Done.
-parsing GTF file: /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.U5nUa6x7eF/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.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
10:37:52 : INFO : Done.
-parsing GTF file: /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

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[910000]   -done parsing /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          ' ** passed ** ' => 3486,
          'small anchor length' => 40,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 12,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 41,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 24,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 160,
          'seq-similar region overlap' => 167,
          'per_id < 96' => 5195,
          'low complexity anchor region' => 27,
          'excessive soft clipping' => 5997
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[585000]   
[586000]   -fusion SPANNING read extraction for scaff: ACTBP6--ACTB

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[84000]   -fusion SPANNING read extraction for scaff: CCDC6--RET

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[101000]   -fusion SPANNING read extraction for scaff: MTA1--PACS2

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[32000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[34000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[31000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[19000]   -fusion SPANNING read extraction for scaff: TFB2M--CNST

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[22000]   
[23000]   
[24000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 580,
          'seq similar region alignment' => 19605
        };
EM: Starting log likelihood: -2305.900463
EM: Round [1] log likelihood: -2305.890338
EM: Round [2] log likelihood: -2305.880368
EM: Round [3] log likelihood: -2305.870549
EM: Round [4] log likelihood: -2305.860878
EM: Round [5] log likelihood: -2305.851353
EM: Round [6] log likelihood: -2305.841971
EM: Round [7] log likelihood: -2305.832729
EM: Round [8] log likelihood: -2305.823623
EM: Round [9] log likelihood: -2305.814653
EM: Round [10] log likelihood: -2305.805814
EM: Round [11] log likelihood: -2305.797104
EM: Round [12] log likelihood: -2305.788522
EM: Round [13] log likelihood: -2305.780064
EM: Round [14] log likelihood: -2305.771728
EM: Round [15] log likelihood: -2305.763513
EM: Round [16] log likelihood: -2305.755415
EM: Round [17] log likelihood: -2305.747432
EM: Round [18] log likelihood: -2305.739564
EM: Round [19] log likelihood: -2305.731807
EM: Round [20] log likelihood: -2305.724159
EM: Round [21] log likelihood: -2305.716619
EM: Round [22] log likelihood: -2305.709184
EM: Round [23] log likelihood: -2305.701853
EM: Round [24] log likelihood: -2305.694624
EM: Round [25] log likelihood: -2305.687496
EM: Round [26] log likelihood: -2305.680465
EM: Round [27] log likelihood: -2305.673532
EM: Round [28] log likelihood: -2305.666693
EM: Round [29] log likelihood: -2305.659948
EM: Round [30] log likelihood: -2305.653295
EM: Round [31] log likelihood: -2305.646732
EM: Round [32] log likelihood: -2305.640258
EM: Round [33] log likelihood: -2305.633871
EM: Round [34] log likelihood: -2305.627570
EM: Round [35] log likelihood: -2305.621354
EM: Round [36] log likelihood: -2305.615220
EM: Round [37] log likelihood: -2305.609169
EM: Round [38] log likelihood: -2305.603197
EM: Round [39] log likelihood: -2305.597305
EM: Round [40] log likelihood: -2305.591491
EM: Round [41] log likelihood: -2305.585753
EM: Round [42] log likelihood: -2305.580090
EM: Round [43] log likelihood: -2305.574501
EM: Round [44] log likelihood: -2305.568986
EM: Round [45] log likelihood: -2305.563542
EM: Round [46] log likelihood: -2305.558169
EM: Round [47] log likelihood: -2305.552865
EM: Round [48] log likelihood: -2305.547630
EM: Round [49] log likelihood: -2305.542463
EM: Round [50] log likelihood: -2305.537361
EM: Round [51] log likelihood: -2305.532325
EM: Round [52] log likelihood: -2305.527354
EM: Round [53] log likelihood: -2305.522446
