Done.
-parsing GTF file: /tmp/nxf.xhfnK1KncH/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.xhfnK1KncH/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.xhfnK1KncH/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.xhfnK1KncH/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.xhfnK1KncH/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.xhfnK1KncH/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:17:21 : INFO : Done.
-parsing GTF file: /tmp/nxf.xhfnK1KncH/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.xhfnK1KncH/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[2270000] -done parsing /tmp/nxf.xhfnK1KncH/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 45,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 57,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 13,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 24,
'num genes matched < 2' => 1,
'excessive soft clipping' => 9735,
'small anchor length' => 99,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 12,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 10,
'low complexity anchor region' => 12,
'per_id < 96' => 6616,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 84,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 63,
'seq-similar region overlap' => 772,
' ** passed ** ' => 15864
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.xhfnK1KncH/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[49000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[88000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6
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[59000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7
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[97000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11
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[103000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12
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[54000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3
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[36000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4
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[44000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
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[151000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[88000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[110000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[59000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[97000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[54000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[35000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[43000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[102000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[79000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[15000] -fusion SPANNING read extraction for scaff: PMS2P8--CCDC146
[1000]
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[5000] -fusion SPANNING read extraction for scaff: RNU6-138P--KCNH8
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[48000] -fusion SPANNING read extraction for scaff: SBF2--PPIAP86
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[48000] -fusion SPANNING read extraction for scaff: SBF2--LINC01299
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[47000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[10000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[14000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[86000]
[87000]
[88000]
[89000]
[90000]
[91000]
[92000]
[93000]
[94000]
[95000]
[96000]
[97000]
[98000]
[99000]
[100000]
[101000]
[102000]
[103000]
[104000]
[105000]
[106000]
[107000]
[108000]
[109000] -fusion SPANNING read extraction for scaff: UBE2O--ZIC1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 320602,
'lacks exon overlap' => 5318
};
EM: Starting log likelihood: -7075.264684
EM: Round [1] log likelihood: -7036.769319
EM: Round [2] log likelihood: -7025.952124
EM: Round [3] log likelihood: -7022.740528
EM: Round [4] log likelihood: -7021.577369
EM: Round [5] log likelihood: -7020.943258
EM: Round [6] log likelihood: -7020.461828
EM: Round [7] log likelihood: -7020.046262
EM: Round [8] log likelihood: -7019.674790
EM: Round [9] log likelihood: -7019.339499
EM: Round [10] log likelihood: -7019.035710
EM: Round [11] log likelihood: -7018.759812
EM: Round [12] log likelihood: -7018.508767
EM: Round [13] log likelihood: -7018.279951
EM: Round [14] log likelihood: -7018.071078
EM: Round [15] log likelihood: -7017.880139
EM: Round [16] log likelihood: -7017.705361
EM: Round [17] log likelihood: -7017.545177
EM: Round [18] log likelihood: -7017.398191
