Done.
-parsing GTF file: /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.vKgislKKwM/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.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-19e09e-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-19e09e-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
10:52:54 : INFO : Done.
-parsing GTF file: /tmp/nxf.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
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[630000] -done parsing /tmp/nxf.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'seq-similar region overlap' => 699,
'per_id < 96' => 2777,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 90,
'exons hit < 2' => 2,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 166,
'low complexity anchor region' => 40,
' ** passed ** ' => 41525,
'small anchor length' => 252,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
'excessive soft clipping' => 3548,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 8
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[159000] -fusion SPANNING read extraction for scaff: CX3CL1--RBPMS
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[29000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA8
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[21000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA9
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6
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[19000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA10
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB7
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[19000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11
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[21000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA12
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[16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[18000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 49863,
'lacks exon overlap' => 1056
};
EM: Starting log likelihood: -5374.922613
EM: Round [1] log likelihood: -5370.144139
EM: Round [2] log likelihood: -5366.183558
EM: Round [3] log likelihood: -5362.886135
EM: Round [4] log likelihood: -5360.129327
EM: Round [5] log likelihood: -5357.815275
EM: Round [6] log likelihood: -5355.865289
EM: Round [7] log likelihood: -5354.215730
EM: Round [8] log likelihood: -5352.814878
EM: Round [9] log likelihood: -5351.620531
EM: Round [10] log likelihood: -5350.598128
EM: Round [11] log likelihood: -5349.719285
EM: Round [12] log likelihood: -5348.960623
EM: Round [13] log likelihood: -5348.302844
EM: Round [14] log likelihood: -5347.729981
EM: Round [15] log likelihood: -5347.228798
EM: Round [16] log likelihood: -5346.788302
EM: Round [17] log likelihood: -5346.399343
EM: Round [18] log likelihood: -5346.054296
EM: Round [19] log likelihood: -5345.746790
EM: Round [20] log likelihood: -5345.471495
EM: Round [21] log likelihood: -5345.223940
EM: Round [22] log likelihood: -5345.000371
EM: Round [23] log likelihood: -5344.797624
EM: Round [24] log likelihood: -5344.613030
EM: Round [25] log likelihood: -5344.444329
EM: Round [26] log likelihood: -5344.289605
EM: Round [27] log likelihood: -5344.147225
EM: Round [28] log likelihood: -5344.015798
EM: Round [29] log likelihood: -5343.894130
EM: Round [30] log likelihood: -5343.781198
EM: Round [31] log likelihood: -5343.676116
EM: Round [32] log likelihood: -5343.578119
EM: Round [33] log likelihood: -5343.486542
EM: Round [34] log likelihood: -5343.400805
EM: Round [35] log likelihood: -5343.320397
EM: Round [36] log likelihood: -5343.244872
EM: Round [37] log likelihood: -5343.173833
EM: Round [38] log likelihood: -5343.106928
EM: Round [39] log likelihood: -5343.043844
EM: Round [40] log likelihood: -5342.984299
