Done.
-parsing GTF file: /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.mozZzLS8CN/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.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_1.fastp.fastq.gz /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00146_B23WHTKLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00146_B23WHTKLT4_2.star.sortedByCoord.out.bam
11:43:27 : INFO : Done.
-parsing GTF file: /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.gtf
-parsing /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam

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[900000]   -done parsing /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'seq-similar region overlap' => 15,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 10,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 210,
          ' ** passed ** ' => 8209,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 9,
          'per_id < 96' => 3268,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 82,
          'excessive soft clipping' => 11193,
          'exons hit < 2' => 6,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 92,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 613,
          'small anchor length' => 29,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 958,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 12,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 15,
          'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1846,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12,
          'low complexity anchor region' => 13,
          'num genes matched < 2' => 51
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[15000]   -fusion SPANNING read extraction for scaff: AC011037.1--CPA6

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[7000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[11000]   -fusion SPANNING read extraction for scaff: AL512590.2--CCDC180

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[9000]   
[10000]   -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1

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[79000]   -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1

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[79000]   -fusion SPANNING read extraction for scaff: IGL-@-ext--PRR7-AS1

[1000]   
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[3000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

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[34000]   -fusion SPANNING read extraction for scaff: PCDHA5--PCDHA13

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[29000]   -fusion SPANNING read extraction for scaff: PCDHA5--PCDHAC2

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[31000]   -fusion SPANNING read extraction for scaff: PCDHA5--PCDHAC1

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[46000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

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[41000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[43000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[6000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[32000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[13000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[119000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[31000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[5000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[23000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[8000]   -fusion SPANNING read extraction for scaff: UPK3B--AC211486.3

