Done.
-parsing GTF file: /tmp/nxf.Wb46F8YMln/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.Wb46F8YMln/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.Wb46F8YMln/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.Wb46F8YMln/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.Wb46F8YMln/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.Wb46F8YMln/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
22:20:50 : INFO : Done.
-parsing GTF file: /tmp/nxf.Wb46F8YMln/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.Wb46F8YMln/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[570000]   -done parsing /tmp/nxf.Wb46F8YMln/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'excessive soft clipping' => 3757,
          'per_id < 96' => 2557,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 98,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12,
          'low complexity anchor region' => 15,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 7,
          'seq-similar region overlap' => 673,
          ' ** passed ** ' => 2082,
          'num genes matched < 2' => 16
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.Wb46F8YMln/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[83000]   -fusion SPANNING read extraction for scaff: ATP9A--KIF3B

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[11000]   -fusion SPANNING read extraction for scaff: MAP1LC3A--TTLL9

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[65000]   
[66000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[60000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[70000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[15000]   -fusion SPANNING read extraction for scaff: RPRD1A--MOCOS

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[89000]   
[90000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[64000]   -fusion SPANNING read extraction for scaff: TOX2--TSHZ2

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[42000]   -fusion SPANNING read extraction for scaff: TOX2--AL109930.1

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[26000]   -fusion SPANNING read extraction for scaff: TTC39C--CABLES1

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[16000]   -fusion SPANNING read extraction for scaff: TTLL9--CABLES1

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[21000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 19735,
          'seq similar region alignment' => 54545
        };
EM: Starting log likelihood: -1663.953912
EM: Round [1] log likelihood: -1663.950762
EM: Round [2] log likelihood: -1663.947643
EM: Round [3] log likelihood: -1663.944553
EM: Round [4] log likelihood: -1663.941492
EM: Round [5] log likelihood: -1663.938459
EM: Round [6] log likelihood: -1663.935455
EM: Round [7] log likelihood: -1663.932480
EM: Round [8] log likelihood: -1663.929532
EM: Round [9] log likelihood: -1663.926611
EM: Round [10] log likelihood: -1663.923717
EM: Round [11] log likelihood: -1663.920850
EM: Round [12] log likelihood: -1663.918010
EM: Round [13] log likelihood: -1663.915195
EM: Round [14] log likelihood: -1663.912406
EM: Round [15] log likelihood: -1663.909643
EM: Round [16] log likelihood: -1663.906905
EM: Round [17] log likelihood: -1663.904191
EM: Round [18] log likelihood: -1663.901502
EM: Round [19] log likelihood: -1663.898838
EM: Round [20] log likelihood: -1663.896197
EM: Round [21] log likelihood: -1663.893580
EM: Round [22] log likelihood: -1663.890987
EM: Round [23] log likelihood: -1663.888417
EM: Round [24] log likelihood: -1663.885869
EM: Round [25] log likelihood: -1663.883345