EM: Round [41] log likelihood: -5342.928041
EM: Round [42] log likelihood: -5342.874842
EM: Round [43] log likelihood: -5342.824495
EM: Round [44] log likelihood: -5342.776811
EM: Round [45] log likelihood: -5342.731619
EM: Round [46] log likelihood: -5342.688762
EM: Round [47] log likelihood: -5342.648095
EM: Round [48] log likelihood: -5342.609485
EM: Round [49] log likelihood: -5342.572808
EM: Round [50] log likelihood: -5342.537950
EM: Round [51] log likelihood: -5342.504806
EM: Round [52] log likelihood: -5342.473277
EM: Round [53] log likelihood: -5342.443270
EM: Round [54] log likelihood: -5342.414701
EM: Round [55] log likelihood: -5342.387489
EM: Round [56] log likelihood: -5342.361558
EM: Round [57] log likelihood: -5342.336839
EM: Round [58] log likelihood: -5342.313265
EM: Round [59] log likelihood: -5342.290774
EM: Round [60] log likelihood: -5342.269308
EM: Round [61] log likelihood: -5342.248811
EM: Round [62] log likelihood: -5342.229231
EM: Round [63] log likelihood: -5342.210521
EM: Round [64] log likelihood: -5342.192632
EM: Round [65] log likelihood: -5342.175523
EM: Round [66] log likelihood: -5342.159152
EM: Round [67] log likelihood: -5342.143480
EM: Round [68] log likelihood: -5342.128470
EM: Round [69] log likelihood: -5342.114089
EM: Round [70] log likelihood: -5342.100302
EM: Round [71] log likelihood: -5342.087079
EM: Round [72] log likelihood: -5342.074391
EM: Round [73] log likelihood: -5342.062210
EM: Round [74] log likelihood: -5342.050510
EM: Round [75] log likelihood: -5342.039266
EM: Round [76] log likelihood: -5342.028454
EM: Round [77] log likelihood: -5342.018052
EM: Round [78] log likelihood: -5342.008039
EM: Round [79] log likelihood: -5341.998395
EM: Round [80] log likelihood: -5341.989101
EM: Round [81] log likelihood: -5341.980140
EM: Round [82] log likelihood: -5341.971494
EM: Round [83] log likelihood: -5341.963147
EM: Round [84] log likelihood: -5341.955084
EM: Round [85] log likelihood: -5341.947290
EM: Round [86] log likelihood: -5341.939752
EM: Round [87] log likelihood: -5341.932458
EM: Round [88] log likelihood: -5341.925394
EM: Round [89] log likelihood: -5341.918549
EM: Round [90] log likelihood: -5341.911912
EM: Round [91] log likelihood: -5341.905473
EM: Round [92] log likelihood: -5341.899221
EM: Round [93] log likelihood: -5341.893148
EM: Round [94] log likelihood: -5341.887244
EM: Round [95] log likelihood: -5341.881502
EM: Round [96] log likelihood: -5341.875912
EM: Round [97] log likelihood: -5341.870468
EM: Round [98] log likelihood: -5341.865162
EM: Round [99] log likelihood: -5341.859988
EM: Round [100] log likelihood: -5341.854939
EM: Round [101] log likelihood: -5341.850009
EM: Round [102] log likelihood: -5341.845192
EM: Round [103] log likelihood: -5341.840483
EM: Round [104] log likelihood: -5341.835877
EM: Round [105] log likelihood: -5341.831368
EM: Round [106] log likelihood: -5341.826952
EM: Round [107] log likelihood: -5341.822625
EM: Round [108] log likelihood: -5341.818382
EM: Round [109] log likelihood: -5341.814219
EM: Round [110] log likelihood: -5341.810133
EM: Round [111] log likelihood: -5341.806120
EM: Round [112] log likelihood: -5341.802177
EM: Round [113] log likelihood: -5341.798300
EM: Round [114] log likelihood: -5341.794486
EM: Round [115] log likelihood: -5341.790733
EM: Round [116] log likelihood: -5341.787038
EM: Round [117] log likelihood: -5341.783398
EM: Round [118] log likelihood: -5341.779810
EM: Round [119] log likelihood: -5341.776273
EM: Round [120] log likelihood: -5341.772784
EM: Round [121] log likelihood: -5341.769341
EM: Round [122] log likelihood: -5341.765943
EM: Round [123] log likelihood: -5341.762586
EM: Round [124] log likelihood: -5341.759269
EM: Round [125] log likelihood: -5341.755992
EM: Round [126] log likelihood: -5341.752751
EM: Round [127] log likelihood: -5341.749546