EM: Round [19] log likelihood: -7017.263160
EM: Round [20] log likelihood: -7017.138972
EM: Round [21] log likelihood: -7017.024633
EM: Round [22] log likelihood: -7016.919250
EM: Round [23] log likelihood: -7016.822018
EM: Round [24] log likelihood: -7016.732216
EM: Round [25] log likelihood: -7016.649190
EM: Round [26] log likelihood: -7016.572352
EM: Round [27] log likelihood: -7016.501170
EM: Round [28] log likelihood: -7016.435160
EM: Round [29] log likelihood: -7016.373888
EM: Round [30] log likelihood: -7016.316956
EM: Round [31] log likelihood: -7016.264005
EM: Round [32] log likelihood: -7016.214710
EM: Round [33] log likelihood: -7016.168772
EM: Round [34] log likelihood: -7016.125922
EM: Round [35] log likelihood: -7016.085913
EM: Round [36] log likelihood: -7016.048522
EM: Round [37] log likelihood: -7016.013544
EM: Round [38] log likelihood: -7015.980792
EM: Round [39] log likelihood: -7015.950096
EM: Round [40] log likelihood: -7015.921301
EM: Round [41] log likelihood: -7015.894263
EM: Round [42] log likelihood: -7015.868852
EM: Round [43] log likelihood: -7015.844949
EM: Round [44] log likelihood: -7015.822444
EM: Round [45] log likelihood: -7015.801237
EM: Round [46] log likelihood: -7015.781237
EM: Round [47] log likelihood: -7015.762358
EM: Round [48] log likelihood: -7015.744522
EM: Round [49] log likelihood: -7015.727659
EM: Round [50] log likelihood: -7015.711702
EM: Round [51] log likelihood: -7015.696592
EM: Round [52] log likelihood: -7015.682271
EM: Round [53] log likelihood: -7015.668689
EM: Round [54] log likelihood: -7015.655798
EM: Round [55] log likelihood: -7015.643554
EM: Round [56] log likelihood: -7015.631917
EM: Round [57] log likelihood: -7015.620849
EM: Round [58] log likelihood: -7015.610316
EM: Round [59] log likelihood: -7015.600284
EM: Round [60] log likelihood: -7015.590725
EM: Round [61] log likelihood: -7015.581611
EM: Round [62] log likelihood: -7015.572915
EM: Round [63] log likelihood: -7015.564615
EM: Round [64] log likelihood: -7015.556687
EM: Round [65] log likelihood: -7015.549112
EM: Round [66] log likelihood: -7015.541869
EM: Round [67] log likelihood: -7015.534941
EM: Round [68] log likelihood: -7015.528312
EM: Round [69] log likelihood: -7015.521964
EM: Round [70] log likelihood: -7015.515884
EM: Round [71] log likelihood: -7015.510058
EM: Round [72] log likelihood: -7015.504474
EM: Round [73] log likelihood: -7015.499118
EM: Round [74] log likelihood: -7015.493980
EM: Round [75] log likelihood: -7015.489049
EM: Round [76] log likelihood: -7015.484315
EM: Round [77] log likelihood: -7015.479770
EM: Round [78] log likelihood: -7015.475403
EM: Round [79] log likelihood: -7015.471207
EM: Round [80] log likelihood: -7015.467174
EM: Round [81] log likelihood: -7015.463296
EM: Round [82] log likelihood: -7015.459567
EM: Round [83] log likelihood: -7015.455980
EM: Round [84] log likelihood: -7015.452528
EM: Round [85] log likelihood: -7015.449206
EM: Round [86] log likelihood: -7015.446009
EM: Round [87] log likelihood: -7015.442930
EM: Round [88] log likelihood: -7015.439966
EM: Round [89] log likelihood: -7015.437110
EM: Round [90] log likelihood: -7015.434359
EM: Round [91] log likelihood: -7015.431709
EM: Round [92] log likelihood: -7015.429155
EM: Round [93] log likelihood: -7015.426693
EM: Round [94] log likelihood: -7015.424320
EM: Round [95] log likelihood: -7015.422032
EM: Round [96] log likelihood: -7015.419826
EM: Round [97] log likelihood: -7015.417698
EM: Round [98] log likelihood: -7015.415646
EM: Round [99] log likelihood: -7015.413667
EM: Round [100] log likelihood: -7015.411757
EM: Round [101] log likelihood: -7015.409915
EM: Round [102] log likelihood: -7015.408137
EM: Round [103] log likelihood: -7015.406422
EM: Round [104] log likelihood: -7015.404766
EM: Round [105] log likelihood: -7015.403168
EM: Round [106] log likelihood: -7015.401625
EM: Round [107] log likelihood: -7015.400136
EM: Round [108] log likelihood: -7015.398699
EM: Round [109] log likelihood: -7015.397311
EM: Round [110] log likelihood: -7015.395971
EM: Round [111] log likelihood: -7015.394677
EM: Round [112] log likelihood: -7015.393427
EM: Round [113] log likelihood: -7015.392220
EM: Round [114] log likelihood: -7015.391055
EM: Round [115] log likelihood: -7015.389929
EM: Round [116] log likelihood: -7015.388842
EM: Round [117] log likelihood: -7015.387791
EM: Round [118] log likelihood: -7015.386777
EM: Round [119] log likelihood: -7015.385797
EM: Round [120] log likelihood: -7015.384850
EM: Round [121] log likelihood: -7015.383935
EM: Round [122] log likelihood: -7015.383051
EM: Round [123] log likelihood: -7015.382197
EM: Round [124] log likelihood: -7015.381372