EM: Round [26] log likelihood: -1663.880842
EM: Round [27] log likelihood: -1663.878362
EM: Round [28] log likelihood: -1663.875904
EM: Round [29] log likelihood: -1663.873467
EM: Round [30] log likelihood: -1663.871052
EM: Round [31] log likelihood: -1663.868658
EM: Round [32] log likelihood: -1663.866284
EM: Round [33] log likelihood: -1663.863932
EM: Round [34] log likelihood: -1663.861600
EM: Round [35] log likelihood: -1663.859288
EM: Round [36] log likelihood: -1663.856996
EM: Round [37] log likelihood: -1663.854724
EM: Round [38] log likelihood: -1663.852471
EM: Round [39] log likelihood: -1663.850238
EM: Round [40] log likelihood: -1663.848024
EM: Round [41] log likelihood: -1663.845829
EM: Round [42] log likelihood: -1663.843653
EM: Round [43] log likelihood: -1663.841495
EM: Round [44] log likelihood: -1663.839355
EM: Round [45] log likelihood: -1663.837234
EM: Round [46] log likelihood: -1663.835131
EM: Round [47] log likelihood: -1663.833045
EM: Round [48] log likelihood: -1663.830977
EM: Round [49] log likelihood: -1663.828927
EM: Round [50] log likelihood: -1663.826893
EM: Round [51] log likelihood: -1663.824877
EM: Round [52] log likelihood: -1663.822877
EM: Round [53] log likelihood: -1663.820895
EM: Round [54] log likelihood: -1663.818928
EM: Round [55] log likelihood: -1663.816978
EM: Round [56] log likelihood: -1663.815045
EM: Round [57] log likelihood: -1663.813127
EM: Round [58] log likelihood: -1663.811225
EM: Round [59] log likelihood: -1663.809339
EM: Round [60] log likelihood: -1663.807468
EM: Round [61] log likelihood: -1663.805613
EM: Round [62] log likelihood: -1663.803773
EM: Round [63] log likelihood: -1663.801948
EM: Round [64] log likelihood: -1663.800138
EM: Round [65] log likelihood: -1663.798343
EM: Round [66] log likelihood: -1663.796562
EM: Round [67] log likelihood: -1663.794796
EM: Round [68] log likelihood: -1663.793044
EM: Round [69] log likelihood: -1663.791306
EM: Round [70] log likelihood: -1663.789583
EM: Round [71] log likelihood: -1663.787873
EM: Round [72] log likelihood: -1663.786177
EM: Round [73] log likelihood: -1663.784495
EM: Round [74] log likelihood: -1663.782826
EM: Round [75] log likelihood: -1663.781170
EM: Round [76] log likelihood: -1663.779528
EM: Round [77] log likelihood: -1663.777899
EM: Round [78] log likelihood: -1663.776283
EM: Round [79] log likelihood: -1663.774680
EM: Round [80] log likelihood: -1663.773090
EM: Round [81] log likelihood: -1663.771512
EM: Round [82] log likelihood: -1663.769947
EM: Round [83] log likelihood: -1663.768394
EM: Round [84] log likelihood: -1663.766853
EM: Round [85] log likelihood: -1663.765325
EM: Round [86] log likelihood: -1663.763809
EM: Round [87] log likelihood: -1663.762304
EM: Round [88] log likelihood: -1663.760812
EM: Round [89] log likelihood: -1663.759331
EM: Round [90] log likelihood: -1663.757861
EM: Round [91] log likelihood: -1663.756404
EM: Round [92] log likelihood: -1663.754957
EM: Round [93] log likelihood: -1663.753522
EM: Round [94] log likelihood: -1663.752098
EM: Round [95] log likelihood: -1663.750685
EM: Round [96] log likelihood: -1663.749283
EM: Round [97] log likelihood: -1663.747892
EM: Round [98] log likelihood: -1663.746512
EM: Round [99] log likelihood: -1663.745142
EM: Round [100] log likelihood: -1663.743783
EM: Round [101] log likelihood: -1663.742435
EM: Round [102] log likelihood: -1663.741097
EM: Round [103] log likelihood: -1663.739769
EM: Round [104] log likelihood: -1663.738451
EM: Round [105] log likelihood: -1663.737144
EM: Round [106] log likelihood: -1663.735846
EM: Round [107] log likelihood: -1663.734559
EM: Round [108] log likelihood: -1663.733281