EM: Round [128] log likelihood: -5341.746375
EM: Round [129] log likelihood: -5341.743236
EM: Round [130] log likelihood: -5341.740129
EM: Round [131] log likelihood: -5341.737053
EM: Round [132] log likelihood: -5341.734005
EM: Round [133] log likelihood: -5341.730985
EM: Round [134] log likelihood: -5341.727991
EM: Round [135] log likelihood: -5341.725024
EM: Round [136] log likelihood: -5341.722081
EM: Round [137] log likelihood: -5341.719163
EM: Round [138] log likelihood: -5341.716267
EM: Round [139] log likelihood: -5341.713394
EM: Round [140] log likelihood: -5341.710542
EM: Round [141] log likelihood: -5341.707711
EM: Round [142] log likelihood: -5341.704899
EM: Round [143] log likelihood: -5341.702108
EM: Round [144] log likelihood: -5341.699335
EM: Round [145] log likelihood: -5341.696580
EM: Round [146] log likelihood: -5341.693842
EM: Round [147] log likelihood: -5341.691122
EM: Round [148] log likelihood: -5341.688418
EM: Round [149] log likelihood: -5341.685730
EM: Round [150] log likelihood: -5341.683058
EM: Round [151] log likelihood: -5341.680401
EM: Round [152] log likelihood: -5341.677758
EM: Round [153] log likelihood: -5341.675130
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EM: Round [618] log likelihood: -5340.974128
EM: Round [619] log likelihood: -5340.973199
EM: Round [620] log likelihood: -5340.972271
EM: Round [621] log likelihood: -5340.971345
EM: Round [622] log likelihood: -5340.970420
EM: Round [623] log likelihood: -5340.969496
EM: Round [624] log likelihood: -5340.968574
EM: Round [625] log likelihood: -5340.967654
EM: Round [626] log likelihood: -5340.966735
EM: Round [627] log likelihood: -5340.965817
EM: Round [628] log likelihood: -5340.964901
EM: Round [629] log likelihood: -5340.963986
EM: Round [630] log likelihood: -5340.963073
EM: Round [631] log likelihood: -5340.962161
EM: Round [632] log likelihood: -5340.961250
EM: Round [633] log likelihood: -5340.960341
EM: Round [634] log likelihood: -5340.959433
EM: Round [635] log likelihood: -5340.958527
EM: Round [636] log likelihood: -5340.957622
EM: Round [637] log likelihood: -5340.956718
EM: Round [638] log likelihood: -5340.955816
EM: Round [639] log likelihood: -5340.954915
EM: Round [640] log likelihood: -5340.954016
EM: Round [641] log likelihood: -5340.953118
EM: Round [642] log likelihood: -5340.952221
EM: Round [643] log likelihood: -5340.951325
EM: Round [644] log likelihood: -5340.950432
EM: Round [645] log likelihood: -5340.949539
EM: Round [646] log likelihood: -5340.948648
EM: Round [647] log likelihood: -5340.947758
EM: Round [648] log likelihood: -5340.946869
EM: Round [649] log likelihood: -5340.945982
EM: Round [650] log likelihood: -5340.945096
EM: Round [651] log likelihood: -5340.944212
EM: Round [652] log likelihood: -5340.943329
EM: Round [653] log likelihood: -5340.942447
EM: Round [654] log likelihood: -5340.941566
EM: Round [655] log likelihood: -5340.940687
EM: Round [656] log likelihood: -5340.939810
EM: Round [657] log likelihood: -5340.938933
EM: Round [658] log likelihood: -5340.938058
EM: Round [659] log likelihood: -5340.937184
EM: Round [660] log likelihood: -5340.936312
EM: Round [661] log likelihood: -5340.935440
EM: Round [662] log likelihood: -5340.934571
EM: Round [663] log likelihood: -5340.933702
EM: Round [664] log likelihood: -5340.932835
EM: Round [665] log likelihood: -5340.931969
EM: Round [666] log likelihood: -5340.931104
EM: Round [667] log likelihood: -5340.930241
EM: Round [668] log likelihood: -5340.929379
EM: Round [669] log likelihood: -5340.928518
EM: Round [670] log likelihood: -5340.927658
EM: Round [671] log likelihood: -5340.926800
EM: Round [672] log likelihood: -5340.925943
EM: Round [673] log likelihood: -5340.925087
EM: Round [674] log likelihood: -5340.924233
