Done.
-parsing GTF file: /tmp/nxf.fUMZj7ojso/659_bGc-T1-TRNA-1_A23MVY2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.fUMZj7ojso/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.fUMZj7ojso/659_bGc-T1-TRNA-1_A23MVY2LT4_1_1.fastp.fastq.gz /tmp/nxf.fUMZj7ojso/659_bGc-T1-TRNA-1_A23MVY2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.fUMZj7ojso/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.fUMZj7ojso/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bGc-T1-TRNA-1_A23MVY2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bGc-T1-TRNA-1_A23MVY2LT4_1.star.sortedByCoord.out.bam
11:38:42 : INFO : Done.
-parsing GTF file: /tmp/nxf.fUMZj7ojso/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_1.gtf
-parsing /tmp/nxf.fUMZj7ojso/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam
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[1790000] -done parsing /tmp/nxf.fUMZj7ojso/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 718,
' ** passed ** ' => 8925,
'per_id < 96' => 8390,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 110,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
'exons hit < 2' => 4,
'low complexity anchor region' => 2,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 578,
'excessive soft clipping' => 13598,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
'seq-similar region overlap' => 245,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 12,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 652,
'num genes matched < 2' => 55,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 42,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 2,
'small anchor length' => 6
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.fUMZj7ojso/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[54000] -fusion SPANNING read extraction for scaff: ADAMTS12--ADAMTS7P3
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[6000] -fusion SPANNING read extraction for scaff: CLIC2--BX571846.1
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[6000] -fusion SPANNING read extraction for scaff: CLIC2--TMLHE-AS1
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[291000] -fusion SPANNING read extraction for scaff: KIF5B--RET
[1000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
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[801000] -fusion SPANNING read extraction for scaff: NOTCH2--NBPF11
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[44000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[44000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[47000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[37000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1
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[36000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2
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[39000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13
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[8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[1000]
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
[1000]
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[8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[66000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[71000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[4000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[22000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 6927,
'seq similar region alignment' => 46745
};
EM: Starting log likelihood: -4950.484307
EM: Round [1] log likelihood: -4948.595730
EM: Round [2] log likelihood: -4947.149642
EM: Round [3] log likelihood: -4945.982083
EM: Round [4] log likelihood: -4945.006425
EM: Round [5] log likelihood: -4944.171270
EM: Round [6] log likelihood: -4943.443665
EM: Round [7] log likelihood: -4942.801221
EM: Round [8] log likelihood: -4942.228002
EM: Round [9] log likelihood: -4941.712232
EM: Round [10] log likelihood: -4941.244937
EM: Round [11] log likelihood: -4940.819104
EM: Round [12] log likelihood: -4940.429135
EM: Round [13] log likelihood: -4940.070488
EM: Round [14] log likelihood: -4939.739418
