Done.
-parsing GTF file: /tmp/nxf.MVS524PpqF/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.MVS524PpqF/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.MVS524PpqF/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.MVS524PpqF/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.MVS524PpqF/fi_workdir/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.MVS524PpqF/fi_workdir/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
11:26:39 : INFO : Done.
-parsing GTF file: /tmp/nxf.MVS524PpqF/fi_workdir/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.MVS524PpqF/fi_workdir/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[1790000] -done parsing /tmp/nxf.MVS524PpqF/fi_workdir/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 101,
'seq-similar region overlap' => 4,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 10,
'per_id < 96' => 8103,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 21,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 3026,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 1071,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 2038,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 9,
' ** passed ** ' => 6916,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 6,
'num genes matched < 2' => 17,
'excessive soft clipping' => 13447,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 114,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 11209,
'exons hit < 2' => 1,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 720,
'small anchor length' => 37
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.MVS524PpqF/fi_workdir/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[132000] -fusion SPANNING read extraction for scaff: AL049555.1--LLGL2
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[836000] -fusion SPANNING read extraction for scaff: PDXDC1--NPIPB5
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[77000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[22000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
[1000]
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[4000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[24000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[10000] -fusion SPANNING read extraction for scaff: UBE2Q2P1--GOLGA6L10
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 11967,
'seq similar region alignment' => 17089
};
EM: Starting log likelihood: -5713.901684
EM: Round [1] log likelihood: -5693.463781
EM: Round [2] log likelihood: -5691.079292
EM: Round [3] log likelihood: -5690.600156
EM: Round [4] log likelihood: -5690.495534
EM: Round [5] log likelihood: -5690.449677
EM: Round [6] log likelihood: -5690.412706
EM: Round [7] log likelihood: -5690.378071
EM: Round [8] log likelihood: -5690.344923
EM: Round [9] log likelihood: -5690.313096
EM: Round [10] log likelihood: -5690.282510
EM: Round [11] log likelihood: -5690.253096
EM: Round [12] log likelihood: -5690.224793
EM: Round [13] log likelihood: -5690.197546
EM: Round [14] log likelihood: -5690.171301
EM: Round [15] log likelihood: -5690.146008
EM: Round [16] log likelihood: -5690.121623
EM: Round [17] log likelihood: -5690.098101
EM: Round [18] log likelihood: -5690.075403
EM: Round [19] log likelihood: -5690.053492
EM: Round [20] log likelihood: -5690.032331
EM: Round [21] log likelihood: -5690.011888
EM: Round [22] log likelihood: -5689.992131
EM: Round [23] log likelihood: -5689.973031
EM: Round [24] log likelihood: -5689.954560
EM: Round [25] log likelihood: -5689.936692
EM: Round [26] log likelihood: -5689.919401
EM: Round [27] log likelihood: -5689.902666
EM: Round [28] log likelihood: -5689.886463
EM: Round [29] log likelihood: -5689.870771
EM: Round [30] log likelihood: -5689.855571
EM: Round [31] log likelihood: -5689.840844
EM: Round [32] log likelihood: -5689.826570
EM: Round [33] log likelihood: -5689.812735
EM: Round [34] log likelihood: -5689.799320
EM: Round [35] log likelihood: -5689.786311
EM: Round [36] log likelihood: -5689.773693
EM: Round [37] log likelihood: -5689.761452
EM: Round [38] log likelihood: -5689.749573
EM: Round [39] log likelihood: -5689.738046
EM: Round [40] log likelihood: -5689.726856
EM: Round [41] log likelihood: -5689.715993
EM: Round [42] log likelihood: -5689.705446
EM: Round [43] log likelihood: -5689.695202
EM: Round [44] log likelihood: -5689.685253
EM: Round [45] log likelihood: -5689.675589
EM: Round [46] log likelihood: -5689.666199
EM: Round [47] log likelihood: -5689.657075
EM: Round [48] log likelihood: -5689.648209
EM: Round [49] log likelihood: -5689.639591
EM: Round [50] log likelihood: -5689.631214
EM: Round [51] log likelihood: -5689.623071
EM: Round [52] log likelihood: -5689.615153
EM: Round [53] log likelihood: -5689.607453
EM: Round [54] log likelihood: -5689.599966
EM: Round [55] log likelihood: -5689.592684