EM: Round [675] log likelihood: -5340.923380
EM: Round [676] log likelihood: -5340.922528
EM: Round [677] log likelihood: -5340.921677
EM: Round [678] log likelihood: -5340.920828
EM: Round [679] log likelihood: -5340.919980
EM: Round [680] log likelihood: -5340.919133
EM: Round [681] log likelihood: -5340.918287
EM: Round [682] log likelihood: -5340.917443
EM: Round [683] log likelihood: -5340.916600
EM: Round [684] log likelihood: -5340.915758
EM: Round [685] log likelihood: -5340.914918
EM: Round [686] log likelihood: -5340.914078
EM: Round [687] log likelihood: -5340.913240
EM: Round [688] log likelihood: -5340.912403
EM: Round [689] log likelihood: -5340.911568
EM: Round [690] log likelihood: -5340.910733
EM: Round [691] log likelihood: -5340.909900
EM: Round [692] log likelihood: -5340.909068
EM: Round [693] log likelihood: -5340.908237
EM: Round [694] log likelihood: -5340.907408
EM: Round [695] log likelihood: -5340.906579
EM: Round [696] log likelihood: -5340.905752
EM: Round [697] log likelihood: -5340.904926
EM: Round [698] log likelihood: -5340.904102
EM: Round [699] log likelihood: -5340.903278
EM: Round [700] log likelihood: -5340.902456
EM: Round [701] log likelihood: -5340.901635
EM: Round [702] log likelihood: -5340.900815
EM: Round [703] log likelihood: -5340.899996
EM: Round [704] log likelihood: -5340.899178
EM: Round [705] log likelihood: -5340.898362
EM: Round [706] log likelihood: -5340.897547
EM: Round [707] log likelihood: -5340.896733
EM: Round [708] log likelihood: -5340.895920
EM: Round [709] log likelihood: -5340.895108
EM: Round [710] log likelihood: -5340.894298
EM: Round [711] log likelihood: -5340.893489
EM: Round [712] log likelihood: -5340.892681
EM: Round [713] log likelihood: -5340.891874
EM: Round [714] log likelihood: -5340.891068
EM: Round [715] log likelihood: -5340.890263
EM: Round [716] log likelihood: -5340.889460
EM: Round [717] log likelihood: -5340.888657
EM: Round [718] log likelihood: -5340.887856
EM: Round [719] log likelihood: -5340.887056
EM: Round [720] log likelihood: -5340.886257
EM: Round [721] log likelihood: -5340.885459
EM: Round [722] log likelihood: -5340.884663
EM: Round [723] log likelihood: -5340.883867
EM: Round [724] log likelihood: -5340.883073
EM: Round [725] log likelihood: -5340.882280
EM: Round [726] log likelihood: -5340.881488
EM: Round [727] log likelihood: -5340.880697
EM: Round [728] log likelihood: -5340.879907
EM: Round [729] log likelihood: -5340.879118
EM: Round [730] log likelihood: -5340.878331
EM: Round [731] log likelihood: -5340.877544
EM: Round [732] log likelihood: -5340.876759
EM: Round [733] log likelihood: -5340.875975
EM: Round [734] log likelihood: -5340.875192
EM: Round [735] log likelihood: -5340.874410
EM: Round [736] log likelihood: -5340.873629
EM: Round [737] log likelihood: -5340.872849
EM: Round [738] log likelihood: -5340.872070
EM: Round [739] log likelihood: -5340.871293
EM: Round [740] log likelihood: -5340.870516
EM: Round [741] log likelihood: -5340.869741
EM: Round [742] log likelihood: -5340.868966
EM: Round [743] log likelihood: -5340.868193
EM: Round [744] log likelihood: -5340.867421
EM: Round [745] log likelihood: -5340.866650
EM: Round [746] log likelihood: -5340.865880
EM: Round [747] log likelihood: -5340.865111
EM: Round [748] log likelihood: -5340.864343
EM: Round [749] log likelihood: -5340.863577
EM: Round [750] log likelihood: -5340.862811
EM: Round [751] log likelihood: -5340.862046
EM: Round [752] log likelihood: -5340.861283
EM: Round [753] log likelihood: -5340.860520
EM: Round [754] log likelihood: -5340.859759
EM: Round [755] log likelihood: -5340.858999
EM: Round [756] log likelihood: -5340.858239
EM: Round [757] log likelihood: -5340.857481
EM: Round [758] log likelihood: -5340.856724
EM: Round [759] log likelihood: -5340.855968