EM: Round [15] log likelihood: -4939.432801
EM: Round [16] log likelihood: -4939.148005
EM: Round [17] log likelihood: -4938.882787
EM: Round [18] log likelihood: -4938.635223
EM: Round [19] log likelihood: -4938.403649
EM: Round [20] log likelihood: -4938.186615
EM: Round [21] log likelihood: -4937.982853
EM: Round [22] log likelihood: -4937.791243
EM: Round [23] log likelihood: -4937.610796
EM: Round [24] log likelihood: -4937.440631
EM: Round [25] log likelihood: -4937.279962
EM: Round [26] log likelihood: -4937.128082
EM: Round [27] log likelihood: -4936.984356
EM: Round [28] log likelihood: -4936.848212
EM: Round [29] log likelihood: -4936.719127
EM: Round [30] log likelihood: -4936.596630
EM: Round [31] log likelihood: -4936.480290
EM: Round [32] log likelihood: -4936.369712
EM: Round [33] log likelihood: -4936.264535
EM: Round [34] log likelihood: -4936.164429
EM: Round [35] log likelihood: -4936.069088
EM: Round [36] log likelihood: -4935.978230
EM: Round [37] log likelihood: -4935.891596
EM: Round [38] log likelihood: -4935.808945
EM: Round [39] log likelihood: -4935.730054
EM: Round [40] log likelihood: -4935.654714
EM: Round [41] log likelihood: -4935.582734
EM: Round [42] log likelihood: -4935.513933
EM: Round [43] log likelihood: -4935.448144
EM: Round [44] log likelihood: -4935.385209
EM: Round [45] log likelihood: -4935.324983
EM: Round [46] log likelihood: -4935.267327
EM: Round [47] log likelihood: -4935.212114
EM: Round [48] log likelihood: -4935.159221
EM: Round [49] log likelihood: -4935.108536
EM: Round [50] log likelihood: -4935.059950
EM: Round [51] log likelihood: -4935.013365
EM: Round [52] log likelihood: -4934.968684
EM: Round [53] log likelihood: -4934.925818
EM: Round [54] log likelihood: -4934.884683
EM: Round [55] log likelihood: -4934.845199
EM: Round [56] log likelihood: -4934.807290
EM: Round [57] log likelihood: -4934.770885
EM: Round [58] log likelihood: -4934.735915
EM: Round [59] log likelihood: -4934.702318
EM: Round [60] log likelihood: -4934.670032
EM: Round [61] log likelihood: -4934.639000
EM: Round [62] log likelihood: -4934.609166
EM: Round [63] log likelihood: -4934.580479
EM: Round [64] log likelihood: -4934.552889
EM: Round [65] log likelihood: -4934.526349
EM: Round [66] log likelihood: -4934.500815
EM: Round [67] log likelihood: -4934.476244
EM: Round [68] log likelihood: -4934.452596
EM: Round [69] log likelihood: -4934.429831
EM: Round [70] log likelihood: -4934.407913
EM: Round [71] log likelihood: -4934.386807
EM: Round [72] log likelihood: -4934.366480
EM: Round [73] log likelihood: -4934.346900
EM: Round [74] log likelihood: -4934.328035
EM: Round [75] log likelihood: -4934.309857
EM: Round [76] log likelihood: -4934.292339
EM: Round [77] log likelihood: -4934.275453
EM: Round [78] log likelihood: -4934.259175
EM: Round [79] log likelihood: -4934.243479
EM: Round [80] log likelihood: -4934.228344
EM: Round [81] log likelihood: -4934.213746
EM: Round [82] log likelihood: -4934.199664
EM: Round [83] log likelihood: -4934.186079
EM: Round [84] log likelihood: -4934.172970
EM: Round [85] log likelihood: -4934.160319
EM: Round [86] log likelihood: -4934.148108
EM: Round [87] log likelihood: -4934.136321
EM: Round [88] log likelihood: -4934.124940
EM: Round [89] log likelihood: -4934.113950
EM: Round [90] log likelihood: -4934.103336
EM: Round [91] log likelihood: -4934.093083
EM: Round [92] log likelihood: -4934.083178
EM: Round [93] log likelihood: -4934.073608
EM: Round [94] log likelihood: -4934.064360
EM: Round [95] log likelihood: -4934.055421
EM: Round [96] log likelihood: -4934.046780
EM: Round [97] log likelihood: -4934.038425
EM: Round [98] log likelihood: -4934.030347
EM: Round [99] log likelihood: -4934.022533
EM: Round [100] log likelihood: -4934.014976
EM: Round [101] log likelihood: -4934.007664
EM: Round [102] log likelihood: -4934.000590
EM: Round [103] log likelihood: -4933.993743
EM: Round [104] log likelihood: -4933.987116
EM: Round [105] log likelihood: -4933.980701
EM: Round [106] log likelihood: -4933.974489
EM: Round [107] log likelihood: -4933.968473