EM: Round [109] log likelihood: -1663.732013
EM: Round [110] log likelihood: -1663.730755
EM: Round [111] log likelihood: -1663.729506
EM: Round [112] log likelihood: -1663.728267
EM: Round [113] log likelihood: -1663.727037
EM: Round [114] log likelihood: -1663.725816
EM: Round [115] log likelihood: -1663.724605
EM: Round [116] log likelihood: -1663.723403
EM: Round [117] log likelihood: -1663.722210
EM: Round [118] log likelihood: -1663.721026
EM: Round [119] log likelihood: -1663.719851
EM: Round [120] log likelihood: -1663.718685
EM: Round [121] log likelihood: -1663.717527
EM: Round [122] log likelihood: -1663.716378
EM: Round [123] log likelihood: -1663.715238
EM: Round [124] log likelihood: -1663.714107
EM: Round [125] log likelihood: -1663.712984
EM: Round [126] log likelihood: -1663.711869
EM: Round [127] log likelihood: -1663.710763
EM: Round [128] log likelihood: -1663.709664
EM: Round [129] log likelihood: -1663.708575
EM: Round [130] log likelihood: -1663.707493
EM: Round [131] log likelihood: -1663.706419
EM: Round [132] log likelihood: -1663.705353
EM: Round [133] log likelihood: -1663.704295
EM: Round [134] log likelihood: -1663.703245
EM: Round [135] log likelihood: -1663.702203
EM: Round [136] log likelihood: -1663.701169
EM: Round [137] log likelihood: -1663.700142
EM: Round [138] log likelihood: -1663.699122
EM: Round [139] log likelihood: -1663.698111
EM: Round [140] log likelihood: -1663.697106
EM: Round [141] log likelihood: -1663.696109
EM: Round [142] log likelihood: -1663.695120
EM: Round [143] log likelihood: -1663.694137
EM: Round [144] log likelihood: -1663.693162
EM: Round [145] log likelihood: -1663.692194
EM: Round [146] log likelihood: -1663.691234
EM: Round [147] log likelihood: -1663.690280
EM: Round [148] log likelihood: -1663.689333
EM: Round [149] log likelihood: -1663.688393
EM: Round [150] log likelihood: -1663.687460
EM: Round [151] log likelihood: -1663.686534
EM: Round [152] log likelihood: -1663.685614
EM: Round [153] log likelihood: -1663.684701
EM: Round [154] log likelihood: -1663.683795
EM: Round [155] log likelihood: -1663.682895
EM: Round [156] log likelihood: -1663.682002
EM: Round [157] log likelihood: -1663.681116
EM: Round [158] log likelihood: -1663.680236
EM: Round [159] log likelihood: -1663.679362
EM: Round [160] log likelihood: -1663.678494
EM: Round [161] log likelihood: -1663.677633
EM: Round [162] log likelihood: -1663.676778
EM: Round [163] log likelihood: -1663.675929
EM: Round [164] log likelihood: -1663.675087
EM: Round [165] log likelihood: -1663.674250
EM: Round [166] log likelihood: -1663.673419
EM: Round [167] log likelihood: -1663.672595
EM: Round [168] log likelihood: -1663.671776
EM: Round [169] log likelihood: -1663.670963
EM: Round [170] log likelihood: -1663.670156
EM: Round [171] log likelihood: -1663.669355
EM: Round [172] log likelihood: -1663.668560
EM: Round [173] log likelihood: -1663.667770
EM: Round [174] log likelihood: -1663.666986
EM: Round [175] log likelihood: -1663.666207
EM: Round [176] log likelihood: -1663.665434
EM: Round [177] log likelihood: -1663.664667
EM: Round [178] log likelihood: -1663.663905
EM: Round [179] log likelihood: -1663.663148
EM: Round [180] log likelihood: -1663.662397
EM: Round [181] log likelihood: -1663.661651
EM: Round [182] log likelihood: -1663.660911
EM: Round [183] log likelihood: -1663.660175
EM: Round [184] log likelihood: -1663.659445
EM: Round [185] log likelihood: -1663.658720
EM: Round [186] log likelihood: -1663.658001
EM: Round [187] log likelihood: -1663.657286
EM: Round [188] log likelihood: -1663.656576
