Done.
-parsing GTF file: /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.Gxw6aZN623/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.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38_1.fastp.fastq.gz /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00118_23H5VFLT4_s38.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00118_23H5VFLT4_s38.star.sortedByCoord.out.bam
10:36:04 : INFO : Done.
-parsing GTF file: /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.gtf
-parsing /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam
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[1180000] -done parsing /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
' ** passed ** ' => 8311,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 20,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 18,
'seq-similar region overlap' => 255,
'num genes matched < 2' => 10,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 17,
'excessive soft clipping' => 8971,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 95,
'small anchor length' => 19,
'exons hit < 2' => 5,
'per_id < 96' => 3520
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[86000] -fusion SPANNING read extraction for scaff: FOXJ3--HIVEP3
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[29000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[86000] -fusion SPANNING read extraction for scaff: TM9SF2--CLYBL
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[16000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[103000] -fusion SPANNING read extraction for scaff: UBAC2--TM9SF2
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[18000] -fusion SPANNING read extraction for scaff: VPS26B--PTPN20
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[13000] -fusion SPANNING read extraction for scaff: VPS26B--GDF10
[1000]
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[10000] -fusion SPANNING read extraction for scaff: ZNF419--ZNF772
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 56273,
'lacks exon overlap' => 14385
};
EM: Starting log likelihood: -6238.480830
EM: Round [1] log likelihood: -6238.249744
EM: Round [2] log likelihood: -6238.235409
EM: Round [3] log likelihood: -6238.223195
EM: Round [4] log likelihood: -6238.211483
EM: Round [5] log likelihood: -6238.200226
EM: Round [6] log likelihood: -6238.189402
EM: Round [7] log likelihood: -6238.178990
EM: Round [8] log likelihood: -6238.168970
EM: Round [9] log likelihood: -6238.159323
EM: Round [10] log likelihood: -6238.150033
EM: Round [11] log likelihood: -6238.141083
EM: Round [12] log likelihood: -6238.132458
EM: Round [13] log likelihood: -6238.124143
EM: Round [14] log likelihood: -6238.116125
EM: Round [15] log likelihood: -6238.108390
EM: Round [16] log likelihood: -6238.100928
EM: Round [17] log likelihood: -6238.093725
EM: Round [18] log likelihood: -6238.086773
EM: Round [19] log likelihood: -6238.080059
EM: Round [20] log likelihood: -6238.073575
EM: Round [21] log likelihood: -6238.067310
EM: Round [22] log likelihood: -6238.061258
EM: Round [23] log likelihood: -6238.055408
EM: Round [24] log likelihood: -6238.049754
EM: Round [25] log likelihood: -6238.044287
EM: Round [26] log likelihood: -6238.039000
EM: Round [27] log likelihood: -6238.033887
EM: Round [28] log likelihood: -6238.028941
EM: Round [29] log likelihood: -6238.024155
EM: Round [30] log likelihood: -6238.019525
EM: Round [31] log likelihood: -6238.015043
EM: Round [32] log likelihood: -6238.010705
EM: Round [33] log likelihood: -6238.006506
EM: Round [34] log likelihood: -6238.002440
EM: Round [35] log likelihood: -6237.998503
EM: Round [36] log likelihood: -6237.994690
EM: Round [37] log likelihood: -6237.990996
EM: Round [38] log likelihood: -6237.987419
EM: Round [39] log likelihood: -6237.983953
EM: Round [40] log likelihood: -6237.980594
EM: Round [41] log likelihood: -6237.977340
EM: Round [42] log likelihood: -6237.974187
EM: Round [43] log likelihood: -6237.971130
EM: Round [44] log likelihood: -6237.968167
EM: Round [45] log likelihood: -6237.965295
EM: Round [46] log likelihood: -6237.962511
EM: Round [47] log likelihood: -6237.959811
EM: Round [48] log likelihood: -6237.957194
EM: Round [49] log likelihood: -6237.954655
EM: Round [50] log likelihood: -6237.952193
EM: Round [51] log likelihood: -6237.949806
EM: Round [52] log likelihood: -6237.947490
EM: Round [53] log likelihood: -6237.945244
EM: Round [54] log likelihood: -6237.943065
EM: Round [55] log likelihood: -6237.940951
EM: Round [56] log likelihood: -6237.938900
EM: Round [57] log likelihood: -6237.936910
EM: Round [58] log likelihood: -6237.934979
EM: Round [59] log likelihood: -6237.933105
EM: Round [60] log likelihood: -6237.931287
EM: Round [61] log likelihood: -6237.929522
EM: Round [62] log likelihood: -6237.927809
EM: Round [63] log likelihood: -6237.926147
EM: Round [64] log likelihood: -6237.924534
EM: Round [65] log likelihood: -6237.922967
EM: Round [66] log likelihood: -6237.921447
EM: Round [67] log likelihood: -6237.919971
EM: Round [68] log likelihood: -6237.918538
EM: Round [69] log likelihood: -6237.917147
EM: Round [70] log likelihood: -6237.915797