EM: Round [108] log likelihood: -4933.962647
EM: Round [109] log likelihood: -4933.957003
EM: Round [110] log likelihood: -4933.951534
EM: Round [111] log likelihood: -4933.946234
EM: Round [112] log likelihood: -4933.941097
EM: Round [113] log likelihood: -4933.936117
EM: Round [114] log likelihood: -4933.931288
EM: Round [115] log likelihood: -4933.926606
EM: Round [116] log likelihood: -4933.922063
EM: Round [117] log likelihood: -4933.917657
EM: Round [118] log likelihood: -4933.913381
EM: Round [119] log likelihood: -4933.909231
EM: Round [120] log likelihood: -4933.905203
EM: Round [121] log likelihood: -4933.901292
EM: Round [122] log likelihood: -4933.897494
EM: Round [123] log likelihood: -4933.893805
EM: Round [124] log likelihood: -4933.890222
EM: Round [125] log likelihood: -4933.886740
EM: Round [126] log likelihood: -4933.883356
EM: Round [127] log likelihood: -4933.880066
EM: Round [128] log likelihood: -4933.876868
EM: Round [129] log likelihood: -4933.873757
EM: Round [130] log likelihood: -4933.870732
EM: Round [131] log likelihood: -4933.867789
EM: Round [132] log likelihood: -4933.864924
EM: Round [133] log likelihood: -4933.862137
EM: Round [134] log likelihood: -4933.859423
EM: Round [135] log likelihood: -4933.856781
EM: Round [136] log likelihood: -4933.854207
EM: Round [137] log likelihood: -4933.851700
EM: Round [138] log likelihood: -4933.849257
EM: Round [139] log likelihood: -4933.846877
EM: Round [140] log likelihood: -4933.844556
EM: Round [141] log likelihood: -4933.842293
EM: Round [142] log likelihood: -4933.840087
EM: Round [143] log likelihood: -4933.837934
EM: Round [144] log likelihood: -4933.835834
EM: Round [145] log likelihood: -4933.833785
EM: Round [146] log likelihood: -4933.831784
EM: Round [147] log likelihood: -4933.829831
EM: Round [148] log likelihood: -4933.827924
EM: Round [149] log likelihood: -4933.826061
EM: Round [150] log likelihood: -4933.824241
EM: Round [151] log likelihood: -4933.822462
EM: Round [152] log likelihood: -4933.820724
EM: Round [153] log likelihood: -4933.819024
EM: Round [154] log likelihood: -4933.817362
EM: Round [155] log likelihood: -4933.815736
EM: Round [156] log likelihood: -4933.814146
EM: Round [157] log likelihood: -4933.812590
EM: Round [158] log likelihood: -4933.811066
EM: Round [159] log likelihood: -4933.809575
EM: Round [160] log likelihood: -4933.808115
EM: Round [161] log likelihood: -4933.806685
EM: Round [162] log likelihood: -4933.805284
EM: Round [163] log likelihood: -4933.803911
EM: Round [164] log likelihood: -4933.802565
EM: Round [165] log likelihood: -4933.801247
EM: Round [166] log likelihood: -4933.799953
EM: Round [167] log likelihood: -4933.798685
EM: Round [168] log likelihood: -4933.797441
EM: Round [169] log likelihood: -4933.796221
EM: Round [170] log likelihood: -4933.795023
EM: Round [171] log likelihood: -4933.793847
EM: Round [172] log likelihood: -4933.792693
EM: Round [173] log likelihood: -4933.791560
EM: Round [174] log likelihood: -4933.790447
EM: Round [175] log likelihood: -4933.789354
EM: Round [176] log likelihood: -4933.788279
EM: Round [177] log likelihood: -4933.787224
EM: Round [178] log likelihood: -4933.786186
EM: Round [179] log likelihood: -4933.785166
EM: Round [180] log likelihood: -4933.784163
EM: Round [181] log likelihood: -4933.783176
EM: Round [182] log likelihood: -4933.782206
EM: Round [183] log likelihood: -4933.781251
EM: Round [184] log likelihood: -4933.780312
EM: Round [185] log likelihood: -4933.779387
EM: Round [186] log likelihood: -4933.778477
EM: Round [187] log likelihood: -4933.777581
EM: Round [188] log likelihood: -4933.776699
EM: Round [189] log likelihood: -4933.775830
EM: Round [190] log likelihood: -4933.774974
EM: Round [191] log likelihood: -4933.774131
EM: Round [192] log likelihood: -4933.773300
EM: Round [193] log likelihood: -4933.772481
EM: Round [194] log likelihood: -4933.771674
EM: Round [195] log likelihood: -4933.770878
EM: Round [196] log likelihood: -4933.770094
EM: Round [197] log likelihood: -4933.769320
EM: Round [198] log likelihood: -4933.768557
