Done.
-parsing GTF file: /tmp/nxf.zYieQzYkmk/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.zYieQzYkmk/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.zYieQzYkmk/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.zYieQzYkmk/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.zYieQzYkmk/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.zYieQzYkmk/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
10:05:02 : INFO : Done.
-parsing GTF file: /tmp/nxf.zYieQzYkmk/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.zYieQzYkmk/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[5810000] -done parsing /tmp/nxf.zYieQzYkmk/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'low complexity anchor region' => 6,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 2978,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 49,
'exons hit < 2' => 33,
'num genes matched < 2' => 22,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 456,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 2070,
'small anchor length' => 20,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 732,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3876,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 6,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 146,
'excessive soft clipping' => 80220,
'seq-similar region overlap' => 380,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 812,
'per_id < 96' => 82136,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 1138,
' ** passed ** ' => 4521,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 4466
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.zYieQzYkmk/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[129000] -fusion SPANNING read extraction for scaff: AC060809.1--ERBB4
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[53000] -fusion SPANNING read extraction for scaff: ARSG--DPH1
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[59000] -fusion SPANNING read extraction for scaff: BMP2K--PTPRT
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[21000] -fusion SPANNING read extraction for scaff: CDK19--ROS1
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[140000] -fusion SPANNING read extraction for scaff: CEP43--ERBB4
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[9000] -fusion SPANNING read extraction for scaff: DECR1--DPYS
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[9000] -fusion SPANNING read extraction for scaff: DECR1--AP002847.1
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[57000] -fusion SPANNING read extraction for scaff: DPH1--PIK3R6
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[35000] -fusion SPANNING read extraction for scaff: EXOC4--TMEM212-AS1
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[77000] -fusion SPANNING read extraction for scaff: EXOC4--NUP205
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[3000] -fusion SPANNING read extraction for scaff: FAM227B--SEMA3D
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[39000] -fusion SPANNING read extraction for scaff: HSPD1--AC068489.1
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[39000] -fusion SPANNING read extraction for scaff: HSPD1--LLPHP3
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[179000] -fusion SPANNING read extraction for scaff: KIAA1109--SPATA5
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[15000] -fusion SPANNING read extraction for scaff: MEIS2--SEMA3D
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[14000] -fusion SPANNING read extraction for scaff: MEIS2--LINC02490
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[14000] -fusion SPANNING read extraction for scaff: MEIS2--AC066614.1
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[16000] -fusion SPANNING read extraction for scaff: MEIS2--FAM227B
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[45000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[43000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[43000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[153000] -fusion SPANNING read extraction for scaff: PIK3CA--TBC1D32
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[34000] -fusion SPANNING read extraction for scaff: RDH10--SPAG1
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[89000] -fusion SPANNING read extraction for scaff: SHANK2--AC104042.1
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[89000] -fusion SPANNING read extraction for scaff: SHANK2--AC061997.1