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[136000]   -fusion SPANNING read extraction for scaff: ZFHX3--LINC01572
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 28464,
          'seq similar region alignment' => 18606
        };
EM: Starting log likelihood: -6205.277206
EM: Round [1] log likelihood: -6200.753596
EM: Round [2] log likelihood: -6200.724714
EM: Round [3] log likelihood: -6200.715455
EM: Round [4] log likelihood: -6200.706321
EM: Round [5] log likelihood: -6200.697273
EM: Round [6] log likelihood: -6200.688309
EM: Round [7] log likelihood: -6200.679428
EM: Round [8] log likelihood: -6200.670630
EM: Round [9] log likelihood: -6200.661912
EM: Round [10] log likelihood: -6200.653275
EM: Round [11] log likelihood: -6200.644718
EM: Round [12] log likelihood: -6200.636238
EM: Round [13] log likelihood: -6200.627837
EM: Round [14] log likelihood: -6200.619511
EM: Round [15] log likelihood: -6200.611262
EM: Round [16] log likelihood: -6200.603087
EM: Round [17] log likelihood: -6200.594985
EM: Round [18] log likelihood: -6200.586957
EM: Round [19] log likelihood: -6200.579001
EM: Round [20] log likelihood: -6200.571116
EM: Round [21] log likelihood: -6200.563302
EM: Round [22] log likelihood: -6200.555557
EM: Round [23] log likelihood: -6200.547881
EM: Round [24] log likelihood: -6200.540273
EM: Round [25] log likelihood: -6200.532733
EM: Round [26] log likelihood: -6200.525259
EM: Round [27] log likelihood: -6200.517851
EM: Round [28] log likelihood: -6200.510507
EM: Round [29] log likelihood: -6200.503229
EM: Round [30] log likelihood: -6200.496013
EM: Round [31] log likelihood: -6200.488861
EM: Round [32] log likelihood: -6200.481771
EM: Round [33] log likelihood: -6200.474742
EM: Round [34] log likelihood: -6200.467774
EM: Round [35] log likelihood: -6200.460866
EM: Round [36] log likelihood: -6200.454018
EM: Round [37] log likelihood: -6200.447228
EM: Round [38] log likelihood: -6200.440497
EM: Round [39] log likelihood: -6200.433824
EM: Round [40] log likelihood: -6200.427207
EM: Round [41] log likelihood: -6200.420647
EM: Round [42] log likelihood: -6200.414142
EM: Round [43] log likelihood: -6200.407693
EM: Round [44] log likelihood: -6200.401298
EM: Round [45] log likelihood: -6200.394957
EM: Round [46] log likelihood: -6200.388670
EM: Round [47] log likelihood: -6200.382436
EM: Round [48] log likelihood: -6200.376253
EM: Round [49] log likelihood: -6200.370123
EM: Round [50] log likelihood: -6200.364044
EM: Round [51] log likelihood: -6200.358015
EM: Round [52] log likelihood: -6200.352037
EM: Round [53] log likelihood: -6200.346109
EM: Round [54] log likelihood: -6200.340229
EM: Round [55] log likelihood: -6200.334398
EM: Round [56] log likelihood: -6200.328616
EM: Round [57] log likelihood: -6200.322881
EM: Round [58] log likelihood: -6200.317193
EM: Round [59] log likelihood: -6200.311552
EM: Round [60] log likelihood: -6200.305957
EM: Round [61] log likelihood: -6200.300408
EM: Round [62] log likelihood: -6200.294904
EM: Round [63] log likelihood: -6200.289445
EM: Round [64] log likelihood: -6200.284031
EM: Round [65] log likelihood: -6200.278660
EM: Round [66] log likelihood: -6200.273333
EM: Round [67] log likelihood: -6200.268049
EM: Round [68] log likelihood: -6200.262808
EM: Round [69] log likelihood: -6200.257609
EM: Round [70] log likelihood: -6200.252452
EM: Round [71] log likelihood: -6200.247336
EM: Round [72] log likelihood: -6200.242262
EM: Round [73] log likelihood: -6200.237228
EM: Round [74] log likelihood: -6200.232234
EM: Round [75] log likelihood: -6200.227280
EM: Round [76] log likelihood: -6200.222366
EM: Round [77] log likelihood: -6200.217490
EM: Round [78] log likelihood: -6200.212654
EM: Round [79] log likelihood: -6200.207856
EM: Round [80] log likelihood: -6200.203096
EM: Round [81] log likelihood: -6200.198373
EM: Round [82] log likelihood: -6200.193688
EM: Round [83] log likelihood: -6200.189039
EM: Round [84] log likelihood: -6200.184427
EM: Round [85] log likelihood: -6200.179852
EM: Round [86] log likelihood: -6200.175312
EM: Round [87] log likelihood: -6200.170808
EM: Round [88] log likelihood: -6200.166339
EM: Round [89] log likelihood: -6200.161905