EM: Round [199] log likelihood: -4933.767804
EM: Round [200] log likelihood: -4933.767062
EM: Round [201] log likelihood: -4933.766329
EM: Round [202] log likelihood: -4933.765606
EM: Round [203] log likelihood: -4933.764893
EM: Round [204] log likelihood: -4933.764189
EM: Round [205] log likelihood: -4933.763493
EM: Round [206] log likelihood: -4933.762807
EM: Round [207] log likelihood: -4933.762129
EM: Round [208] log likelihood: -4933.761460
EM: Round [209] log likelihood: -4933.760799
EM: Round [210] log likelihood: -4933.760146
EM: Round [211] log likelihood: -4933.759501
EM: Round [212] log likelihood: -4933.758863
EM: Round [213] log likelihood: -4933.758233
EM: Round [214] log likelihood: -4933.757611
EM: Round [215] log likelihood: -4933.756996
EM: Round [216] log likelihood: -4933.756388
EM: Round [217] log likelihood: -4933.755786
EM: Round [218] log likelihood: -4933.755192
EM: Round [219] log likelihood: -4933.754605
EM: Round [220] log likelihood: -4933.754024
EM: Round [221] log likelihood: -4933.753449
EM: Round [222] log likelihood: -4933.752881
EM: Round [223] log likelihood: -4933.752319
EM: Round [224] log likelihood: -4933.751763
EM: Round [225] log likelihood: -4933.751213
EM: Round [226] log likelihood: -4933.750669
EM: Round [227] log likelihood: -4933.750130
EM: Round [228] log likelihood: -4933.749598
EM: Round [229] log likelihood: -4933.749071
EM: Round [230] log likelihood: -4933.748549
EM: Round [231] log likelihood: -4933.748033
EM: Round [232] log likelihood: -4933.747522
EM: Round [233] log likelihood: -4933.747016
EM: Round [234] log likelihood: -4933.746515
EM: Round [235] log likelihood: -4933.746019
EM: Round [236] log likelihood: -4933.745528
EM: Round [237] log likelihood: -4933.745043
EM: Round [238] log likelihood: -4933.744561
EM: Round [239] log likelihood: -4933.744085
EM: Round [240] log likelihood: -4933.743613
EM: Round [241] log likelihood: -4933.743146
EM: Round [242] log likelihood: -4933.742683
EM: Round [243] log likelihood: -4933.742225
EM: Round [244] log likelihood: -4933.741771
EM: Round [245] log likelihood: -4933.741321
EM: Round [246] log likelihood: -4933.740875
EM: Round [247] log likelihood: -4933.740434
EM: Round [248] log likelihood: -4933.739997
EM: Round [249] log likelihood: -4933.739563
EM: Round [250] log likelihood: -4933.739134
EM: Round [251] log likelihood: -4933.738709
EM: Round [252] log likelihood: -4933.738288
EM: Round [253] log likelihood: -4933.737870
EM: Round [254] log likelihood: -4933.737456
EM: Round [255] log likelihood: -4933.737046
EM: Round [256] log likelihood: -4933.736640
EM: Round [257] log likelihood: -4933.736237
EM: Round [258] log likelihood: -4933.735838
EM: Round [259] log likelihood: -4933.735442
EM: Round [260] log likelihood: -4933.735050
EM: Round [261] log likelihood: -4933.734661
EM: Round [262] log likelihood: -4933.734276
EM: Round [263] log likelihood: -4933.733894
EM: Round [264] log likelihood: -4933.733515
EM: Round [265] log likelihood: -4933.733140
EM: Round [266] log likelihood: -4933.732767
EM: Round [267] log likelihood: -4933.732398
EM: Round [268] log likelihood: -4933.732033
EM: Round [269] log likelihood: -4933.731670
EM: Round [270] log likelihood: -4933.731310
EM: Round [271] log likelihood: -4933.730954
EM: Round [272] log likelihood: -4933.730600
EM: Round [273] log likelihood: -4933.730250
EM: Round [274] log likelihood: -4933.729902
EM: Round [275] log likelihood: -4933.729558
EM: Round [276] log likelihood: -4933.729216
EM: Round [277] log likelihood: -4933.728877
EM: Round [278] log likelihood: -4933.728541
EM: Round [279] log likelihood: -4933.728207
EM: Round [280] log likelihood: -4933.727877
EM: Round [281] log likelihood: -4933.727549
EM: Round [282] log likelihood: -4933.727224
EM: Round [283] log likelihood: -4933.726901
EM: Round [284] log likelihood: -4933.726581
EM: Round [285] log likelihood: -4933.726264
EM: Round [286] log likelihood: -4933.725950
EM: Round [287] log likelihood: -4933.725638
EM: Round [288] log likelihood: -4933.725328
EM: Round [289] log likelihood: -4933.725021
EM: Round [290] log likelihood: -4933.724717