EM: Round [189] log likelihood: -1663.655872
EM: Round [190] log likelihood: -1663.655172
EM: Round [191] log likelihood: -1663.654478
EM: Round [192] log likelihood: -1663.653788
EM: Round [193] log likelihood: -1663.653103
EM: Round [194] log likelihood: -1663.652423
EM: Round [195] log likelihood: -1663.651748
EM: Round [196] log likelihood: -1663.651077
EM: Round [197] log likelihood: -1663.650411
EM: Round [198] log likelihood: -1663.649750
EM: Round [199] log likelihood: -1663.649094
EM: Round [200] log likelihood: -1663.648442
EM: Round [201] log likelihood: -1663.647795
EM: Round [202] log likelihood: -1663.647152
EM: Round [203] log likelihood: -1663.646514
EM: Round [204] log likelihood: -1663.645880
EM: Round [205] log likelihood: -1663.645251
EM: Round [206] log likelihood: -1663.644626
EM: Round [207] log likelihood: -1663.644005
EM: Round [208] log likelihood: -1663.643389
EM: Round [209] log likelihood: -1663.642777
EM: Round [210] log likelihood: -1663.642169
EM: Round [211] log likelihood: -1663.641566
EM: Round [212] log likelihood: -1663.640967
EM: Round [213] log likelihood: -1663.640371
EM: Round [214] log likelihood: -1663.639781
EM: Round [215] log likelihood: -1663.639194
EM: Round [216] log likelihood: -1663.638611
EM: Round [217] log likelihood: -1663.638032
EM: Round [218] log likelihood: -1663.637458
EM: Round [219] log likelihood: -1663.636887
EM: Round [220] log likelihood: -1663.636320
EM: Round [221] log likelihood: -1663.635757
EM: Round [222] log likelihood: -1663.635199
EM: Round [223] log likelihood: -1663.634644
EM: Round [224] log likelihood: -1663.634092
EM: Round [225] log likelihood: -1663.633545
EM: Round [226] log likelihood: -1663.633001
EM: Round [227] log likelihood: -1663.632462
EM: Round [228] log likelihood: -1663.631925
EM: Round [229] log likelihood: -1663.631393
EM: Round [230] log likelihood: -1663.630864
EM: Round [231] log likelihood: -1663.630339
EM: Round [232] log likelihood: -1663.629818
EM: Round [233] log likelihood: -1663.629300
EM: Round [234] log likelihood: -1663.628785
EM: Round [235] log likelihood: -1663.628275
EM: Round [236] log likelihood: -1663.627767
EM: Round [237] log likelihood: -1663.627264
EM: Round [238] log likelihood: -1663.626763
EM: Round [239] log likelihood: -1663.626266
EM: Round [240] log likelihood: -1663.625773
EM: Round [241] log likelihood: -1663.625283
EM: Round [242] log likelihood: -1663.624796
EM: Round [243] log likelihood: -1663.624313
EM: Round [244] log likelihood: -1663.623833
EM: Round [245] log likelihood: -1663.623356
EM: Round [246] log likelihood: -1663.622882
EM: Round [247] log likelihood: -1663.622412
EM: Round [248] log likelihood: -1663.621945
EM: Round [249] log likelihood: -1663.621481
EM: Round [250] log likelihood: -1663.621020
EM: Round [251] log likelihood: -1663.620563
EM: Round [252] log likelihood: -1663.620108
EM: Round [253] log likelihood: -1663.619657
EM: Round [254] log likelihood: -1663.619208
EM: Round [255] log likelihood: -1663.618763
EM: Round [256] log likelihood: -1663.618321
EM: Round [257] log likelihood: -1663.617882
EM: Round [258] log likelihood: -1663.617446
EM: Round [259] log likelihood: -1663.617012
EM: Round [260] log likelihood: -1663.616582
EM: Round [261] log likelihood: -1663.616155
EM: Round [262] log likelihood: -1663.615730
EM: Round [263] log likelihood: -1663.615309
EM: Round [264] log likelihood: -1663.614890
EM: Round [265] log likelihood: -1663.614474
EM: Round [266] log likelihood: -1663.614061
EM: Round [267] log likelihood: -1663.613651
EM: Round [268] log likelihood: -1663.613243
EM: Round [269] log likelihood: -1663.612838