EM: Round [760] log likelihood: -5340.855213
EM: Round [761] log likelihood: -5340.854459
EM: Round [762] log likelihood: -5340.853706
EM: Round [763] log likelihood: -5340.852954
EM: Round [764] log likelihood: -5340.852203
EM: Round [765] log likelihood: -5340.851453
EM: Round [766] log likelihood: -5340.850705
EM: Round [767] log likelihood: -5340.849957
EM: Round [768] log likelihood: -5340.849210
EM: Round [769] log likelihood: -5340.848464
EM: Round [770] log likelihood: -5340.847720
EM: Round [771] log likelihood: -5340.846976
EM: Round [772] log likelihood: -5340.846233
EM: Round [773] log likelihood: -5340.845492
EM: Round [774] log likelihood: -5340.844751
EM: Round [775] log likelihood: -5340.844012
EM: Round [776] log likelihood: -5340.843273
EM: Round [777] log likelihood: -5340.842536
EM: Round [778] log likelihood: -5340.841799
EM: Round [779] log likelihood: -5340.841063
EM: Round [780] log likelihood: -5340.840329
EM: Round [781] log likelihood: -5340.839595
EM: Round [782] log likelihood: -5340.838863
EM: Round [783] log likelihood: -5340.838131
EM: Round [784] log likelihood: -5340.837401
EM: Round [785] log likelihood: -5340.836671
EM: Round [786] log likelihood: -5340.835943
EM: Round [787] log likelihood: -5340.835215
EM: Round [788] log likelihood: -5340.834489
EM: Round [789] log likelihood: -5340.833763
EM: Round [790] log likelihood: -5340.833039
EM: Round [791] log likelihood: -5340.832315
EM: Round [792] log likelihood: -5340.831593
EM: Round [793] log likelihood: -5340.830871
EM: Round [794] log likelihood: -5340.830150
EM: Round [795] log likelihood: -5340.829431
EM: Round [796] log likelihood: -5340.828712
EM: Round [797] log likelihood: -5340.827994
EM: Round [798] log likelihood: -5340.827277
EM: Round [799] log likelihood: -5340.826562
EM: Round [800] log likelihood: -5340.825847
EM: Round [801] log likelihood: -5340.825133
EM: Round [802] log likelihood: -5340.824420
EM: Round [803] log likelihood: -5340.823708
EM: Round [804] log likelihood: -5340.822997
EM: Round [805] log likelihood: -5340.822287
EM: Round [806] log likelihood: -5340.821578
EM: Round [807] log likelihood: -5340.820870
EM: Round [808] log likelihood: -5340.820163
EM: Round [809] log likelihood: -5340.819457
EM: Round [810] log likelihood: -5340.818751
EM: Round [811] log likelihood: -5340.818047
EM: Round [812] log likelihood: -5340.817344
EM: Round [813] log likelihood: -5340.816641
EM: Round [814] log likelihood: -5340.815940
EM: Round [815] log likelihood: -5340.815239
EM: Round [816] log likelihood: -5340.814539
EM: Round [817] log likelihood: -5340.813841
EM: Round [818] log likelihood: -5340.813143
EM: Round [819] log likelihood: -5340.812446
EM: Round [820] log likelihood: -5340.811750
EM: Round [821] log likelihood: -5340.811055
EM: Round [822] log likelihood: -5340.810361
EM: Round [823] log likelihood: -5340.809668
EM: Round [824] log likelihood: -5340.808976
EM: Round [825] log likelihood: -5340.808284
EM: Round [826] log likelihood: -5340.807594
EM: Round [827] log likelihood: -5340.806905
EM: Round [828] log likelihood: -5340.806216
EM: Round [829] log likelihood: -5340.805528
EM: Round [830] log likelihood: -5340.804842
EM: Round [831] log likelihood: -5340.804156
EM: Round [832] log likelihood: -5340.803471
EM: Round [833] log likelihood: -5340.802787
EM: Round [834] log likelihood: -5340.802104
EM: Round [835] log likelihood: -5340.801421
EM: Round [836] log likelihood: -5340.800740
EM: Round [837] log likelihood: -5340.800060
EM: Round [838] log likelihood: -5340.799380
EM: Round [839] log likelihood: -5340.798701
EM: Round [840] log likelihood: -5340.798024
EM: Round [841] log likelihood: -5340.797347
EM: Round [842] log likelihood: -5340.796671
EM: Round [843] log likelihood: -5340.795996
EM: Round [844] log likelihood: -5340.795321