EM: Round [71] log likelihood: -6237.914486
EM: Round [72] log likelihood: -6237.913212
EM: Round [73] log likelihood: -6237.911976
EM: Round [74] log likelihood: -6237.910776
EM: Round [75] log likelihood: -6237.909610
EM: Round [76] log likelihood: -6237.908478
EM: Round [77] log likelihood: -6237.907378
EM: Round [78] log likelihood: -6237.906311
EM: Round [79] log likelihood: -6237.905274
EM: Round [80] log likelihood: -6237.904267
EM: Round [81] log likelihood: -6237.903289
EM: Round [82] log likelihood: -6237.902339
EM: Round [83] log likelihood: -6237.901416
EM: Round [84] log likelihood: -6237.900519
EM: Round [85] log likelihood: -6237.899649
EM: Round [86] log likelihood: -6237.898803
EM: Round [87] log likelihood: -6237.897981
EM: Round [88] log likelihood: -6237.897183
EM: Round [89] log likelihood: -6237.896408
EM: Round [90] log likelihood: -6237.895654
EM: Round [91] log likelihood: -6237.894923
EM: Round [92] log likelihood: -6237.894212
EM: Round [93] log likelihood: -6237.893521
EM: Round [94] log likelihood: -6237.892850
EM: Round [95] log likelihood: -6237.892198
EM: Round [96] log likelihood: -6237.891565
EM: Round [97] log likelihood: -6237.890949
EM: Round [98] log likelihood: -6237.890351
EM: Round [99] log likelihood: -6237.889770
EM: Round [100] log likelihood: -6237.889205
EM: Round [101] log likelihood: -6237.888657
EM: Round [102] log likelihood: -6237.888124
EM: Round [103] log likelihood: -6237.887606
EM: Round [104] log likelihood: -6237.887102
EM: Round [105] log likelihood: -6237.886613
EM: Round [106] log likelihood: -6237.886138
EM: Round [107] log likelihood: -6237.885676
EM: Round [108] log likelihood: -6237.885227
EM: Round [109] log likelihood: -6237.884791
EM: Round [110] log likelihood: -6237.884367
EM: Round [111] log likelihood: -6237.883955
EM: Round [112] log likelihood: -6237.883555
EM: Round [113] log likelihood: -6237.883165
EM: Round [114] log likelihood: -6237.882787
EM: Round [115] log likelihood: -6237.882420
EM: Round [116] log likelihood: -6237.882063
EM: Round [117] log likelihood: -6237.881716
EM: Round [118] log likelihood: -6237.881378
EM: Round [119] log likelihood: -6237.881050
EM: Round [120] log likelihood: -6237.880732
EM: Round [121] log likelihood: -6237.880422
EM: Round [122] log likelihood: -6237.880121
EM: Round [123] log likelihood: -6237.879828
EM: Round [124] log likelihood: -6237.879544
EM: Round [125] log likelihood: -6237.879268
EM: Round [126] log likelihood: -6237.878999
EM: Round [127] log likelihood: -6237.878738
EM: Round [128] log likelihood: -6237.878484
EM: Round [129] log likelihood: -6237.878238
EM: Round [130] log likelihood: -6237.877998
EM: Round [131] log likelihood: -6237.877765
EM: Round [132] log likelihood: -6237.877538
EM: Round [133] log likelihood: -6237.877318
EM: Round [134] log likelihood: -6237.877104
EM: Round [135] log likelihood: -6237.876896
EM: Round [136] log likelihood: -6237.876694
EM: Round [137] log likelihood: -6237.876497
EM: Round [138] log likelihood: -6237.876306
EM: Round [139] log likelihood: -6237.876120
EM: Round [140] log likelihood: -6237.875940
EM: Round [141] log likelihood: -6237.875764
EM: Round [142] log likelihood: -6237.875594
EM: Round [143] log likelihood: -6237.875428
EM: Round [144] log likelihood: -6237.875267
EM: Round [145] log likelihood: -6237.875110
EM: Round [146] log likelihood: -6237.874958
EM: Round [147] log likelihood: -6237.874810
EM: Round [148] log likelihood: -6237.874666
EM: Round [149] log likelihood: -6237.874526
EM: Round [150] log likelihood: -6237.874390
EM: Round [151] log likelihood: -6237.874258
EM: Round [152] log likelihood: -6237.874129
EM: Round [153] log likelihood: -6237.874004
EM: Round [154] log likelihood: -6237.873883
EM: Round [155] log likelihood: -6237.873765
EM: Round [156] log likelihood: -6237.873650
EM: Round [157] log likelihood: -6237.873539
EM: Round [158] log likelihood: -6237.873430
EM: Round [159] log likelihood: -6237.873325
EM: Round [160] log likelihood: -6237.873222
EM: Round [161] log likelihood: -6237.873123
EM: Stopping iterations at round 161 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam into /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam.read_coords
CMD: touch /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam.read_coords > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam.frag_coords > /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.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.Gxw6aZN623/fi_workdir/tih_rna_sample_00118_23H5VFLT4_s38.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -5999.148165
EM: Round [1] log likelihood: -5999.100045
EM: Round [2] log likelihood: -5999.099520
EM: Round [3] log likelihood: -5999.099506
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38_1.fastp.fastq.gz: 296764304
Warning - not locating file: /tmp/nxf.Gxw6aZN623/tih_rna_sample_00118_23H5VFLT4_s38.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
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 [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 [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
ls: cannot access 'IGV_inputs': No such file or directory