likelihood: -3832.721413
EM: Round [907] log likelihood: -3832.721271
EM: Round [908] log likelihood: -3832.721129
EM: Round [909] log likelihood: -3832.720988
EM: Round [910] log likelihood: -3832.720847
EM: Round [911] log likelihood: -3832.720706
EM: Round [912] log likelihood: -3832.720565
EM: Round [913] log likelihood: -3832.720425
EM: Round [914] log likelihood: -3832.720286
EM: Round [915] log likelihood: -3832.720146
EM: Round [916] log likelihood: -3832.720007
EM: Round [917] log likelihood: -3832.719869
EM: Round [918] log likelihood: -3832.719731
EM: Round [919] log likelihood: -3832.719593
EM: Round [920] log likelihood: -3832.719455
EM: Round [921] log likelihood: -3832.719318
EM: Round [922] log likelihood: -3832.719181
EM: Round [923] log likelihood: -3832.719045
EM: Round [924] log likelihood: -3832.718908
EM: Round [925] log likelihood: -3832.718773
EM: Round [926] log likelihood: -3832.718637
EM: Round [927] log likelihood: -3832.718502
EM: Round [928] log likelihood: -3832.718367
EM: Round [929] log likelihood: -3832.718233
EM: Round [930] log likelihood: -3832.718099
EM: Round [931] log likelihood: -3832.717965
EM: Round [932] log likelihood: -3832.717832
EM: Round [933] log likelihood: -3832.717699
EM: Round [934] log likelihood: -3832.717566
EM: Round [935] log likelihood: -3832.717434
EM: Round [936] log likelihood: -3832.717302
EM: Round [937] log likelihood: -3832.717170
EM: Round [938] log likelihood: -3832.717039
EM: Round [939] log likelihood: -3832.716908
EM: Round [940] log likelihood: -3832.716777
EM: Round [941] log likelihood: -3832.716647
EM: Round [942] log likelihood: -3832.716517
EM: Round [943] log likelihood: -3832.716387
EM: Round [944] log likelihood: -3832.716258
EM: Round [945] log likelihood: -3832.716129
EM: Round [946] log likelihood: -3832.716000
EM: Round [947] log likelihood: -3832.715872
EM: Round [948] log likelihood: -3832.715744
EM: Round [949] log likelihood: -3832.715616
EM: Round [950] log likelihood: -3832.715489
EM: Round [951] log likelihood: -3832.715362
EM: Round [952] log likelihood: -3832.715235
EM: Round [953] log likelihood: -3832.715109
EM: Round [954] log likelihood: -3832.714983
EM: Round [955] log likelihood: -3832.714857
EM: Round [956] log likelihood: -3832.714731
EM: Round [957] log likelihood: -3832.714606
EM: Round [958] log likelihood: -3832.714482
EM: Round [959] log likelihood: -3832.714357
EM: Round [960] log likelihood: -3832.714233
EM: Round [961] log likelihood: -3832.714109
EM: Round [962] log likelihood: -3832.713986
EM: Round [963] log likelihood: -3832.713863
EM: Round [964] log likelihood: -3832.713740
EM: Round [965] log likelihood: -3832.713617
EM: Round [966] log likelihood: -3832.713495
EM: Round [967] log likelihood: -3832.713373
EM: Round [968] log likelihood: -3832.713251
EM: Round [969] log likelihood: -3832.713130
EM: Round [970] log likelihood: -3832.713009
EM: Round [971] log likelihood: -3832.712888
EM: Round [972] log likelihood: -3832.712768
EM: Round [973] log likelihood: -3832.712648
EM: Round [974] log likelihood: -3832.712528
EM: Round [975] log likelihood: -3832.712409
EM: Round [976] log likelihood: -3832.712290
EM: Round [977] log likelihood: -3832.712171
EM: Round [978] log likelihood: -3832.712052
EM: Round [979] log likelihood: -3832.711934
EM: Round [980] log likelihood: -3832.711816
EM: Round [981] log likelihood: -3832.711698
EM: Round [982] log likelihood: -3832.711581
EM: Round [983] log likelihood: -3832.711464
EM: Round [984] log likelihood: -3832.711347
EM: Round [985] log likelihood: -3832.711231
EM: Round [986] log likelihood: -3832.711115
EM: Round [987] log likelihood: -3832.710999
EM: Round [988] log likelihood: -3832.710883
EM: Round [989] log likelihood: -3832.710768
EM: Round [990] log likelihood: -3832.710653
EM: Round [991] log likelihood: -3832.710538
EM: Round [992] log likelihood: -3832.710424