EM: Round [54] log likelihood: -2305.517600
EM: Round [55] log likelihood: -2305.512816
EM: Round [56] log likelihood: -2305.508092
EM: Round [57] log likelihood: -2305.503428
EM: Round [58] log likelihood: -2305.498823
EM: Round [59] log likelihood: -2305.494276
EM: Round [60] log likelihood: -2305.489785
EM: Round [61] log likelihood: -2305.485351
EM: Round [62] log likelihood: -2305.480972
EM: Round [63] log likelihood: -2305.476648
EM: Round [64] log likelihood: -2305.472378
EM: Round [65] log likelihood: -2305.468160
EM: Round [66] log likelihood: -2305.463995
EM: Round [67] log likelihood: -2305.459882
EM: Round [68] log likelihood: -2305.455819
EM: Round [69] log likelihood: -2305.451805
EM: Round [70] log likelihood: -2305.447842
EM: Round [71] log likelihood: -2305.443927
EM: Round [72] log likelihood: -2305.440059
EM: Round [73] log likelihood: -2305.436239
EM: Round [74] log likelihood: -2305.432466
EM: Round [75] log likelihood: -2305.428738
EM: Round [76] log likelihood: -2305.425056
EM: Round [77] log likelihood: -2305.421418
EM: Round [78] log likelihood: -2305.417824
EM: Round [79] log likelihood: -2305.414274
EM: Round [80] log likelihood: -2305.410767
EM: Round [81] log likelihood: -2305.407301
EM: Round [82] log likelihood: -2305.403878
EM: Round [83] log likelihood: -2305.400495
EM: Round [84] log likelihood: -2305.397153
EM: Round [85] log likelihood: -2305.393851
EM: Round [86] log likelihood: -2305.390588
EM: Round [87] log likelihood: -2305.387364
EM: Round [88] log likelihood: -2305.384178
EM: Round [89] log likelihood: -2305.381031
EM: Round [90] log likelihood: -2305.377920
EM: Round [91] log likelihood: -2305.374847
EM: Round [92] log likelihood: -2305.371809
EM: Round [93] log likelihood: -2305.368808
EM: Round [94] log likelihood: -2305.365842
EM: Round [95] log likelihood: -2305.362911
EM: Round [96] log likelihood: -2305.360014
EM: Round [97] log likelihood: -2305.357151
EM: Round [98] log likelihood: -2305.354322
EM: Round [99] log likelihood: -2305.351526
EM: Round [100] log likelihood: -2305.348763
EM: Round [101] log likelihood: -2305.346031
EM: Round [102] log likelihood: -2305.343332
EM: Round [103] log likelihood: -2305.340664
EM: Round [104] log likelihood: -2305.338027
EM: Round [105] log likelihood: -2305.335421
EM: Round [106] log likelihood: -2305.332845
EM: Round [107] log likelihood: -2305.330299
EM: Round [108] log likelihood: -2305.327782
EM: Round [109] log likelihood: -2305.325294
EM: Round [110] log likelihood: -2305.322835
EM: Round [111] log likelihood: -2305.320404
EM: Round [112] log likelihood: -2305.318001
EM: Round [113] log likelihood: -2305.315626
EM: Round [114] log likelihood: -2305.313278
EM: Round [115] log likelihood: -2305.310957
EM: Round [116] log likelihood: -2305.308663
EM: Round [117] log likelihood: -2305.306394
EM: Round [118] log likelihood: -2305.304152
EM: Round [119] log likelihood: -2305.301935
EM: Round [120] log likelihood: -2305.299744
EM: Round [121] log likelihood: -2305.297577
EM: Round [122] log likelihood: -2305.295436
EM: Round [123] log likelihood: -2305.293318
EM: Round [124] log likelihood: -2305.291225
EM: Round [125] log likelihood: -2305.289155
EM: Round [126] log likelihood: -2305.287109
EM: Round [127] log likelihood: -2305.285086
EM: Round [128] log likelihood: -2305.283085
EM: Round [129] log likelihood: -2305.281108
EM: Round [130] log likelihood: -2305.279152
EM: Round [131] log likelihood: -2305.277219
EM: Round [132] log likelihood: -2305.275307
EM: Round [133] log likelihood: -2305.273417
EM: Round [134] log likelihood: -2305.271548
EM: Round [135] log likelihood: -2305.269701
EM: Round [136] log likelihood: -2305.267874
EM: Round [137] log likelihood: -2305.266067
EM: Round [138] log likelihood: -2305.264281
EM: Round [139] log likelihood: -2305.262514
EM: Round [140] log likelihood: -2305.260768
EM: Round [141] log likelihood: -2305.259040
EM: Round [142] log likelihood: -2305.257333
EM: Round [143] log likelihood: -2305.255644
EM: Round [144] log likelihood: -2305.253974
EM: Round [145] log likelihood: -2305.252322
EM: Round [146] log likelihood: -2305.250689