EM: Round [270] log likelihood: -1663.612436
EM: Round [271] log likelihood: -1663.612037
EM: Round [272] log likelihood: -1663.611641
EM: Round [273] log likelihood: -1663.611247
EM: Round [274] log likelihood: -1663.610855
EM: Round [275] log likelihood: -1663.610467
EM: Round [276] log likelihood: -1663.610081
EM: Round [277] log likelihood: -1663.609698
EM: Round [278] log likelihood: -1663.609317
EM: Round [279] log likelihood: -1663.608939
EM: Round [280] log likelihood: -1663.608563
EM: Round [281] log likelihood: -1663.608190
EM: Round [282] log likelihood: -1663.607819
EM: Round [283] log likelihood: -1663.607451
EM: Round [284] log likelihood: -1663.607086
EM: Round [285] log likelihood: -1663.606722
EM: Round [286] log likelihood: -1663.606362
EM: Round [287] log likelihood: -1663.606003
EM: Round [288] log likelihood: -1663.605648
EM: Round [289] log likelihood: -1663.605294
EM: Round [290] log likelihood: -1663.604943
EM: Round [291] log likelihood: -1663.604594
EM: Round [292] log likelihood: -1663.604248
EM: Round [293] log likelihood: -1663.603904
EM: Round [294] log likelihood: -1663.603562
EM: Round [295] log likelihood: -1663.603222
EM: Round [296] log likelihood: -1663.602885
EM: Round [297] log likelihood: -1663.602550
EM: Round [298] log likelihood: -1663.602218
EM: Round [299] log likelihood: -1663.601887
EM: Round [300] log likelihood: -1663.601559
EM: Round [301] log likelihood: -1663.601233
EM: Round [302] log likelihood: -1663.600909
EM: Round [303] log likelihood: -1663.600587
EM: Round [304] log likelihood: -1663.600268
EM: Round [305] log likelihood: -1663.599950
EM: Round [306] log likelihood: -1663.599635
EM: Round [307] log likelihood: -1663.599322
EM: Round [308] log likelihood: -1663.599011
EM: Round [309] log likelihood: -1663.598702
EM: Round [310] log likelihood: -1663.598395
EM: Round [311] log likelihood: -1663.598090
EM: Round [312] log likelihood: -1663.597787
EM: Round [313] log likelihood: -1663.597486
EM: Round [314] log likelihood: -1663.597187
EM: Round [315] log likelihood: -1663.596890
EM: Round [316] log likelihood: -1663.596595
EM: Round [317] log likelihood: -1663.596302
EM: Round [318] log likelihood: -1663.596011
EM: Round [319] log likelihood: -1663.595722
EM: Round [320] log likelihood: -1663.595435
EM: Round [321] log likelihood: -1663.595150
EM: Round [322] log likelihood: -1663.594867
EM: Round [323] log likelihood: -1663.594585
EM: Round [324] log likelihood: -1663.594306
EM: Round [325] log likelihood: -1663.594028
EM: Round [326] log likelihood: -1663.593752
EM: Round [327] log likelihood: -1663.593478
EM: Round [328] log likelihood: -1663.593206
EM: Round [329] log likelihood: -1663.592936
EM: Round [330] log likelihood: -1663.592667
EM: Round [331] log likelihood: -1663.592400
EM: Round [332] log likelihood: -1663.592135
EM: Round [333] log likelihood: -1663.591872
EM: Round [334] log likelihood: -1663.591610
EM: Round [335] log likelihood: -1663.591351
EM: Round [336] log likelihood: -1663.591093
EM: Round [337] log likelihood: -1663.590836
EM: Round [338] log likelihood: -1663.590581
EM: Round [339] log likelihood: -1663.590328
EM: Round [340] log likelihood: -1663.590077
EM: Round [341] log likelihood: -1663.589828
EM: Round [342] log likelihood: -1663.589580
EM: Round [343] log likelihood: -1663.589333
EM: Round [344] log likelihood: -1663.589088
EM: Round [345] log likelihood: -1663.588845
EM: Round [346] log likelihood: -1663.588604
EM: Round [347] log likelihood: -1663.588364
EM: Round [348] log likelihood: -1663.588126
EM: Round [349] log likelihood: -1663.587889
EM: Round [350] log likelihood: -1663.587654