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[159000] -fusion SPANNING read extraction for scaff: SKIL--NCEH1
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[30000] -fusion SPANNING read extraction for scaff: SPATA5--DCHS2
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[47000] -fusion SPANNING read extraction for scaff: SPIDR--ZNF595
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[41000] -fusion SPANNING read extraction for scaff: TUBGCP2--AC104640.2
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[41000] -fusion SPANNING read extraction for scaff: TUBGCP2--AC117434.1
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[20000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[76000] -fusion SPANNING read extraction for scaff: UAP1--INO80
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[3979000] -fusion SPANNING read extraction for scaff: ZCCHC14--IGH-@-ext
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 18509,
'seq similar region alignment' => 37114
};
EM: Starting log likelihood: -4029.453824
EM: Round [1] log likelihood: -4028.974694
EM: Round [2] log likelihood: -4028.920074
EM: Round [3] log likelihood: -4028.890623
EM: Round [4] log likelihood: -4028.863222
EM: Round [5] log likelihood: -4028.836496
EM: Round [6] log likelihood: -4028.810349
EM: Round [7] log likelihood: -4028.784760
EM: Round [8] log likelihood: -4028.759713
EM: Round [9] log likelihood: -4028.735194
EM: Round [10] log likelihood: -4028.711189
EM: Round [11] log likelihood: -4028.687683
EM: Round [12] log likelihood: -4028.664663
EM: Round [13] log likelihood: -4028.642117
EM: Round [14] log likelihood: -4028.620032
EM: Round [15] log likelihood: -4028.598397
EM: Round [16] log likelihood: -4028.577200
EM: Round [17] log likelihood: -4028.556429
EM: Round [18] log likelihood: -4028.536075
EM: Round [19] log likelihood: -4028.516126
EM: Round [20] log likelihood: -4028.496573
EM: Round [21] log likelihood: -4028.477406
EM: Round [22] log likelihood: -4028.458615
EM: Round [23] log likelihood: -4028.440192
EM: Round [24] log likelihood: -4028.422127
EM: Round [25] log likelihood: -4028.404412
EM: Round [26] log likelihood: -4028.387039
EM: Round [27] log likelihood: -4028.370000
EM: Round [28] log likelihood: -4028.353287
EM: Round [29] log likelihood: -4028.336892
EM: Round [30] log likelihood: -4028.320808
EM: Round [31] log likelihood: -4028.305028
EM: Round [32] log likelihood: -4028.289545
EM: Round [33] log likelihood: -4028.274353
EM: Round [34] log likelihood: -4028.259444
EM: Round [35] log likelihood: -4028.244813
EM: Round [36] log likelihood: -4028.230453
EM: Round [37] log likelihood: -4028.216358
EM: Round [38] log likelihood: -4028.202523
EM: Round [39] log likelihood: -4028.188942
EM: Round [40] log likelihood: -4028.175609
EM: Round [41] log likelihood: -4028.162520
EM: Round [42] log likelihood: -4028.149668
EM: Round [43] log likelihood: -4028.137049
EM: Round [44] log likelihood: -4028.124657
EM: Round [45] log likelihood: -4028.112489
EM: Round [46] log likelihood: -4028.100539
EM: Round [47] log likelihood: -4028.088803
EM: Round [48] log likelihood: -4028.077277
EM: Round [49] log likelihood: -4028.065955
EM: Round [50] log likelihood: -4028.054835
EM: Round [51] log likelihood: -4028.043911
EM: Round [52] log likelihood: -4028.033179
EM: Round [53] log likelihood: -4028.022637
EM: Round [54] log likelihood: -4028.012280
EM: Round [55] log likelihood: -4028.002104
EM: Round [56] log likelihood: -4027.992105
EM: Round [57] log likelihood: -4027.982281
EM: Round [58] log likelihood: -4027.972628
EM: Round [59] log likelihood: -4027.963142
EM: Round [60] log likelihood: -4027.953819
EM: Round [61] log likelihood: -4027.944658
EM: Round [62] log likelihood: -4027.935655
EM: Round [63] log likelihood: -4027.926806
EM: Round [64] log likelihood: -4027.918109
EM: Round [65] log likelihood: -4027.909560
EM: Round [66] log likelihood: -4027.901158
EM: Round [67] log likelihood: -4027.892898
EM: Round [68] log likelihood: -4027.884779
EM: Round [69] log likelihood: -4027.876798
EM: Round [70] log likelihood: -4027.868952
EM: Round [71] log likelihood: -4027.861238
EM: Round [72] log likelihood: -4027.853654
EM: Round [73] log likelihood: -4027.846198
EM: Round [74] log likelihood: -4027.838868
EM: Round [75] log likelihood: -4027.831660
EM: Round [76] log likelihood: -4027.824573
EM: Round [77] log likelihood: -4027.817604
EM: Round [78] log likelihood: -4027.810752
EM: Round [79] log likelihood: -4027.804013
EM: Round [80] log likelihood: -4027.797387