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EM: Round [91] log likelihood: -6200.153141
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EM: Round [94] log likelihood: -6200.140247
EM: Round [95] log likelihood: -6200.136016
EM: Round [96] log likelihood: -6200.131818
EM: Round [97] log likelihood: -6200.127652
EM: Round [98] log likelihood: -6200.123517
EM: Round [99] log likelihood: -6200.119415
EM: Round [100] log likelihood: -6200.115345
EM: Round [101] log likelihood: -6200.111305
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EM: Round [103] log likelihood: -6200.103319
EM: Round [104] log likelihood: -6200.099372
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EM: Round [107] log likelihood: -6200.087709
EM: Round [108] log likelihood: -6200.083881
EM: Round [109] log likelihood: -6200.080082
EM: Round [110] log likelihood: -6200.076311
EM: Round [111] log likelihood: -6200.072569
EM: Round [112] log likelihood: -6200.068856
EM: Round [113] log likelihood: -6200.065170
EM: Round [114] log likelihood: -6200.061513
EM: Round [115] log likelihood: -6200.057883
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EM: Round [117] log likelihood: -6200.050704
EM: Round [118] log likelihood: -6200.047156
EM: Round [119] log likelihood: -6200.043634
EM: Round [120] log likelihood: -6200.040138
EM: Round [121] log likelihood: -6200.036668
EM: Round [122] log likelihood: -6200.033225
EM: Round [123] log likelihood: -6200.029807
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EM: Round [125] log likelihood: -6200.023047
EM: Round [126] log likelihood: -6200.019705
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EM: Round [128] log likelihood: -6200.013096
EM: Round [129] log likelihood: -6200.009828
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EM: Round [132] log likelihood: -6200.000168
EM: Round [133] log likelihood: -6199.996995
EM: Round [134] log likelihood: -6199.993846
EM: Round [135] log likelihood: -6199.990721
EM: Round [136] log likelihood: -6199.987618
EM: Round [137] log likelihood: -6199.984538
EM: Round [138] log likelihood: -6199.981481
EM: Round [139] log likelihood: -6199.978446
EM: Round [140] log likelihood: -6199.975433
EM: Round [141] log likelihood: -6199.972443
EM: Round [142] log likelihood: -6199.969474
EM: Round [143] log likelihood: -6199.966527
EM: Round [144] log likelihood: -6199.963602
EM: Round [145] log likelihood: -6199.960698
EM: Round [146] log likelihood: -6199.957815
EM: Round [147] log likelihood: -6199.954953
EM: Round [148] log likelihood: -6199.952112
EM: Round [149] log likelihood: -6199.949292
EM: Round [150] log likelihood: -6199.946492
EM: Round [151] log likelihood: -6199.943712
EM: Round [152] log likelihood: -6199.940953
EM: Round [153] log likelihood: -6199.938213
EM: Round [154] log likelihood: -6199.935494
EM: Round [155] log likelihood: -6199.932794
EM: Round [156] log likelihood: -6199.930114
EM: Round [157] log likelihood: -6199.927452
EM: Round [158] log likelihood: -6199.924811
EM: Round [159] log likelihood: -6199.922188
EM: Round [160] log likelihood: -6199.919584
EM: Round [161] log likelihood: -6199.916999
EM: Round [162] log likelihood: -6199.914432
EM: Round [163] log likelihood: -6199.911884
EM: Round [164] log likelihood: -6199.909354
EM: Round [165] log likelihood: -6199.906842
EM: Round [166] log likelihood: -6199.904348
EM: Round [167] log likelihood: -6199.901872
EM: Round [168] log likelihood: -6199.899414
EM: Round [169] log likelihood: -6199.896973
EM: Round [170] log likelihood: -6199.894550
EM: Round [171] log likelihood: -6199.892144
EM: Round [172] log likelihood: -6199.889755
EM: Round [173] log likelihood: -6199.887383
EM: Round [174] log likelihood: -6199.885028
EM: Round [175] log likelihood: -6199.882690
EM: Round [176] log likelihood: -6199.880368
EM: Round [177] log likelihood: -6199.878063
EM: Round [178] log likelihood: -6199.875775
EM: Round [179] log likelihood: -6199.873502
EM: Round [180] log likelihood: -6199.871246
EM: Round [181] log likelihood: -6199.869005
EM: Round [182] log likelihood: -6199.866780
EM: Round [183] log likelihood: -6199.864572
EM: Round [184] log likelihood: -6199.862378