EM: Round [291] log likelihood: -4933.724415
EM: Round [292] log likelihood: -4933.724115
EM: Round [293] log likelihood: -4933.723818
EM: Round [294] log likelihood: -4933.723523
EM: Round [295] log likelihood: -4933.723230
EM: Round [296] log likelihood: -4933.722940
EM: Round [297] log likelihood: -4933.722653
EM: Round [298] log likelihood: -4933.722367
EM: Round [299] log likelihood: -4933.722084
EM: Round [300] log likelihood: -4933.721803
EM: Round [301] log likelihood: -4933.721524
EM: Round [302] log likelihood: -4933.721248
EM: Round [303] log likelihood: -4933.720973
EM: Round [304] log likelihood: -4933.720701
EM: Round [305] log likelihood: -4933.720431
EM: Round [306] log likelihood: -4933.720163
EM: Round [307] log likelihood: -4933.719898
EM: Round [308] log likelihood: -4933.719634
EM: Round [309] log likelihood: -4933.719372
EM: Round [310] log likelihood: -4933.719113
EM: Round [311] log likelihood: -4933.718855
EM: Round [312] log likelihood: -4933.718600
EM: Round [313] log likelihood: -4933.718347
EM: Round [314] log likelihood: -4933.718095
EM: Round [315] log likelihood: -4933.717846
EM: Round [316] log likelihood: -4933.717598
EM: Round [317] log likelihood: -4933.717352
EM: Round [318] log likelihood: -4933.717109
EM: Round [319] log likelihood: -4933.716867
EM: Round [320] log likelihood: -4933.716627
EM: Round [321] log likelihood: -4933.716389
EM: Round [322] log likelihood: -4933.716153
EM: Round [323] log likelihood: -4933.715918
EM: Round [324] log likelihood: -4933.715686
EM: Round [325] log likelihood: -4933.715455
EM: Round [326] log likelihood: -4933.715226
EM: Round [327] log likelihood: -4933.714998
EM: Round [328] log likelihood: -4933.714773
EM: Round [329] log likelihood: -4933.714549
EM: Round [330] log likelihood: -4933.714327
EM: Round [331] log likelihood: -4933.714107
EM: Round [332] log likelihood: -4933.713888
EM: Round [333] log likelihood: -4933.713671
EM: Round [334] log likelihood: -4933.713456
EM: Round [335] log likelihood: -4933.713242
EM: Round [336] log likelihood: -4933.713031
EM: Round [337] log likelihood: -4933.712820
EM: Round [338] log likelihood: -4933.712611
EM: Round [339] log likelihood: -4933.712404
EM: Round [340] log likelihood: -4933.712199
EM: Round [341] log likelihood: -4933.711995
EM: Round [342] log likelihood: -4933.711792
EM: Round [343] log likelihood: -4933.711592
EM: Round [344] log likelihood: -4933.711392
EM: Round [345] log likelihood: -4933.711194
EM: Round [346] log likelihood: -4933.710998
EM: Round [347] log likelihood: -4933.710803
EM: Round [348] log likelihood: -4933.710610
EM: Round [349] log likelihood: -4933.710418
EM: Round [350] log likelihood: -4933.710228
EM: Round [351] log likelihood: -4933.710039
EM: Round [352] log likelihood: -4933.709851
EM: Round [353] log likelihood: -4933.709665
EM: Round [354] log likelihood: -4933.709481
EM: Round [355] log likelihood: -4933.709297
EM: Round [356] log likelihood: -4933.709115
EM: Round [357] log likelihood: -4933.708935
EM: Round [358] log likelihood: -4933.708756
EM: Round [359] log likelihood: -4933.708578
EM: Round [360] log likelihood: -4933.708402
EM: Round [361] log likelihood: -4933.708227
EM: Round [362] log likelihood: -4933.708053
EM: Round [363] log likelihood: -4933.707880
EM: Round [364] log likelihood: -4933.707709
EM: Round [365] log likelihood: -4933.707540
EM: Round [366] log likelihood: -4933.707371
EM: Round [367] log likelihood: -4933.707204
EM: Round [368] log likelihood: -4933.707038
EM: Round [369] log likelihood: -4933.706873
EM: Round [370] log likelihood: -4933.706709
EM: Round [371] log likelihood: -4933.706547
EM: Round [372] log likelihood: -4933.706386
EM: Round [373] log likelihood: -4933.706226
EM: Round [374] log likelihood: -4933.706068
EM: Round [375] log likelihood: -4933.705910
EM: Round [376] log likelihood: -4933.705754
EM: Round [377] log likelihood: -4933.705599
EM: Round [378] log likelihood: -4933.705445
EM: Round [379] log likelihood: -4933.705292
EM: Round [380] log likelihood: -4933.705141
EM: Round [381] log likelihood: -4933.704990