EM: Round [56] log likelihood: -5689.585600
EM: Round [57] log likelihood: -5689.578709
EM: Round [58] log likelihood: -5689.572006
EM: Round [59] log likelihood: -5689.565483
EM: Round [60] log likelihood: -5689.559136
EM: Round [61] log likelihood: -5689.552960
EM: Round [62] log likelihood: -5689.546949
EM: Round [63] log likelihood: -5689.541099
EM: Round [64] log likelihood: -5689.535404
EM: Round [65] log likelihood: -5689.529861
EM: Round [66] log likelihood: -5689.524464
EM: Round [67] log likelihood: -5689.519210
EM: Round [68] log likelihood: -5689.514094
EM: Round [69] log likelihood: -5689.509112
EM: Round [70] log likelihood: -5689.504261
EM: Round [71] log likelihood: -5689.499537
EM: Round [72] log likelihood: -5689.494936
EM: Round [73] log likelihood: -5689.490455
EM: Round [74] log likelihood: -5689.486091
EM: Round [75] log likelihood: -5689.481839
EM: Round [76] log likelihood: -5689.477697
EM: Round [77] log likelihood: -5689.473662
EM: Round [78] log likelihood: -5689.469731
EM: Round [79] log likelihood: -5689.465901
EM: Round [80] log likelihood: -5689.462170
EM: Round [81] log likelihood: -5689.458533
EM: Round [82] log likelihood: -5689.454990
EM: Round [83] log likelihood: -5689.451537
EM: Round [84] log likelihood: -5689.448173
EM: Round [85] log likelihood: -5689.444893
EM: Round [86] log likelihood: -5689.441697
EM: Round [87] log likelihood: -5689.438582
EM: Round [88] log likelihood: -5689.435546
EM: Round [89] log likelihood: -5689.432587
EM: Round [90] log likelihood: -5689.429702
EM: Round [91] log likelihood: -5689.426890
EM: Round [92] log likelihood: -5689.424149
EM: Round [93] log likelihood: -5689.421476
EM: Round [94] log likelihood: -5689.418871
EM: Round [95] log likelihood: -5689.416331
EM: Round [96] log likelihood: -5689.413854
EM: Round [97] log likelihood: -5689.411440
EM: Round [98] log likelihood: -5689.409085
EM: Round [99] log likelihood: -5689.406790
EM: Round [100] log likelihood: -5689.404552
EM: Round [101] log likelihood: -5689.402369
EM: Round [102] log likelihood: -5689.400241
EM: Round [103] log likelihood: -5689.398165
EM: Round [104] log likelihood: -5689.396141
EM: Round [105] log likelihood: -5689.394167
EM: Round [106] log likelihood: -5689.392242
EM: Round [107] log likelihood: -5689.390365
EM: Round [108] log likelihood: -5689.388534
EM: Round [109] log likelihood: -5689.386748
EM: Round [110] log likelihood: -5689.385007
EM: Round [111] log likelihood: -5689.383308
EM: Round [112] log likelihood: -5689.381651
EM: Round [113] log likelihood: -5689.380035
EM: Round [114] log likelihood: -5689.378458
EM: Round [115] log likelihood: -5689.376921
EM: Round [116] log likelihood: -5689.375421
EM: Round [117] log likelihood: -5689.373958
EM: Round [118] log likelihood: -5689.372530
EM: Round [119] log likelihood: -5689.371138
EM: Round [120] log likelihood: -5689.369780
EM: Round [121] log likelihood: -5689.368455
EM: Round [122] log likelihood: -5689.367162
EM: Round [123] log likelihood: -5689.365901
EM: Round [124] log likelihood: -5689.364671
EM: Round [125] log likelihood: -5689.363471
EM: Round [126] log likelihood: -5689.362300
EM: Round [127] log likelihood: -5689.361157
EM: Round [128] log likelihood: -5689.360043
EM: Round [129] log likelihood: -5689.358955
EM: Round [130] log likelihood: -5689.357894
EM: Round [131] log likelihood: -5689.356859
EM: Round [132] log likelihood: -5689.355849
EM: Round [133] log likelihood: -5689.354864
EM: Round [134] log likelihood: -5689.353902
EM: Round [135] log likelihood: -5689.352964
EM: Round [136] log likelihood: -5689.352049
EM: Round [137] log likelihood: -5689.351155
EM: Round [138] log likelihood: -5689.350284
EM: Round [139] log likelihood: -5689.349433
EM: Round [140] log likelihood: -5689.348604
EM: Round [141] log likelihood: -5689.347794
EM: Round [142] log likelihood: -5689.347004
EM: Round [143] log likelihood: -5689.346233
EM: Round [144] log likelihood: -5689.345480
EM: Round [145] log likelihood: -5689.344746
EM: Round [146] log likelihood: -5689.344029
EM: Round [147] log likelihood: -5689.343330
EM: Round [148] log likelihood: -5689.342648
EM: Round [149] log likelihood: -5689.341982
EM: Round [150] log likelihood: -5689.341332
EM: Round [151] log likelihood: -5689.340698
EM: Round [152] log likelihood: -5689.340080
EM: Round [153] log likelihood: -5689.339476
EM: Round [154] log likelihood: -5689.338886
EM: Round [155] log likelihood: -5689.338311
EM: Round [156] log likelihood: -5689.337750
EM: Round [157] log likelihood: -5689.337202
EM: Round [158] log likelihood: -5689.336668
EM: Round [159] log likelihood: -5689.336146
EM: Round [160] log likelihood: -5689.335637
EM: Round [161] log likelihood: -5689.335140
EM: Round [162] log likelihood: -5689.334655
EM: Round [163] log likelihood: -5689.334182
EM: Round [164] log likelihood: -5689.333720