EM: Round [351] log likelihood: -1663.587420
EM: Round [352] log likelihood: -1663.587188
EM: Round [353] log likelihood: -1663.586957
EM: Round [354] log likelihood: -1663.586728
EM: Round [355] log likelihood: -1663.586501
EM: Round [356] log likelihood: -1663.586275
EM: Round [357] log likelihood: -1663.586050
EM: Round [358] log likelihood: -1663.585827
EM: Round [359] log likelihood: -1663.585606
EM: Round [360] log likelihood: -1663.585386
EM: Round [361] log likelihood: -1663.585167
EM: Round [362] log likelihood: -1663.584950
EM: Round [363] log likelihood: -1663.584734
EM: Round [364] log likelihood: -1663.584519
EM: Round [365] log likelihood: -1663.584306
EM: Round [366] log likelihood: -1663.584095
EM: Round [367] log likelihood: -1663.583885
EM: Round [368] log likelihood: -1663.583676
EM: Round [369] log likelihood: -1663.583468
EM: Round [370] log likelihood: -1663.583262
EM: Round [371] log likelihood: -1663.583058
EM: Round [372] log likelihood: -1663.582854
EM: Round [373] log likelihood: -1663.582652
EM: Round [374] log likelihood: -1663.582452
EM: Round [375] log likelihood: -1663.582252
EM: Round [376] log likelihood: -1663.582054
EM: Round [377] log likelihood: -1663.581857
EM: Round [378] log likelihood: -1663.581662
EM: Round [379] log likelihood: -1663.581468
EM: Round [380] log likelihood: -1663.581275
EM: Round [381] log likelihood: -1663.581083
EM: Round [382] log likelihood: -1663.580893
EM: Round [383] log likelihood: -1663.580704
EM: Round [384] log likelihood: -1663.580516
EM: Round [385] log likelihood: -1663.580329
EM: Round [386] log likelihood: -1663.580144
EM: Round [387] log likelihood: -1663.579959
EM: Round [388] log likelihood: -1663.579776
EM: Round [389] log likelihood: -1663.579594
EM: Round [390] log likelihood: -1663.579414
EM: Round [391] log likelihood: -1663.579234
EM: Round [392] log likelihood: -1663.579056
EM: Round [393] log likelihood: -1663.578879
EM: Round [394] log likelihood: -1663.578703
EM: Round [395] log likelihood: -1663.578528
EM: Round [396] log likelihood: -1663.578355
EM: Round [397] log likelihood: -1663.578182
EM: Round [398] log likelihood: -1663.578011
EM: Round [399] log likelihood: -1663.577840
EM: Round [400] log likelihood: -1663.577671
EM: Round [401] log likelihood: -1663.577503
EM: Round [402] log likelihood: -1663.577336
EM: Round [403] log likelihood: -1663.577170
EM: Round [404] log likelihood: -1663.577006
EM: Round [405] log likelihood: -1663.576842
EM: Round [406] log likelihood: -1663.576679
EM: Round [407] log likelihood: -1663.576518
EM: Round [408] log likelihood: -1663.576357
EM: Round [409] log likelihood: -1663.576198
EM: Round [410] log likelihood: -1663.576039
EM: Round [411] log likelihood: -1663.575882
EM: Round [412] log likelihood: -1663.575725
EM: Round [413] log likelihood: -1663.575570
EM: Round [414] log likelihood: -1663.575416
EM: Round [415] log likelihood: -1663.575262
EM: Round [416] log likelihood: -1663.575110
EM: Round [417] log likelihood: -1663.574959
EM: Round [418] log likelihood: -1663.574808
EM: Round [419] log likelihood: -1663.574659
EM: Round [420] log likelihood: -1663.574511
EM: Round [421] log likelihood: -1663.574363
EM: Round [422] log likelihood: -1663.574217
EM: Round [423] log likelihood: -1663.574071
EM: Round [424] log likelihood: -1663.573927
EM: Round [425] log likelihood: -1663.573783
EM: Round [426] log likelihood: -1663.573640
EM: Round [427] log likelihood: -1663.573499
EM: Round [428] log likelihood: -1663.573358
EM: Round [429] log likelihood: -1663.573218
EM: Round [430] log likelihood: -1663.573079