EM: Round [81] log likelihood: -4027.790871
EM: Round [82] log likelihood: -4027.784462
EM: Round [83] log likelihood: -4027.778160
EM: Round [84] log likelihood: -4027.771962
EM: Round [85] log likelihood: -4027.765866
EM: Round [86] log likelihood: -4027.759870
EM: Round [87] log likelihood: -4027.753973
EM: Round [88] log likelihood: -4027.748173
EM: Round [89] log likelihood: -4027.742468
EM: Round [90] log likelihood: -4027.736857
EM: Round [91] log likelihood: -4027.731337
EM: Round [92] log likelihood: -4027.725907
EM: Round [93] log likelihood: -4027.720566
EM: Round [94] log likelihood: -4027.715311
EM: Round [95] log likelihood: -4027.710143
EM: Round [96] log likelihood: -4027.705058
EM: Round [97] log likelihood: -4027.700056
EM: Round [98] log likelihood: -4027.695134
EM: Round [99] log likelihood: -4027.690293
EM: Round [100] log likelihood: -4027.685529
EM: Round [101] log likelihood: -4027.680843
EM: Round [102] log likelihood: -4027.676232
EM: Round [103] log likelihood: -4027.671695
EM: Round [104] log likelihood: -4027.667232
EM: Round [105] log likelihood: -4027.662840
EM: Round [106] log likelihood: -4027.658518
EM: Round [107] log likelihood: -4027.654266
EM: Round [108] log likelihood: -4027.650082
EM: Round [109] log likelihood: -4027.645965
EM: Round [110] log likelihood: -4027.641914
EM: Round [111] log likelihood: -4027.637927
EM: Round [112] log likelihood: -4027.634005
EM: Round [113] log likelihood: -4027.630144
EM: Round [114] log likelihood: -4027.626345
EM: Round [115] log likelihood: -4027.622607
EM: Round [116] log likelihood: -4027.618928
EM: Round [117] log likelihood: -4027.615307
EM: Round [118] log likelihood: -4027.611744
EM: Round [119] log likelihood: -4027.608237
EM: Round [120] log likelihood: -4027.604786
EM: Round [121] log likelihood: -4027.601389
EM: Round [122] log likelihood: -4027.598047
EM: Round [123] log likelihood: -4027.594757
EM: Round [124] log likelihood: -4027.591518
EM: Round [125] log likelihood: -4027.588331
EM: Round [126] log likelihood: -4027.585195
EM: Round [127] log likelihood: -4027.582107
EM: Round [128] log likelihood: -4027.579068
EM: Round [129] log likelihood: -4027.576077
EM: Round [130] log likelihood: -4027.573133
EM: Round [131] log likelihood: -4027.570235
EM: Round [132] log likelihood: -4027.567383
EM: Round [133] log likelihood: -4027.564575
EM: Round [134] log likelihood: -4027.561812
EM: Round [135] log likelihood: -4027.559091
EM: Round [136] log likelihood: -4027.556413
EM: Round [137] log likelihood: -4027.553777
EM: Round [138] log likelihood: -4027.551183
EM: Round [139] log likelihood: -4027.548628
EM: Round [140] log likelihood: -4027.546114
EM: Round [141] log likelihood: -4027.543639
EM: Round [142] log likelihood: -4027.541202
EM: Round [143] log likelihood: -4027.538804
EM: Round [144] log likelihood: -4027.536442
EM: Round [145] log likelihood: -4027.534118
EM: Round [146] log likelihood: -4027.531829
EM: Round [147] log likelihood: -4027.529576
EM: Round [148] log likelihood: -4027.527358
EM: Round [149] log likelihood: -4027.525175
EM: Round [150] log likelihood: -4027.523025
EM: Round [151] log likelihood: -4027.520909
EM: Round [152] log likelihood: -4027.518826
EM: Round [153] log likelihood: -4027.516774
EM: Round [154] log likelihood: -4027.514755
EM: Round [155] log likelihood: -4027.512767
EM: Round [156] log likelihood: -4027.510809
EM: Round [157] log likelihood: -4027.508882
EM: Round [158] log likelihood: -4027.506985
EM: Round [159] log likelihood: -4027.505117
EM: Round [160] log likelihood: -4027.503278
EM: Round [161] log likelihood: -4027.501467
EM: Round [162] log likelihood: -4027.499684
EM: Round [163] log likelihood: -4027.497928
EM: Round [164] log likelihood: -4027.496200
EM: Round [165] log likelihood: -4027.494498
EM: Round [166] log likelihood: -4027.492823
EM: Round [167] log likelihood: -4027.491173
EM: Round [168] log likelihood: -4027.489549
EM: Round [169] log likelihood: -4027.487949
EM: Round [170] log likelihood: -4027.486374
EM: Round [171] log likelihood: -4027.484824
EM: Round [172] log likelihood: -4027.483297
EM: Round [173] log likelihood: -4027.481793
EM: Round [174] log likelihood: -4027.480313
EM: Round [175] log likelihood: -4027.478856
EM: Round [176] log likelihood: -4027.477420
EM: Round [177] log likelihood: -4027.476007
EM: Round [178] log likelihood: -4027.474616
EM: Round [179] log likelihood: -4027.473245
EM: Round [180] log likelihood: -4027.471896
EM: Round [181] log likelihood: -4027.470568