EM: Round [147] log likelihood: -2305.249074
EM: Round [148] log likelihood: -2305.247477
EM: Round [149] log likelihood: -2305.245898
EM: Round [150] log likelihood: -2305.244336
EM: Round [151] log likelihood: -2305.242792
EM: Round [152] log likelihood: -2305.241264
EM: Round [153] log likelihood: -2305.239754
EM: Round [154] log likelihood: -2305.238260
EM: Round [155] log likelihood: -2305.236783
EM: Round [156] log likelihood: -2305.235322
EM: Round [157] log likelihood: -2305.233877
EM: Round [158] log likelihood: -2305.232448
EM: Round [159] log likelihood: -2305.231035
EM: Round [160] log likelihood: -2305.229637
EM: Round [161] log likelihood: -2305.228255
EM: Round [162] log likelihood: -2305.226888
EM: Round [163] log likelihood: -2305.225536
EM: Round [164] log likelihood: -2305.224199
EM: Round [165] log likelihood: -2305.222876
EM: Round [166] log likelihood: -2305.221568
EM: Round [167] log likelihood: -2305.220274
EM: Round [168] log likelihood: -2305.218995
EM: Round [169] log likelihood: -2305.217729
EM: Round [170] log likelihood: -2305.216477
EM: Round [171] log likelihood: -2305.215239
EM: Round [172] log likelihood: -2305.214015
EM: Round [173] log likelihood: -2305.212803
EM: Round [174] log likelihood: -2305.211605
EM: Round [175] log likelihood: -2305.210420
EM: Round [176] log likelihood: -2305.209248
EM: Round [177] log likelihood: -2305.208089
EM: Round [178] log likelihood: -2305.206942
EM: Round [179] log likelihood: -2305.205808
EM: Round [180] log likelihood: -2305.204686
EM: Round [181] log likelihood: -2305.203577
EM: Round [182] log likelihood: -2305.202479
EM: Round [183] log likelihood: -2305.201393
EM: Round [184] log likelihood: -2305.200319
EM: Round [185] log likelihood: -2305.199257
EM: Round [186] log likelihood: -2305.198206
EM: Round [187] log likelihood: -2305.197167
EM: Round [188] log likelihood: -2305.196139
EM: Round [189] log likelihood: -2305.195122
EM: Round [190] log likelihood: -2305.194116
EM: Round [191] log likelihood: -2305.193120
EM: Round [192] log likelihood: -2305.192136
EM: Round [193] log likelihood: -2305.191162
EM: Round [194] log likelihood: -2305.190199
EM: Round [195] log likelihood: -2305.189246
EM: Round [196] log likelihood: -2305.188303
EM: Round [197] log likelihood: -2305.187371
EM: Round [198] log likelihood: -2305.186448
EM: Round [199] log likelihood: -2305.185536
EM: Round [200] log likelihood: -2305.184633
EM: Round [201] log likelihood: -2305.183740
EM: Round [202] log likelihood: -2305.182857
EM: Round [203] log likelihood: -2305.181983
EM: Round [204] log likelihood: -2305.181118
EM: Round [205] log likelihood: -2305.180263
EM: Round [206] log likelihood: -2305.179417
EM: Round [207] log likelihood: -2305.178580
EM: Round [208] log likelihood: -2305.177752
EM: Round [209] log likelihood: -2305.176933
EM: Round [210] log likelihood: -2305.176122
EM: Round [211] log likelihood: -2305.175320
EM: Round [212] log likelihood: -2305.174527
EM: Round [213] log likelihood: -2305.173743
EM: Round [214] log likelihood: -2305.172966
EM: Round [215] log likelihood: -2305.172199
EM: Round [216] log likelihood: -2305.171439
EM: Round [217] log likelihood: -2305.170687
EM: Round [218] log likelihood: -2305.169944
EM: Round [219] log likelihood: -2305.169208
EM: Round [220] log likelihood: -2305.168480
EM: Round [221] log likelihood: -2305.167760
EM: Round [222] log likelihood: -2305.167048
EM: Round [223] log likelihood: -2305.166343
EM: Round [224] log likelihood: -2305.165646
EM: Round [225] log likelihood: -2305.164956
EM: Round [226] log likelihood: -2305.164273
EM: Round [227] log likelihood: -2305.163598
EM: Round [228] log likelihood: -2305.162930
EM: Round [229] log likelihood: -2305.162269
EM: Round [230] log likelihood: -2305.161615
EM: Round [231] log likelihood: -2305.160968
EM: Round [232] log likelihood: -2305.160328
EM: Round [233] log likelihood: -2305.159695
EM: Round [234] log likelihood: -2305.159068
EM: Round [235] log likelihood: -2305.158448
EM: Round [236] log likelihood: -2305.157835
EM: Round [237] log likelihood: -2305.157228
EM: Round [238] log likelihood: -2305.156628