EM: Round [185] log likelihood: -6199.860200
EM: Round [186] log likelihood: -6199.858038
EM: Round [187] log likelihood: -6199.855891
EM: Round [188] log likelihood: -6199.853759
EM: Round [189] log likelihood: -6199.851641
EM: Round [190] log likelihood: -6199.849539
EM: Round [191] log likelihood: -6199.847452
EM: Round [192] log likelihood: -6199.845379
EM: Round [193] log likelihood: -6199.843321
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EM: Round [195] log likelihood: -6199.839247
EM: Round [196] log likelihood: -6199.837232
EM: Round [197] log likelihood: -6199.835231
EM: Round [198] log likelihood: -6199.833244
EM: Round [199] log likelihood: -6199.831270
EM: Round [200] log likelihood: -6199.829311
EM: Round [201] log likelihood: -6199.827365
EM: Round [202] log likelihood: -6199.825433
EM: Round [203] log likelihood: -6199.823514
EM: Round [204] log likelihood: -6199.821608
EM: Round [205] log likelihood: -6199.819716
EM: Round [206] log likelihood: -6199.817837
EM: Round [207] log likelihood: -6199.815971
EM: Round [208] log likelihood: -6199.814118
EM: Round [209] log likelihood: -6199.812278
EM: Round [210] log likelihood: -6199.810451
EM: Round [211] log likelihood: -6199.808636
EM: Round [212] log likelihood: -6199.806834
EM: Round [213] log likelihood: -6199.805044
EM: Round [214] log likelihood: -6199.803267
EM: Round [215] log likelihood: -6199.801502
EM: Round [216] log likelihood: -6199.799749
EM: Round [217] log likelihood: -6199.798009
EM: Round [218] log likelihood: -6199.796280
EM: Round [219] log likelihood: -6199.794564
EM: Round [220] log likelihood: -6199.792859
EM: Round [221] log likelihood: -6199.791166
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EM: Round [235] log likelihood: -6199.768649
EM: Round [236] log likelihood: -6199.767122
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EM: Round [442] log likelihood: -6199.597182
EM: Round [443] log likelihood: -6199.596794
EM: Round [444] log likelihood: -6199.596409
EM: Round [445] log likelihood: -6199.596027
EM: Round [446] log likelihood: -6199.595647
EM: Round [447] log likelihood: -6199.595269
EM: Round [448] log likelihood: -6199.594894
EM: Round [449] log likelihood: -6199.594521
EM: Round [450] log likelihood: -6199.594151
EM: Round [451] log likelihood: -6199.593783
EM: Round [452] log likelihood: -6199.593417
EM: Round [453] log likelihood: -6199.593054
EM: Round [454] log likelihood: -6199.592693
EM: Round [455] log likelihood: -6199.592335
EM: Round [456] log likelihood: -6199.591978
EM: Round [457] log likelihood: -6199.591624
EM: Round [458] log likelihood: -6199.591273
EM: Round [459] log likelihood: -6199.590923
EM: Round [460] log likelihood: -6199.590576
EM: Round [461] log likelihood: -6199.590231
EM: Round [462] log likelihood: -6199.589889
EM: Round [463] log likelihood: -6199.589548
EM: Round [464] log likelihood: -6199.589210
EM: Round [465] log likelihood: -6199.588874
EM: Round [466] log likelihood: -6199.588540
EM: Round [467] log likelihood: -6199.588208
EM: Round [468] log likelihood: -6199.587878
EM: Round [469] log likelihood: -6199.587551
EM: Round [470] log likelihood: -6199.587225
EM: Round [471] log likelihood: -6199.586902
EM: Round [472] log likelihood: -6199.586580
EM: Round [473] log likelihood: -6199.586261
EM: Round [474] log likelihood: -6199.585944
EM: Round [475] log likelihood: -6199.585629
EM: Round [476] log likelihood: -6199.585316
EM: Round [477] log likelihood: -6199.585005
EM: Round [478] log likelihood: -6199.584696
EM: Round [479] log likelihood: -6199.584389
EM: Round [480] log likelihood: -6199.584084
EM: Round [481] log likelihood: -6199.583780
EM: Round [482] log likelihood: -6199.583479
EM: Round [483] log likelihood: -6199.583180
EM: Round [484] log likelihood: -6199.582883
EM: Round [485] log likelihood: -6199.582587
EM: Round [486] log likelihood: -6199.582294
EM: Round [487] log likelihood: -6199.582002
EM: Round [488] log likelihood: -6199.581712
EM: Round [489] log likelihood: -6199.581424
EM: Round [490] log likelihood: -6199.581138
EM: Round [491] log likelihood: -6199.580854
EM: Round [492] log likelihood: -6199.580571