EM: Round [431] log likelihood: -1663.572941
EM: Round [432] log likelihood: -1663.572803
EM: Round [433] log likelihood: -1663.572667
EM: Round [434] log likelihood: -1663.572532
EM: Round [435] log likelihood: -1663.572397
EM: Round [436] log likelihood: -1663.572263
EM: Round [437] log likelihood: -1663.572131
EM: Round [438] log likelihood: -1663.571999
EM: Round [439] log likelihood: -1663.571868
EM: Round [440] log likelihood: -1663.571737
EM: Round [441] log likelihood: -1663.571608
EM: Round [442] log likelihood: -1663.571479
EM: Round [443] log likelihood: -1663.571352
EM: Round [444] log likelihood: -1663.571225
EM: Round [445] log likelihood: -1663.571099
EM: Round [446] log likelihood: -1663.570974
EM: Round [447] log likelihood: -1663.570849
EM: Round [448] log likelihood: -1663.570726
EM: Round [449] log likelihood: -1663.570603
EM: Round [450] log likelihood: -1663.570481
EM: Round [451] log likelihood: -1663.570360
EM: Round [452] log likelihood: -1663.570239
EM: Round [453] log likelihood: -1663.570119
EM: Round [454] log likelihood: -1663.570001
EM: Round [455] log likelihood: -1663.569882
EM: Round [456] log likelihood: -1663.569765
EM: Round [457] log likelihood: -1663.569649
EM: Round [458] log likelihood: -1663.569533
EM: Round [459] log likelihood: -1663.569418
EM: Round [460] log likelihood: -1663.569303
EM: Round [461] log likelihood: -1663.569190
EM: Round [462] log likelihood: -1663.569077
EM: Round [463] log likelihood: -1663.568965
EM: Round [464] log likelihood: -1663.568853
EM: Round [465] log likelihood: -1663.568743
EM: Round [466] log likelihood: -1663.568633
EM: Round [467] log likelihood: -1663.568523
EM: Round [468] log likelihood: -1663.568415
EM: Round [469] log likelihood: -1663.568307
EM: Round [470] log likelihood: -1663.568200
EM: Round [471] log likelihood: -1663.568094
EM: Round [472] log likelihood: -1663.567988
EM: Round [473] log likelihood: -1663.567883
EM: Round [474] log likelihood: -1663.567778
EM: Round [475] log likelihood: -1663.567675
EM: Round [476] log likelihood: -1663.567572
EM: Round [477] log likelihood: -1663.567469
EM: Round [478] log likelihood: -1663.567367
EM: Round [479] log likelihood: -1663.567266
EM: Round [480] log likelihood: -1663.567166
EM: Round [481] log likelihood: -1663.567066
EM: Stopping iterations at round 481 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.Wb46F8YMln/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.Wb46F8YMln/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.Wb46F8YMln/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Wb46F8YMln/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.Wb46F8YMln/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Wb46F8YMln/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.Wb46F8YMln/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Wb46F8YMln/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_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.Wb46F8YMln/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_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.Wb46F8YMln/fi_workdir/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Wb46F8YMln/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.Wb46F8YMln/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1629.060032
EM: Round [1] log likelihood: -1629.060032
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.Wb46F8YMln/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296445688
Warning - not locating file: /tmp/nxf.Wb46F8YMln/aih-tih-sc-f8efb2-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
ls: cannot access 'IGV_inputs': No such file or directory