EM: Round [165] log likelihood: -5689.333269
EM: Round [166] log likelihood: -5689.332829
EM: Round [167] log likelihood: -5689.332399
EM: Round [168] log likelihood: -5689.331980
EM: Round [169] log likelihood: -5689.331571
EM: Round [170] log likelihood: -5689.331172
EM: Round [171] log likelihood: -5689.330782
EM: Round [172] log likelihood: -5689.330402
EM: Round [173] log likelihood: -5689.330031
EM: Round [174] log likelihood: -5689.329669
EM: Round [175] log likelihood: -5689.329315
EM: Round [176] log likelihood: -5689.328970
EM: Round [177] log likelihood: -5689.328633
EM: Round [178] log likelihood: -5689.328305
EM: Round [179] log likelihood: -5689.327984
EM: Round [180] log likelihood: -5689.327671
EM: Round [181] log likelihood: -5689.327365
EM: Round [182] log likelihood: -5689.327067
EM: Round [183] log likelihood: -5689.326775
EM: Round [184] log likelihood: -5689.326491
EM: Round [185] log likelihood: -5689.326214
EM: Round [186] log likelihood: -5689.325943
EM: Round [187] log likelihood: -5689.325679
EM: Round [188] log likelihood: -5689.325421
EM: Round [189] log likelihood: -5689.325169
EM: Round [190] log likelihood: -5689.324923
EM: Round [191] log likelihood: -5689.324683
EM: Round [192] log likelihood: -5689.324449
EM: Round [193] log likelihood: -5689.324220
EM: Round [194] log likelihood: -5689.323997
EM: Round [195] log likelihood: -5689.323780
EM: Round [196] log likelihood: -5689.323567
EM: Round [197] log likelihood: -5689.323360
EM: Round [198] log likelihood: -5689.323157
EM: Round [199] log likelihood: -5689.322960
EM: Round [200] log likelihood: -5689.322767
EM: Round [201] log likelihood: -5689.322578
EM: Round [202] log likelihood: -5689.322394
EM: Round [203] log likelihood: -5689.322215
EM: Round [204] log likelihood: -5689.322040
EM: Round [205] log likelihood: -5689.321869
EM: Round [206] log likelihood: -5689.321702
EM: Round [207] log likelihood: -5689.321539
EM: Round [208] log likelihood: -5689.321380
EM: Round [209] log likelihood: -5689.321225
EM: Round [210] log likelihood: -5689.321074
EM: Round [211] log likelihood: -5689.320926
EM: Round [212] log likelihood: -5689.320781
EM: Round [213] log likelihood: -5689.320640
EM: Round [214] log likelihood: -5689.320503
EM: Round [215] log likelihood: -5689.320369
EM: Round [216] log likelihood: -5689.320238
EM: Round [217] log likelihood: -5689.320110
EM: Round [218] log likelihood: -5689.319985
EM: Round [219] log likelihood: -5689.319863
EM: Round [220] log likelihood: -5689.319744
EM: Round [221] log likelihood: -5689.319628
EM: Round [222] log likelihood: -5689.319515
EM: Round [223] log likelihood: -5689.319404
EM: Round [224] log likelihood: -5689.319296
EM: Round [225] log likelihood: -5689.319190
EM: Round [226] log likelihood: -5689.319088
EM: Round [227] log likelihood: -5689.318987
EM: Round [228] log likelihood: -5689.318889
EM: Stopping iterations at round 228 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.MVS524PpqF/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.MVS524PpqF/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.MVS524PpqF/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.MVS524PpqF/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.MVS524PpqF/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.MVS524PpqF/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.MVS524PpqF/aih-tih-sc-e08fa3-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.MVS524PpqF/fi_workdir/aih-tih-sc-e08fa3-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.MVS524PpqF/fi_workdir/aih-tih-sc-e08fa3-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.MVS524PpqF/fi_workdir/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.MVS524PpqF/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.MVS524PpqF/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -5385.605993
EM: Round [1] log likelihood: -5374.497496
EM: Round [2] log likelihood: -5372.194449
EM: Round [3] log likelihood: -5371.756333
EM: Round [4] log likelihood: -5371.690929
EM: Round [5] log likelihood: -5371.682627
EM: Round [6] log likelihood: -5371.681649
EM: Round [7] log likelihood: -5371.681537
EM: Round [8] log likelihood: -5371.681525
EM: Stopping iterations at round 8 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.MVS524PpqF/aih-tih-sc-e08fa3-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296109161
Warning - not locating file: /tmp/nxf.MVS524PpqF/aih-tih-sc-e08fa3-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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000254560.6]
WARNING, no entry stored in dbm for [ENSG00000189136.9]
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 [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000261116.1]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
ls: cannot access 'IGV_inputs': No such file or directory