EM: Round [182] log likelihood: -4027.469259
EM: Round [183] log likelihood: -4027.467971
EM: Round [184] log likelihood: -4027.466702
EM: Round [185] log likelihood: -4027.465453
EM: Round [186] log likelihood: -4027.464223
EM: Round [187] log likelihood: -4027.463012
EM: Round [188] log likelihood: -4027.461819
EM: Round [189] log likelihood: -4027.460645
EM: Round [190] log likelihood: -4027.459488
EM: Round [191] log likelihood: -4027.458349
EM: Round [192] log likelihood: -4027.457228
EM: Round [193] log likelihood: -4027.456123
EM: Round [194] log likelihood: -4027.455036
EM: Round [195] log likelihood: -4027.453965
EM: Round [196] log likelihood: -4027.452910
EM: Round [197] log likelihood: -4027.451871
EM: Round [198] log likelihood: -4027.450848
EM: Round [199] log likelihood: -4027.449841
EM: Round [200] log likelihood: -4027.448849
EM: Round [201] log likelihood: -4027.447873
EM: Round [202] log likelihood: -4027.446911
EM: Round [203] log likelihood: -4027.445963
EM: Round [204] log likelihood: -4027.445031
EM: Round [205] log likelihood: -4027.444112
EM: Round [206] log likelihood: -4027.443207
EM: Round [207] log likelihood: -4027.442316
EM: Round [208] log likelihood: -4027.441439
EM: Round [209] log likelihood: -4027.440575
EM: Round [210] log likelihood: -4027.439724
EM: Round [211] log likelihood: -4027.438886
EM: Round [212] log likelihood: -4027.438060
EM: Round [213] log likelihood: -4027.437248
EM: Round [214] log likelihood: -4027.436447
EM: Round [215] log likelihood: -4027.435659
EM: Round [216] log likelihood: -4027.434883
EM: Round [217] log likelihood: -4027.434118
EM: Round [218] log likelihood: -4027.433365
EM: Round [219] log likelihood: -4027.432624
EM: Round [220] log likelihood: -4027.431893
EM: Round [221] log likelihood: -4027.431174
EM: Round [222] log likelihood: -4027.430466
EM: Round [223] log likelihood: -4027.429768
EM: Round [224] log likelihood: -4027.429081
EM: Round [225] log likelihood: -4027.428404
EM: Round [226] log likelihood: -4027.427738
EM: Round [227] log likelihood: -4027.427082
EM: Round [228] log likelihood: -4027.426436
EM: Round [229] log likelihood: -4027.425799
EM: Round [230] log likelihood: -4027.425172
EM: Round [231] log likelihood: -4027.424555
EM: Round [232] log likelihood: -4027.423947
EM: Round [233] log likelihood: -4027.423348
EM: Round [234] log likelihood: -4027.422758
EM: Round [235] log likelihood: -4027.422177
EM: Round [236] log likelihood: -4027.421605
EM: Round [237] log likelihood: -4027.421041
EM: Round [238] log likelihood: -4027.420486
EM: Round [239] log likelihood: -4027.419940
EM: Round [240] log likelihood: -4027.419402
EM: Round [241] log likelihood: -4027.418871
EM: Round [242] log likelihood: -4027.418349
EM: Round [243] log likelihood: -4027.417835
EM: Round [244] log likelihood: -4027.417329
EM: Round [245] log likelihood: -4027.416830
EM: Round [246] log likelihood: -4027.416338
EM: Round [247] log likelihood: -4027.415854
EM: Round [248] log likelihood: -4027.415378
EM: Round [249] log likelihood: -4027.414909
EM: Round [250] log likelihood: -4027.414446
EM: Round [251] log likelihood: -4027.413991
EM: Round [252] log likelihood: -4027.413542
EM: Round [253] log likelihood: -4027.413101
EM: Round [254] log likelihood: -4027.412666
EM: Round [255] log likelihood: -4027.412237
EM: Round [256] log likelihood: -4027.411815
EM: Round [257] log likelihood: -4027.411400
EM: Round [258] log likelihood: -4027.410990
EM: Round [259] log likelihood: -4027.410587
EM: Round [260] log likelihood: -4027.410190
EM: Round [261] log likelihood: -4027.409799
EM: Round [262] log likelihood: -4027.409414
EM: Round [263] log likelihood: -4027.409034
EM: Round [264] log likelihood: -4027.408661
EM: Round [265] log likelihood: -4027.408293
EM: Round [266] log likelihood: -4027.407930
EM: Round [267] log likelihood: -4027.407573
EM: Round [268] log likelihood: -4027.407221
EM: Round [269] log likelihood: -4027.406875
EM: Round [270] log likelihood: -4027.406534
EM: Round [271] log likelihood: -4027.406198
EM: Round [272] log likelihood: -4027.405867
EM: Round [273] log likelihood: -4027.405541
EM: Round [274] log likelihood: -4027.405220
EM: Round [275] log likelihood: -4027.404904
EM: Round [276] log likelihood: -4027.404592
EM: Round [277] log likelihood: -4027.404285
EM: Round [278] log likelihood: -4027.403983
EM: Round [279] log likelihood: -4027.403686
EM: Round [280] log likelihood: -4027.403393
EM: Round [281] log likelihood: -4027.403104
EM: Round [282] log likelihood: -4027.402819