EM: Round [239] log likelihood: -2305.156034
EM: Round [240] log likelihood: -2305.155446
EM: Round [241] log likelihood: -2305.154865
EM: Round [242] log likelihood: -2305.154289
EM: Round [243] log likelihood: -2305.153720
EM: Round [244] log likelihood: -2305.153157
EM: Round [245] log likelihood: -2305.152600
EM: Round [246] log likelihood: -2305.152049
EM: Round [247] log likelihood: -2305.151503
EM: Round [248] log likelihood: -2305.150963
EM: Round [249] log likelihood: -2305.150429
EM: Round [250] log likelihood: -2305.149901
EM: Round [251] log likelihood: -2305.149378
EM: Round [252] log likelihood: -2305.148861
EM: Round [253] log likelihood: -2305.148349
EM: Round [254] log likelihood: -2305.147843
EM: Round [255] log likelihood: -2305.147342
EM: Round [256] log likelihood: -2305.146846
EM: Round [257] log likelihood: -2305.146355
EM: Round [258] log likelihood: -2305.145870
EM: Round [259] log likelihood: -2305.145390
EM: Round [260] log likelihood: -2305.144914
EM: Round [261] log likelihood: -2305.144444
EM: Round [262] log likelihood: -2305.143979
EM: Round [263] log likelihood: -2305.143519
EM: Round [264] log likelihood: -2305.143063
EM: Round [265] log likelihood: -2305.142613
EM: Round [266] log likelihood: -2305.142167
EM: Round [267] log likelihood: -2305.141726
EM: Round [268] log likelihood: -2305.141289
EM: Round [269] log likelihood: -2305.140857
EM: Round [270] log likelihood: -2305.140430
EM: Round [271] log likelihood: -2305.140007
EM: Round [272] log likelihood: -2305.139588
EM: Round [273] log likelihood: -2305.139174
EM: Round [274] log likelihood: -2305.138764
EM: Round [275] log likelihood: -2305.138359
EM: Round [276] log likelihood: -2305.137958
EM: Round [277] log likelihood: -2305.137561
EM: Round [278] log likelihood: -2305.137168
EM: Round [279] log likelihood: -2305.136779
EM: Round [280] log likelihood: -2305.136395
EM: Round [281] log likelihood: -2305.136014
EM: Round [282] log likelihood: -2305.135638
EM: Round [283] log likelihood: -2305.135265
EM: Round [284] log likelihood: -2305.134896
EM: Round [285] log likelihood: -2305.134532
EM: Round [286] log likelihood: -2305.134171
EM: Round [287] log likelihood: -2305.133813
EM: Round [288] log likelihood: -2305.133460
EM: Round [289] log likelihood: -2305.133110
EM: Round [290] log likelihood: -2305.132764
EM: Round [291] log likelihood: -2305.132422
EM: Round [292] log likelihood: -2305.132083
EM: Round [293] log likelihood: -2305.131747
EM: Round [294] log likelihood: -2305.131416
EM: Round [295] log likelihood: -2305.131087
EM: Round [296] log likelihood: -2305.130762
EM: Round [297] log likelihood: -2305.130441
EM: Round [298] log likelihood: -2305.130123
EM: Round [299] log likelihood: -2305.129808
EM: Round [300] log likelihood: -2305.129497
EM: Round [301] log likelihood: -2305.129188
EM: Round [302] log likelihood: -2305.128883
EM: Round [303] log likelihood: -2305.128581
EM: Round [304] log likelihood: -2305.128283
EM: Round [305] log likelihood: -2305.127987
EM: Round [306] log likelihood: -2305.127695
EM: Round [307] log likelihood: -2305.127405
EM: Round [308] log likelihood: -2305.127119
EM: Round [309] log likelihood: -2305.126836
EM: Round [310] log likelihood: -2305.126555
EM: Round [311] log likelihood: -2305.126278
EM: Round [312] log likelihood: -2305.126003
EM: Round [313] log likelihood: -2305.125731
EM: Round [314] log likelihood: -2305.125462
EM: Round [315] log likelihood: -2305.125196
EM: Round [316] log likelihood: -2305.124933
EM: Round [317] log likelihood: -2305.124672
EM: Round [318] log likelihood: -2305.124415
EM: Round [319] log likelihood: -2305.124159
EM: Round [320] log likelihood: -2305.123907
EM: Round [321] log likelihood: -2305.123657
EM: Round [322] log likelihood: -2305.123410
EM: Round [323] log likelihood: -2305.123165
EM: Round [324] log likelihood: -2305.122923
EM: Round [325] log likelihood: -2305.122684
EM: Round [326] log likelihood: -2305.122446
EM: Round [327] log likelihood: -2305.122212
EM: Round [328] log likelihood: -2305.121980
EM: Round [329] log likelihood: -2305.121750
EM: Round [330] log likelihood: -2305.121523