EM: Round [993] log likelihood: -3832.710310
EM: Round [994] log likelihood: -3832.710196
EM: Round [995] log likelihood: -3832.710083
EM: Round [996] log likelihood: -3832.709969
EM: Round [997] log likelihood: -3832.709856
EM: Round [998] log likelihood: -3832.709744
EM: Round [999] log likelihood: -3832.709631
EM: Round [1000] log likelihood: -3832.709519
EM: Round [1001] log likelihood: -3832.709408
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_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.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_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.YfmKDMcENe/fi_workdir/tih_rna_sample_00624_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1331.313153
EM: Round [1] log likelihood: -1331.270596
EM: Round [2] log likelihood: -1331.267795
EM: Round [3] log likelihood: -1331.265396
EM: Round [4] log likelihood: -1331.263012
EM: Round [5] log likelihood: -1331.260640
EM: Round [6] log likelihood: -1331.258280
EM: Round [7] log likelihood: -1331.255930
EM: Round [8] log likelihood: -1331.253592
EM: Round [9] log likelihood: -1331.251265
EM: Round [10] log likelihood: -1331.248949
EM: Round [11] log likelihood: -1331.246644
EM: Round [12] log likelihood: -1331.244350
EM: Round [13] log likelihood: -1331.242066
EM: Round [14] log likelihood: -1331.239794
EM: Round [15] log likelihood: -1331.237532
EM: Round [16] log likelihood: -1331.235280
EM: Round [17] log likelihood: -1331.233039
EM: Round [18] log likelihood: -1331.230809
EM: Round [19] log likelihood: -1331.228589
EM: Round [20] log likelihood: -1331.226379
EM: Round [21] log likelihood: -1331.224180
EM: Round [22] log likelihood: -1331.221990
EM: Round [23] log likelihood: -1331.219811
EM: Round [24] log likelihood: -1331.217642
EM: Round [25] log likelihood: -1331.215482
EM: Round [26] log likelihood: -1331.213333
EM: Round [27] log likelihood: -1331.211194
EM: Round [28] log likelihood: -1331.209064
EM: Round [29] log likelihood: -1331.206944
EM: Round [30] log likelihood: -1331.204833
EM: Round [31] log likelihood: -1331.202732
EM: Round [32] log likelihood: -1331.200641
EM: Round [33] log likelihood: -1331.198559
EM: Round [34] log likelihood: -1331.196486
EM: Round [35] log likelihood: -1331.194423
EM: Round [36] log likelihood: -1331.192369
EM: Round [37] log likelihood: -1331.190324
EM: Round [38] log likelihood: -1331.188288
EM: Round [39] log likelihood: -1331.186262
EM: Round [40] log likelihood: -1331.184244
EM: Round [41] log likelihood: -1331.182235
EM: Round [42] log likelihood: -1331.180235
EM: Round [43] log likelihood: -1331.178245
EM: Round [44] log likelihood: -1331.176262
EM: Round [45] log likelihood: -1331.174289
EM: Round [46] log likelihood: -1331.172324
EM: Round [47] log likelihood: -1331.170368
EM: Round [48] log likelihood: -1331.168420
EM: Round [49] log likelihood: -1331.166481
EM: Round [50] log likelihood: -1331.164551
EM: Round [51] log likelihood: -1331.162629
EM: Round [52] log likelihood: -1331.160715
EM: Round [53] log likelihood: -1331.158809
EM: Round [54] log likelihood: -1331.156912
EM: Round [55] log likelihood: -1331.155023
EM: Round [56] log likelihood: -1331.153142
EM: Round [57] log likelihood: -1331.151269
EM: Round [58] log likelihood: -1331.149404
EM: Round [59] log likelihood: -1331.147547
EM: Round [60] log likelihood: -1331.145699
EM: Round [61] log likelihood: -1331.143858
EM: Round [62] log likelihood: -1331.142024
EM: Round [63] log likelihood: -1331.140199
EM: Round [64] log likelihood: -1331.138382
EM: Round [65] log likelihood: -1331.136572
EM: Round [66] log likelihood: -1331.134770
EM: Round [67] log likelihood: -1331.132975
EM: Round [68] log likelihood: -1331.131188
EM: Round [69] log likelihood: -1331.129408
EM: Round [70] log likelihood: -1331.127636
EM: Round [71] log likelihood: -1331.125872
EM: Round [72] log likelihood: -1331.124115
EM: Round [73] log likelihood: -1331.122365