EM: Round [283] log likelihood: -4027.402539
EM: Round [284] log likelihood: -4027.402264
EM: Round [285] log likelihood: -4027.401992
EM: Round [286] log likelihood: -4027.401724
EM: Round [287] log likelihood: -4027.401461
EM: Round [288] log likelihood: -4027.401201
EM: Round [289] log likelihood: -4027.400945
EM: Round [290] log likelihood: -4027.400693
EM: Round [291] log likelihood: -4027.400445
EM: Round [292] log likelihood: -4027.400201
EM: Round [293] log likelihood: -4027.399960
EM: Round [294] log likelihood: -4027.399723
EM: Round [295] log likelihood: -4027.399490
EM: Round [296] log likelihood: -4027.399260
EM: Round [297] log likelihood: -4027.399033
EM: Round [298] log likelihood: -4027.398810
EM: Round [299] log likelihood: -4027.398590
EM: Round [300] log likelihood: -4027.398374
EM: Round [301] log likelihood: -4027.398161
EM: Round [302] log likelihood: -4027.397951
EM: Round [303] log likelihood: -4027.397744
EM: Round [304] log likelihood: -4027.397540
EM: Round [305] log likelihood: -4027.397339
EM: Round [306] log likelihood: -4027.397142
EM: Round [307] log likelihood: -4027.396947
EM: Round [308] log likelihood: -4027.396755
EM: Round [309] log likelihood: -4027.396566
EM: Round [310] log likelihood: -4027.396380
EM: Round [311] log likelihood: -4027.396197
EM: Round [312] log likelihood: -4027.396016
EM: Round [313] log likelihood: -4027.395839
EM: Round [314] log likelihood: -4027.395664
EM: Round [315] log likelihood: -4027.395491
EM: Round [316] log likelihood: -4027.395321
EM: Round [317] log likelihood: -4027.395154
EM: Round [318] log likelihood: -4027.394989
EM: Round [319] log likelihood: -4027.394827
EM: Round [320] log likelihood: -4027.394667
EM: Round [321] log likelihood: -4027.394509
EM: Round [322] log likelihood: -4027.394354
EM: Round [323] log likelihood: -4027.394201
EM: Round [324] log likelihood: -4027.394051
EM: Round [325] log likelihood: -4027.393903
EM: Round [326] log likelihood: -4027.393757
EM: Round [327] log likelihood: -4027.393613
EM: Round [328] log likelihood: -4027.393471
EM: Round [329] log likelihood: -4027.393331
EM: Round [330] log likelihood: -4027.393194
EM: Round [331] log likelihood: -4027.393059
EM: Round [332] log likelihood: -4027.392925
EM: Round [333] log likelihood: -4027.392794
EM: Round [334] log likelihood: -4027.392665
EM: Round [335] log likelihood: -4027.392537
EM: Round [336] log likelihood: -4027.392412
EM: Round [337] log likelihood: -4027.392288
EM: Round [338] log likelihood: -4027.392166
EM: Round [339] log likelihood: -4027.392046
EM: Round [340] log likelihood: -4027.391928
EM: Round [341] log likelihood: -4027.391812
EM: Round [342] log likelihood: -4027.391697
EM: Round [343] log likelihood: -4027.391584
EM: Round [344] log likelihood: -4027.391473
EM: Round [345] log likelihood: -4027.391363
EM: Round [346] log likelihood: -4027.391255
EM: Round [347] log likelihood: -4027.391149
EM: Round [348] log likelihood: -4027.391044
EM: Round [349] log likelihood: -4027.390941
EM: Round [350] log likelihood: -4027.390840
EM: Round [351] log likelihood: -4027.390740
EM: Round [352] log likelihood: -4027.390641
EM: Stopping iterations at round 352 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.zYieQzYkmk/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.zYieQzYkmk/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.zYieQzYkmk/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.zYieQzYkmk/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.zYieQzYkmk/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.zYieQzYkmk/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.zYieQzYkmk/aih-tih-sc-ffd2af-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.zYieQzYkmk/fi_workdir/aih-tih-sc-ffd2af-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.zYieQzYkmk/fi_workdir/aih-tih-sc-ffd2af-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.zYieQzYkmk/fi_workdir/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.zYieQzYkmk/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.zYieQzYkmk/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3755.283441
EM: Round [1] log likelihood: -3755.283441
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.zYieQzYkmk/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 219597035
Warning - not locating file: /tmp/nxf.zYieQzYkmk/aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000259543.1]
WARNING, no entry stored in dbm for [ENSG00000234717.2]
ls: cannot access 'IGV_inputs': No such file or directory