EM: Round [125] log likelihood: -7015.380575
EM: Round [126] log likelihood: -7015.379805
EM: Round [127] log likelihood: -7015.379060
EM: Round [128] log likelihood: -7015.378341
EM: Round [129] log likelihood: -7015.377646
EM: Round [130] log likelihood: -7015.376974
EM: Round [131] log likelihood: -7015.376325
EM: Round [132] log likelihood: -7015.375698
EM: Round [133] log likelihood: -7015.375091
EM: Round [134] log likelihood: -7015.374505
EM: Round [135] log likelihood: -7015.373939
EM: Round [136] log likelihood: -7015.373392
EM: Round [137] log likelihood: -7015.372862
EM: Round [138] log likelihood: -7015.372351
EM: Round [139] log likelihood: -7015.371857
EM: Round [140] log likelihood: -7015.371379
EM: Round [141] log likelihood: -7015.370917
EM: Round [142] log likelihood: -7015.370471
EM: Round [143] log likelihood: -7015.370039
EM: Round [144] log likelihood: -7015.369622
EM: Round [145] log likelihood: -7015.369219
EM: Round [146] log likelihood: -7015.368829
EM: Round [147] log likelihood: -7015.368453
EM: Round [148] log likelihood: -7015.368088
EM: Round [149] log likelihood: -7015.367736
EM: Round [150] log likelihood: -7015.367396
EM: Round [151] log likelihood: -7015.367067
EM: Round [152] log likelihood: -7015.366749
EM: Round [153] log likelihood: -7015.366442
EM: Round [154] log likelihood: -7015.366144
EM: Round [155] log likelihood: -7015.365857
EM: Round [156] log likelihood: -7015.365579
EM: Round [157] log likelihood: -7015.365311
EM: Round [158] log likelihood: -7015.365051
EM: Round [159] log likelihood: -7015.364800
EM: Round [160] log likelihood: -7015.364557
EM: Round [161] log likelihood: -7015.364323
EM: Round [162] log likelihood: -7015.364096
EM: Round [163] log likelihood: -7015.363877
EM: Round [164] log likelihood: -7015.363665
EM: Round [165] log likelihood: -7015.363460
EM: Round [166] log likelihood: -7015.363262
EM: Round [167] log likelihood: -7015.363070
EM: Round [168] log likelihood: -7015.362885
EM: Round [169] log likelihood: -7015.362706
EM: Round [170] log likelihood: -7015.362533
EM: Round [171] log likelihood: -7015.362365
EM: Round [172] log likelihood: -7015.362204
EM: Round [173] log likelihood: -7015.362047
EM: Round [174] log likelihood: -7015.361896
EM: Round [175] log likelihood: -7015.361750
EM: Round [176] log likelihood: -7015.361608
EM: Round [177] log likelihood: -7015.361472
EM: Round [178] log likelihood: -7015.361339
EM: Round [179] log likelihood: -7015.361212
EM: Round [180] log likelihood: -7015.361088
EM: Round [181] log likelihood: -7015.360969
EM: Round [182] log likelihood: -7015.360853
EM: Round [183] log likelihood: -7015.360741
EM: Round [184] log likelihood: -7015.360634
EM: Round [185] log likelihood: -7015.360529
EM: Round [186] log likelihood: -7015.360428
EM: Round [187] log likelihood: -7015.360331
EM: Stopping iterations at round 187 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.xhfnK1KncH/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.xhfnK1KncH/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.xhfnK1KncH/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.xhfnK1KncH/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.xhfnK1KncH/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.xhfnK1KncH/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.xhfnK1KncH/aih-tih-sc-5519ab-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.xhfnK1KncH/fi_workdir/aih-tih-sc-5519ab-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.xhfnK1KncH/fi_workdir/aih-tih-sc-5519ab-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.xhfnK1KncH/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.xhfnK1KncH/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.xhfnK1KncH/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -6420.561296
EM: Round [1] log likelihood: -6382.907410
EM: Round [2] log likelihood: -6372.823955
EM: Round [3] log likelihood: -6370.258193
EM: Round [4] log likelihood: -6369.667570
EM: Round [5] log likelihood: -6369.543887
EM: Round [6] log likelihood: -6369.519595
EM: Round [7] log likelihood: -6369.514985
EM: Round [8] log likelihood: -6369.514124
EM: Round [9] log likelihood: -6369.513964
EM: Round [10] log likelihood: -6369.513934
EM: Stopping iterations at round 10 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.xhfnK1KncH/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296543195
Warning - not locating file: /tmp/nxf.xhfnK1KncH/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000226240.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
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 [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000223698.3]
ls: cannot access 'IGV_inputs': No such file or directory