EM: Round [845] log likelihood: -5340.794648
EM: Round [846] log likelihood: -5340.793975
EM: Round [847] log likelihood: -5340.793304
EM: Round [848] log likelihood: -5340.792633
EM: Round [849] log likelihood: -5340.791963
EM: Round [850] log likelihood: -5340.791294
EM: Round [851] log likelihood: -5340.790626
EM: Round [852] log likelihood: -5340.789959
EM: Round [853] log likelihood: -5340.789293
EM: Round [854] log likelihood: -5340.788627
EM: Round [855] log likelihood: -5340.787963
EM: Round [856] log likelihood: -5340.787299
EM: Round [857] log likelihood: -5340.786636
EM: Round [858] log likelihood: -5340.785974
EM: Round [859] log likelihood: -5340.785313
EM: Round [860] log likelihood: -5340.784652
EM: Round [861] log likelihood: -5340.783993
EM: Round [862] log likelihood: -5340.783334
EM: Round [863] log likelihood: -5340.782676
EM: Round [864] log likelihood: -5340.782019
EM: Round [865] log likelihood: -5340.781363
EM: Round [866] log likelihood: -5340.780708
EM: Round [867] log likelihood: -5340.780054
EM: Round [868] log likelihood: -5340.779400
EM: Round [869] log likelihood: -5340.778748
EM: Round [870] log likelihood: -5340.778096
EM: Round [871] log likelihood: -5340.777445
EM: Round [872] log likelihood: -5340.776794
EM: Round [873] log likelihood: -5340.776145
EM: Round [874] log likelihood: -5340.775497
EM: Round [875] log likelihood: -5340.774849
EM: Round [876] log likelihood: -5340.774202
EM: Round [877] log likelihood: -5340.773556
EM: Round [878] log likelihood: -5340.772911
EM: Round [879] log likelihood: -5340.772266
EM: Round [880] log likelihood: -5340.771623
EM: Round [881] log likelihood: -5340.770980
EM: Round [882] log likelihood: -5340.770338
EM: Round [883] log likelihood: -5340.769697
EM: Round [884] log likelihood: -5340.769057
EM: Round [885] log likelihood: -5340.768417
EM: Round [886] log likelihood: -5340.767779
EM: Round [887] log likelihood: -5340.767141
EM: Round [888] log likelihood: -5340.766504
EM: Round [889] log likelihood: -5340.765867
EM: Round [890] log likelihood: -5340.765232
EM: Round [891] log likelihood: -5340.764597
EM: Round [892] log likelihood: -5340.763964
EM: Round [893] log likelihood: -5340.763331
EM: Round [894] log likelihood: -5340.762698
EM: Round [895] log likelihood: -5340.762067
EM: Round [896] log likelihood: -5340.761436
EM: Round [897] log likelihood: -5340.760807
EM: Round [898] log likelihood: -5340.760178
EM: Round [899] log likelihood: -5340.759549
EM: Round [900] log likelihood: -5340.758922
EM: Round [901] log likelihood: -5340.758295
EM: Round [902] log likelihood: -5340.757669
EM: Round [903] log likelihood: -5340.757044
EM: Round [904] log likelihood: -5340.756420
EM: Round [905] log likelihood: -5340.755797
EM: Round [906] log likelihood: -5340.755174
EM: Round [907] log likelihood: -5340.754552
EM: Round [908] log likelihood: -5340.753931
EM: Round [909] log likelihood: -5340.753310
EM: Round [910] log likelihood: -5340.752691
EM: Round [911] log likelihood: -5340.752072
EM: Round [912] log likelihood: -5340.751454
EM: Round [913] log likelihood: -5340.750837
EM: Round [914] log likelihood: -5340.750220
EM: Round [915] log likelihood: -5340.749605
EM: Round [916] log likelihood: -5340.748990
EM: Round [917] log likelihood: -5340.748375
EM: Round [918] log likelihood: -5340.747762
EM: Round [919] log likelihood: -5340.747149
EM: Round [920] log likelihood: -5340.746537
EM: Round [921] log likelihood: -5340.745926
EM: Round [922] log likelihood: -5340.745316
EM: Round [923] log likelihood: -5340.744706
EM: Round [924] log likelihood: -5340.744098
EM: Round [925] log likelihood: -5340.743489
EM: Round [926] log likelihood: -5340.742882
EM: Round [927] log likelihood: -5340.742276
EM: Round [928] log likelihood: -5340.741670
EM: Round [929] log likelihood: -5340.741065