EM: Round [493] log likelihood: -6199.580291
EM: Round [494] log likelihood: -6199.580012
EM: Round [495] log likelihood: -6199.579735
EM: Round [496] log likelihood: -6199.579460
EM: Round [497] log likelihood: -6199.579186
EM: Round [498] log likelihood: -6199.578915
EM: Round [499] log likelihood: -6199.578645
EM: Round [500] log likelihood: -6199.578376
EM: Round [501] log likelihood: -6199.578110
EM: Round [502] log likelihood: -6199.577845
EM: Round [503] log likelihood: -6199.577582
EM: Round [504] log likelihood: -6199.577320
EM: Round [505] log likelihood: -6199.577061
EM: Round [506] log likelihood: -6199.576803
EM: Round [507] log likelihood: -6199.576546
EM: Round [508] log likelihood: -6199.576291
EM: Round [509] log likelihood: -6199.576038
EM: Round [510] log likelihood: -6199.575787
EM: Round [511] log likelihood: -6199.575537
EM: Round [512] log likelihood: -6199.575288
EM: Round [513] log likelihood: -6199.575042
EM: Round [514] log likelihood: -6199.574797
EM: Round [515] log likelihood: -6199.574553
EM: Round [516] log likelihood: -6199.574311
EM: Round [517] log likelihood: -6199.574070
EM: Round [518] log likelihood: -6199.573832
EM: Round [519] log likelihood: -6199.573594
EM: Round [520] log likelihood: -6199.573358
EM: Round [521] log likelihood: -6199.573124
EM: Round [522] log likelihood: -6199.572891
EM: Round [523] log likelihood: -6199.572660
EM: Round [524] log likelihood: -6199.572430
EM: Round [525] log likelihood: -6199.572201
EM: Round [526] log likelihood: -6199.571974
EM: Round [527] log likelihood: -6199.571749
EM: Round [528] log likelihood: -6199.571525
EM: Round [529] log likelihood: -6199.571302
EM: Round [530] log likelihood: -6199.571081
EM: Round [531] log likelihood: -6199.570861
EM: Round [532] log likelihood: -6199.570643
EM: Round [533] log likelihood: -6199.570426
EM: Round [534] log likelihood: -6199.570210
EM: Round [535] log likelihood: -6199.569996
EM: Round [536] log likelihood: -6199.569783
EM: Round [537] log likelihood: -6199.569572
EM: Round [538] log likelihood: -6199.569361
EM: Round [539] log likelihood: -6199.569153
EM: Round [540] log likelihood: -6199.568945
EM: Round [541] log likelihood: -6199.568739
EM: Round [542] log likelihood: -6199.568534
EM: Round [543] log likelihood: -6199.568331
EM: Round [544] log likelihood: -6199.568128
EM: Round [545] log likelihood: -6199.567927
EM: Round [546] log likelihood: -6199.567728
EM: Round [547] log likelihood: -6199.567529
EM: Round [548] log likelihood: -6199.567332
EM: Round [549] log likelihood: -6199.567137
EM: Round [550] log likelihood: -6199.566942
EM: Round [551] log likelihood: -6199.566749
EM: Round [552] log likelihood: -6199.566557
EM: Round [553] log likelihood: -6199.566366
EM: Round [554] log likelihood: -6199.566176
EM: Round [555] log likelihood: -6199.565988
EM: Round [556] log likelihood: -6199.565800
EM: Round [557] log likelihood: -6199.565614
EM: Round [558] log likelihood: -6199.565429
EM: Round [559] log likelihood: -6199.565246
EM: Round [560] log likelihood: -6199.565063
EM: Round [561] log likelihood: -6199.564882
EM: Round [562] log likelihood: -6199.564702
EM: Round [563] log likelihood: -6199.564523
EM: Round [564] log likelihood: -6199.564345
EM: Round [565] log likelihood: -6199.564168
EM: Round [566] log likelihood: -6199.563992
EM: Round [567] log likelihood: -6199.563818
EM: Round [568] log likelihood: -6199.563644
EM: Round [569] log likelihood: -6199.563472
EM: Round [570] log likelihood: -6199.563301
EM: Round [571] log likelihood: -6199.563131
EM: Round [572] log likelihood: -6199.562962
EM: Round [573] log likelihood: -6199.562794
EM: Round [574] log likelihood: -6199.562627
EM: Round [575] log likelihood: -6199.562461
EM: Round [576] log likelihood: -6199.562296
EM: Round [577] log likelihood: -6199.562133
EM: Round [578] log likelihood: -6199.561970
EM: Round [579] log likelihood: -6199.561808
EM: Round [580] log likelihood: -6199.561648
EM: Round [581] log likelihood: -6199.561488
EM: Round [582] log likelihood: -6199.561330
EM: Round [583] log likelihood: -6199.561172
EM: Round [584] log likelihood: -6199.561016
EM: Round [585] log likelihood: -6199.560860