EM: Round [382] log likelihood: -4933.704841
EM: Round [383] log likelihood: -4933.704693
EM: Round [384] log likelihood: -4933.704546
EM: Round [385] log likelihood: -4933.704400
EM: Round [386] log likelihood: -4933.704255
EM: Round [387] log likelihood: -4933.704111
EM: Round [388] log likelihood: -4933.703969
EM: Round [389] log likelihood: -4933.703827
EM: Round [390] log likelihood: -4933.703686
EM: Round [391] log likelihood: -4933.703547
EM: Round [392] log likelihood: -4933.703408
EM: Round [393] log likelihood: -4933.703271
EM: Round [394] log likelihood: -4933.703135
EM: Round [395] log likelihood: -4933.702999
EM: Round [396] log likelihood: -4933.702865
EM: Round [397] log likelihood: -4933.702732
EM: Round [398] log likelihood: -4933.702599
EM: Round [399] log likelihood: -4933.702468
EM: Round [400] log likelihood: -4933.702338
EM: Round [401] log likelihood: -4933.702208
EM: Round [402] log likelihood: -4933.702080
EM: Round [403] log likelihood: -4933.701952
EM: Round [404] log likelihood: -4933.701826
EM: Round [405] log likelihood: -4933.701700
EM: Round [406] log likelihood: -4933.701576
EM: Round [407] log likelihood: -4933.701452
EM: Round [408] log likelihood: -4933.701329
EM: Round [409] log likelihood: -4933.701208
EM: Round [410] log likelihood: -4933.701087
EM: Round [411] log likelihood: -4933.700967
EM: Round [412] log likelihood: -4933.700848
EM: Round [413] log likelihood: -4933.700729
EM: Round [414] log likelihood: -4933.700612
EM: Round [415] log likelihood: -4933.700496
EM: Round [416] log likelihood: -4933.700380
EM: Round [417] log likelihood: -4933.700265
EM: Round [418] log likelihood: -4933.700151
EM: Round [419] log likelihood: -4933.700038
EM: Round [420] log likelihood: -4933.699926
EM: Round [421] log likelihood: -4933.699815
EM: Round [422] log likelihood: -4933.699704
EM: Round [423] log likelihood: -4933.699595
EM: Round [424] log likelihood: -4933.699486
EM: Round [425] log likelihood: -4933.699378
EM: Round [426] log likelihood: -4933.699271
EM: Round [427] log likelihood: -4933.699164
EM: Round [428] log likelihood: -4933.699059
EM: Round [429] log likelihood: -4933.698954
EM: Round [430] log likelihood: -4933.698850
EM: Round [431] log likelihood: -4933.698746
EM: Round [432] log likelihood: -4933.698644
EM: Round [433] log likelihood: -4933.698542
EM: Round [434] log likelihood: -4933.698441
EM: Round [435] log likelihood: -4933.698341
EM: Round [436] log likelihood: -4933.698241
EM: Stopping iterations at round 436 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.fUMZj7ojso/659_bGc-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam into /tmp/nxf.fUMZj7ojso/659_bGc-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.fUMZj7ojso/659_bGc-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.fUMZj7ojso/659_bGc-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.read_coords > /tmp/nxf.fUMZj7ojso/659_bGc-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.fUMZj7ojso/659_bGc-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.fUMZj7ojso/659_bGc-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.fUMZj7ojso/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_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.fUMZj7ojso/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_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.fUMZj7ojso/fi_workdir/659_bGc-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.fUMZj7ojso/659_bGc-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.fUMZj7ojso/659_bGc-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3859.767099
EM: Round [1] log likelihood: -3859.767099
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.fUMZj7ojso/659_bGc-T1-TRNA-1_A23MVY2LT4_1_1.fastp.fastq.gz: 295166157
Warning - not locating file: /tmp/nxf.fUMZj7ojso/659_bGc-T1-TRNA-1_A23MVY2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000261143.1]
WARNING, no entry stored in dbm for [ENSG00000225393.1]
WARNING, no entry stored in dbm for [ENSG00000224533.4]
WARNING, no entry stored in dbm for [ENSG00000224533.4]
ls: cannot access 'IGV_inputs': No such file or directory