EM: Round [74] log likelihood: -1331.120622
EM: Round [75] log likelihood: -1331.118887
EM: Round [76] log likelihood: -1331.117159
EM: Round [77] log likelihood: -1331.115438
EM: Round [78] log likelihood: -1331.113724
EM: Round [79] log likelihood: -1331.112018
EM: Round [80] log likelihood: -1331.110318
EM: Round [81] log likelihood: -1331.108625
EM: Round [82] log likelihood: -1331.106940
EM: Round [83] log likelihood: -1331.105261
EM: Round [84] log likelihood: -1331.103589
EM: Round [85] log likelihood: -1331.101924
EM: Round [86] log likelihood: -1331.100266
EM: Round [87] log likelihood: -1331.098615
EM: Round [88] log likelihood: -1331.096970
EM: Round [89] log likelihood: -1331.095332
EM: Round [90] log likelihood: -1331.093701
EM: Round [91] log likelihood: -1331.092076
EM: Round [92] log likelihood: -1331.090458
EM: Round [93] log likelihood: -1331.088846
EM: Round [94] log likelihood: -1331.087241
EM: Round [95] log likelihood: -1331.085643
EM: Round [96] log likelihood: -1331.084051
EM: Round [97] log likelihood: -1331.082465
EM: Round [98] log likelihood: -1331.080885
EM: Round [99] log likelihood: -1331.079312
EM: Round [100] log likelihood: -1331.077745
EM: Round [101] log likelihood: -1331.076185
EM: Round [102] log likelihood: -1331.074631
EM: Round [103] log likelihood: -1331.073082
EM: Round [104] log likelihood: -1331.071540
EM: Round [105] log likelihood: -1331.070005
EM: Round [106] log likelihood: -1331.068475
EM: Round [107] log likelihood: -1331.066951
EM: Round [108] log likelihood: -1331.065433
EM: Round [109] log likelihood: -1331.063922
EM: Round [110] log likelihood: -1331.062416
EM: Round [111] log likelihood: -1331.060916
EM: Round [112] log likelihood: -1331.059422
EM: Round [113] log likelihood: -1331.057934
EM: Round [114] log likelihood: -1331.056451
EM: Round [115] log likelihood: -1331.054975
EM: Round [116] log likelihood: -1331.053504
EM: Round [117] log likelihood: -1331.052039
EM: Round [118] log likelihood: -1331.050580
EM: Round [119] log likelihood: -1331.049126
EM: Round [120] log likelihood: -1331.047678
EM: Round [121] log likelihood: -1331.046236
EM: Round [122] log likelihood: -1331.044799
EM: Round [123] log likelihood: -1331.043368
EM: Round [124] log likelihood: -1331.041942
EM: Round [125] log likelihood: -1331.040522
EM: Round [126] log likelihood: -1331.039107
EM: Round [127] log likelihood: -1331.037698
EM: Round [128] log likelihood: -1331.036294
EM: Round [129] log likelihood: -1331.034895
EM: Round [130] log likelihood: -1331.033502
EM: Round [131] log likelihood: -1331.032114
EM: Round [132] log likelihood: -1331.030731
EM: Round [133] log likelihood: -1331.029354
EM: Round [134] log likelihood: -1331.027982
EM: Round [135] log likelihood: -1331.026615
EM: Round [136] log likelihood: -1331.025253
EM: Round [137] log likelihood: -1331.023897
EM: Round [138] log likelihood: -1331.022545
EM: Round [139] log likelihood: -1331.021199
EM: Round [140] log likelihood: -1331.019858
EM: Round [141] log likelihood: -1331.018521
EM: Round [142] log likelihood: -1331.017190
EM: Round [143] log likelihood: -1331.015864
EM: Round [144] log likelihood: -1331.014543
EM: Round [145] log likelihood: -1331.013227
EM: Round [146] log likelihood: -1331.011915
EM: Round [147] log likelihood: -1331.010609
EM: Round [148] log likelihood: -1331.009307
EM: Round [149] log likelihood: -1331.008011
EM: Round [150] log likelihood: -1331.006719
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-total frags in /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1_1.fastp.fastq.gz: 222722746
Warning - not locating file: /tmp/nxf.YfmKDMcENe/tih_rna_sample_00624_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
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WARNING, no entry stored in dbm for [ENSG00000203413.3]
ls: cannot access 'IGV_inputs': No such file or directory