EM: Round [930] log likelihood: -5340.740460
EM: Round [931] log likelihood: -5340.739857
EM: Round [932] log likelihood: -5340.739254
EM: Round [933] log likelihood: -5340.738652
EM: Round [934] log likelihood: -5340.738050
EM: Round [935] log likelihood: -5340.737450
EM: Round [936] log likelihood: -5340.736850
EM: Round [937] log likelihood: -5340.736251
EM: Round [938] log likelihood: -5340.735652
EM: Round [939] log likelihood: -5340.735055
EM: Round [940] log likelihood: -5340.734458
EM: Round [941] log likelihood: -5340.733862
EM: Round [942] log likelihood: -5340.733266
EM: Round [943] log likelihood: -5340.732671
EM: Round [944] log likelihood: -5340.732078
EM: Round [945] log likelihood: -5340.731484
EM: Round [946] log likelihood: -5340.730892
EM: Round [947] log likelihood: -5340.730300
EM: Round [948] log likelihood: -5340.729709
EM: Round [949] log likelihood: -5340.729118
EM: Round [950] log likelihood: -5340.728529
EM: Round [951] log likelihood: -5340.727940
EM: Round [952] log likelihood: -5340.727352
EM: Round [953] log likelihood: -5340.726764
EM: Round [954] log likelihood: -5340.726178
EM: Round [955] log likelihood: -5340.725591
EM: Round [956] log likelihood: -5340.725006
EM: Round [957] log likelihood: -5340.724422
EM: Round [958] log likelihood: -5340.723838
EM: Round [959] log likelihood: -5340.723254
EM: Round [960] log likelihood: -5340.722672
EM: Round [961] log likelihood: -5340.722090
EM: Round [962] log likelihood: -5340.721509
EM: Round [963] log likelihood: -5340.720929
EM: Round [964] log likelihood: -5340.720349
EM: Round [965] log likelihood: -5340.719770
EM: Round [966] log likelihood: -5340.719192
EM: Round [967] log likelihood: -5340.718614
EM: Round [968] log likelihood: -5340.718037
EM: Round [969] log likelihood: -5340.717461
EM: Round [970] log likelihood: -5340.716886
EM: Round [971] log likelihood: -5340.716311
EM: Round [972] log likelihood: -5340.715737
EM: Round [973] log likelihood: -5340.715164
EM: Round [974] log likelihood: -5340.714591
EM: Round [975] log likelihood: -5340.714019
EM: Round [976] log likelihood: -5340.713448
EM: Round [977] log likelihood: -5340.712877
EM: Round [978] log likelihood: -5340.712307
EM: Round [979] log likelihood: -5340.711738
EM: Round [980] log likelihood: -5340.711169
EM: Round [981] log likelihood: -5340.710601
EM: Round [982] log likelihood: -5340.710034
EM: Round [983] log likelihood: -5340.709468
EM: Round [984] log likelihood: -5340.708902
EM: Round [985] log likelihood: -5340.708337
EM: Round [986] log likelihood: -5340.707772
EM: Round [987] log likelihood: -5340.707209
EM: Round [988] log likelihood: -5340.706645
EM: Round [989] log likelihood: -5340.706083
EM: Round [990] log likelihood: -5340.705521
EM: Round [991] log likelihood: -5340.704960
EM: Round [992] log likelihood: -5340.704400
EM: Round [993] log likelihood: -5340.703840
EM: Round [994] log likelihood: -5340.703281
EM: Round [995] log likelihood: -5340.702722
EM: Round [996] log likelihood: -5340.702165
EM: Round [997] log likelihood: -5340.701607
EM: Round [998] log likelihood: -5340.701051
EM: Round [999] log likelihood: -5340.700495
EM: Round [1000] log likelihood: -5340.699940
EM: Round [1001] log likelihood: -5340.699386
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_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.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_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.vKgislKKwM/fi_workdir/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3872.296876
EM: Round [1] log likelihood: -3872.296876
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 226554601
Warning - not locating file: /tmp/nxf.vKgislKKwM/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.gmap_trinity_GG.fusions.gff3.bed
ls: cannot access 'IGV_inputs': No such file or directory