EM: Round [586] log likelihood: -6199.560706
EM: Round [587] log likelihood: -6199.560552
EM: Round [588] log likelihood: -6199.560399
EM: Round [589] log likelihood: -6199.560248
EM: Round [590] log likelihood: -6199.560097
EM: Round [591] log likelihood: -6199.559948
EM: Round [592] log likelihood: -6199.559799
EM: Round [593] log likelihood: -6199.559651
EM: Round [594] log likelihood: -6199.559504
EM: Round [595] log likelihood: -6199.559358
EM: Round [596] log likelihood: -6199.559213
EM: Round [597] log likelihood: -6199.559069
EM: Round [598] log likelihood: -6199.558926
EM: Round [599] log likelihood: -6199.558784
EM: Round [600] log likelihood: -6199.558643
EM: Round [601] log likelihood: -6199.558502
EM: Round [602] log likelihood: -6199.558363
EM: Round [603] log likelihood: -6199.558224
EM: Round [604] log likelihood: -6199.558086
EM: Round [605] log likelihood: -6199.557949
EM: Round [606] log likelihood: -6199.557813
EM: Round [607] log likelihood: -6199.557678
EM: Round [608] log likelihood: -6199.557544
EM: Round [609] log likelihood: -6199.557411
EM: Round [610] log likelihood: -6199.557278
EM: Round [611] log likelihood: -6199.557146
EM: Round [612] log likelihood: -6199.557015
EM: Round [613] log likelihood: -6199.556885
EM: Round [614] log likelihood: -6199.556756
EM: Round [615] log likelihood: -6199.556628
EM: Round [616] log likelihood: -6199.556500
EM: Round [617] log likelihood: -6199.556373
EM: Round [618] log likelihood: -6199.556247
EM: Round [619] log likelihood: -6199.556122
EM: Round [620] log likelihood: -6199.555998
EM: Round [621] log likelihood: -6199.555874
EM: Round [622] log likelihood: -6199.555752
EM: Round [623] log likelihood: -6199.555629
EM: Round [624] log likelihood: -6199.555508
EM: Round [625] log likelihood: -6199.555388
EM: Round [626] log likelihood: -6199.555268
EM: Round [627] log likelihood: -6199.555149
EM: Round [628] log likelihood: -6199.555031
EM: Round [629] log likelihood: -6199.554914
EM: Round [630] log likelihood: -6199.554797
EM: Round [631] log likelihood: -6199.554681
EM: Round [632] log likelihood: -6199.554566
EM: Round [633] log likelihood: -6199.554451
EM: Round [634] log likelihood: -6199.554338
EM: Round [635] log likelihood: -6199.554224
EM: Round [636] log likelihood: -6199.554112
EM: Round [637] log likelihood: -6199.554001
EM: Round [638] log likelihood: -6199.553890
EM: Round [639] log likelihood: -6199.553780
EM: Round [640] log likelihood: -6199.553670
EM: Round [641] log likelihood: -6199.553561
EM: Round [642] log likelihood: -6199.553453
EM: Round [643] log likelihood: -6199.553346
EM: Round [644] log likelihood: -6199.553239
EM: Round [645] log likelihood: -6199.553133
EM: Round [646] log likelihood: -6199.553028
EM: Round [647] log likelihood: -6199.552923
EM: Round [648] log likelihood: -6199.552819
EM: Round [649] log likelihood: -6199.552716
EM: Round [650] log likelihood: -6199.552613
EM: Round [651] log likelihood: -6199.552511
EM: Round [652] log likelihood: -6199.552409
EM: Round [653] log likelihood: -6199.552309
EM: Round [654] log likelihood: -6199.552209
EM: Round [655] log likelihood: -6199.552109
EM: Stopping iterations at round 655 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam into /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.read_coords > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.frag_coords > /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.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.mozZzLS8CN/fi_workdir/tih_rna_sample_00146_B23WHTKLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -5147.304091
EM: Round [1] log likelihood: -5145.617989
EM: Round [2] log likelihood: -5145.615491
EM: Round [3] log likelihood: -5145.615485
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2_1.fastp.fastq.gz: 296087706
Warning - not locating file: /tmp/nxf.mozZzLS8CN/tih_rna_sample_00146_B23WHTKLT4_2.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000273598.1]
WARNING, no entry stored in dbm for [ENSG00000273598.1]
WARNING, no entry stored in dbm for [ENSG00000273598.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
ls: cannot access 'IGV_inputs': No such file or directory