EM: Round [331] log likelihood: -2305.121298
EM: Round [332] log likelihood: -2305.121075
EM: Round [333] log likelihood: -2305.120855
EM: Round [334] log likelihood: -2305.120637
EM: Round [335] log likelihood: -2305.120421
EM: Round [336] log likelihood: -2305.120207
EM: Round [337] log likelihood: -2305.119996
EM: Round [338] log likelihood: -2305.119787
EM: Round [339] log likelihood: -2305.119580
EM: Round [340] log likelihood: -2305.119375
EM: Round [341] log likelihood: -2305.119173
EM: Round [342] log likelihood: -2305.118972
EM: Round [343] log likelihood: -2305.118774
EM: Round [344] log likelihood: -2305.118577
EM: Round [345] log likelihood: -2305.118383
EM: Round [346] log likelihood: -2305.118191
EM: Round [347] log likelihood: -2305.118000
EM: Round [348] log likelihood: -2305.117812
EM: Round [349] log likelihood: -2305.117626
EM: Round [350] log likelihood: -2305.117441
EM: Round [351] log likelihood: -2305.117259
EM: Round [352] log likelihood: -2305.117078
EM: Round [353] log likelihood: -2305.116899
EM: Round [354] log likelihood: -2305.116723
EM: Round [355] log likelihood: -2305.116548
EM: Round [356] log likelihood: -2305.116374
EM: Round [357] log likelihood: -2305.116203
EM: Round [358] log likelihood: -2305.116033
EM: Round [359] log likelihood: -2305.115865
EM: Round [360] log likelihood: -2305.115699
EM: Round [361] log likelihood: -2305.115535
EM: Round [362] log likelihood: -2305.115372
EM: Round [363] log likelihood: -2305.115211
EM: Round [364] log likelihood: -2305.115052
EM: Round [365] log likelihood: -2305.114894
EM: Round [366] log likelihood: -2305.114738
EM: Round [367] log likelihood: -2305.114584
EM: Round [368] log likelihood: -2305.114431
EM: Round [369] log likelihood: -2305.114280
EM: Round [370] log likelihood: -2305.114130
EM: Round [371] log likelihood: -2305.113982
EM: Round [372] log likelihood: -2305.113836
EM: Round [373] log likelihood: -2305.113690
EM: Round [374] log likelihood: -2305.113547
EM: Round [375] log likelihood: -2305.113405
EM: Round [376] log likelihood: -2305.113264
EM: Round [377] log likelihood: -2305.113125
EM: Round [378] log likelihood: -2305.112988
EM: Round [379] log likelihood: -2305.112851
EM: Round [380] log likelihood: -2305.112716
EM: Round [381] log likelihood: -2305.112583
EM: Round [382] log likelihood: -2305.112451
EM: Round [383] log likelihood: -2305.112320
EM: Round [384] log likelihood: -2305.112191
EM: Round [385] log likelihood: -2305.112063
EM: Round [386] log likelihood: -2305.111936
EM: Round [387] log likelihood: -2305.111811
EM: Round [388] log likelihood: -2305.111687
EM: Round [389] log likelihood: -2305.111564
EM: Round [390] log likelihood: -2305.111443
EM: Round [391] log likelihood: -2305.111323
EM: Round [392] log likelihood: -2305.111204
EM: Round [393] log likelihood: -2305.111086
EM: Round [394] log likelihood: -2305.110969
EM: Round [395] log likelihood: -2305.110854
EM: Round [396] log likelihood: -2305.110740
EM: Round [397] log likelihood: -2305.110627
EM: Round [398] log likelihood: -2305.110515
EM: Round [399] log likelihood: -2305.110405
EM: Round [400] log likelihood: -2305.110295
EM: Round [401] log likelihood: -2305.110187
EM: Round [402] log likelihood: -2305.110080
EM: Round [403] log likelihood: -2305.109974
EM: Round [404] log likelihood: -2305.109869
EM: Round [405] log likelihood: -2305.109765
EM: Round [406] log likelihood: -2305.109662
EM: Round [407] log likelihood: -2305.109560
EM: Round [408] log likelihood: -2305.109460
EM: Round [409] log likelihood: -2305.109360
EM: Stopping iterations at round 409 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_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.U5nUa6x7eF/fi_workdir/659_Lx-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1682.840867
EM: Round [1] log likelihood: -1682.840867
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 248185552
Warning - not locating file: /tmp/nxf.U5nUa6x7eF/659_Lx-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000203413.3]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
ls: cannot access 'IGV_inputs': No such file or directory