Done.
-parsing GTF file: /tmp/nxf.YkRoeD1bYA/tih_rna_sample_00736_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.YkRoeD1bYA/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.YkRoeD1bYA/tih_rna_sample_00736_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.YkRoeD1bYA/tih_rna_sample_00736_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.YkRoeD1bYA/fi_workdir/tih_rna_sample_00736_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.YkRoeD1bYA/fi_workdir/tih_rna_sample_00736_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00736_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00736_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:27:29 : INFO : Done.
-parsing GTF file: /tmp/nxf.YkRoeD1bYA/fi_workdir/tih_rna_sample_00736_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.YkRoeD1bYA/fi_workdir/tih_rna_sample_00736_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[5880000] -done parsing /tmp/nxf.YkRoeD1bYA/fi_workdir/tih_rna_sample_00736_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num genes matched < 2' => 17,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 309,
'per_id < 96' => 39967,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 76,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 600,
'seq-similar region overlap' => 317,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 492,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 30,
'small anchor length' => 15,
'low complexity anchor region' => 7,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 171,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4782,
'excessive soft clipping' => 148285,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8,
' ** passed ** ' => 5798,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 96,
'exons hit < 2' => 4,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1105,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 14,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 5775,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 1350
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.YkRoeD1bYA/fi_workdir/tih_rna_sample_00736_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[199000] -fusion SPANNING read extraction for scaff: AC136431.1--PKD1P5
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[210000] -fusion SPANNING read extraction for scaff: CASC3--PSMD3
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[20000] -fusion SPANNING read extraction for scaff: DNA2--CDCA2
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[88000] -fusion SPANNING read extraction for scaff: FBXL20--TNS4
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[4707000] -fusion SPANNING read extraction for scaff: IGH@-ext--C1QBP
[1000]
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[29000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[23000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[20000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[4000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[5000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[7000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[25000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[4000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[106000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[30000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[20000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 37682,
'lacks exon overlap' => 6201
};
EM: Starting log likelihood: -3148.340697
EM: Round [1] log likelihood: -3148.005618
EM: Round [2] log likelihood: -3147.709796
EM: Round [3] log likelihood: -3147.438241
EM: Round [4] log likelihood: -3147.188386
EM: Round [5] log likelihood: -3146.958100
EM: Round [6] log likelihood: -3146.745522
EM: Round [7] log likelihood: -3146.549012
EM: Round [8] log likelihood: -3146.367125
EM: Round [9] log likelihood: -3146.198576
EM: Round [10] log likelihood: -3146.042220
EM: Round [11] log likelihood: -3145.897034
EM: Round [12] log likelihood: -3145.762100
EM: Round [13] log likelihood: -3145.636591
EM: Round [14] log likelihood: -3145.519761
EM: Round [15] log likelihood: -3145.410934
EM: Round [16] log likelihood: -3145.309496
EM: Round [17] log likelihood: -3145.214891
EM: Round [18] log likelihood: -3145.126608
EM: Round [19] log likelihood: -3145.044185
EM: Round [20] log likelihood: -3144.967196
EM: Round [21] log likelihood: -3144.895250
EM: Round [22] log likelihood: -3144.827991
EM: Round [23] log likelihood: -3144.765090
EM: Round [24] log likelihood: -3144.706243
EM: Round [25] log likelihood: -3144.651172
EM: Round [26] log likelihood: -3144.599618
EM: Round [27] log likelihood: -3144.551343
EM: Round [28] log likelihood: -3144.506126
EM: Round [29] log likelihood: -3144.463764
EM: Round [30] log likelihood: -3144.424067
EM: Round [31] log likelihood: -3144.386860
EM: Round [32] log likelihood: -3144.351978
EM: Round [33] log likelihood: -3144.319272
EM: Round [34] log likelihood: -3144.288599
EM: Round [35] log likelihood: -3144.259828
EM: Round [36] log likelihood: -3144.232838
EM: Round [37] log likelihood: -3144.207515
EM: Round [38] log likelihood: -3144.183752
EM: Round [39] log likelihood: -3144.161451
EM: Round [40] log likelihood: -3144.140519
EM: Round [41] log likelihood: -3144.120869
EM: Round [42] log likelihood: -3144.102423
EM: Round [43] log likelihood: -3144.085103
EM: Round [44] log likelihood: -3144.068840
EM: Round [45] log likelihood: -3144.053568
EM: Round [46] log likelihood: -3144.039226
EM: Round [47] log likelihood: -3144.025755
EM: Round [48] log likelihood: -3144.013102
EM: Round [49] log likelihood: -3144.001217
EM: Round [50] log likelihood: -3143.990053
EM: Round [51] log likelihood: -3143.979564
EM: Round [52] log likelihood: -3143.969710
EM: Round [53] log likelihood: -3143.960451
EM: Round [54] log likelihood: -3143.951752
EM: Round [55] log likelihood: -3143.943578
EM: Round [56] log likelihood: -3143.935897
EM: Round [57] log likelihood: -3143.928679
EM: Round [58] log likelihood: -3143.921896
EM: Round [59] log likelihood: -3143.915521
EM: Round [60] log likelihood: -3143.909530
EM: Round [61] log likelihood: -3143.903899
EM: Round [62] log likelihood: -3143.898607
EM: Round [63] log likelihood: -3143.893633
EM: Round [64] log likelihood: -3143.888958
EM: Round [65] log likelihood: -3143.884564
EM: Round [66] log likelihood: -3143.880433
EM: Round [67] log likelihood: -3143.876551
EM: Round [68] log likelihood: -3143.872901
EM: Round [69] log likelihood: -3143.869470
EM: Round [70] log likelihood: -3143.866245
EM: Round [71] log likelihood: -3143.863213
EM: Round [72] log likelihood: -3143.860363
EM: Round [73] log likelihood: -3143.857684
EM: Round [74] log likelihood: -3143.855165
EM: Round [75] log likelihood: -3143.852797
EM: Round [76] log likelihood: -3143.850571
EM: Round [77] log likelihood: -3143.848478
EM: Round [78] log likelihood: -3143.846511
EM: Round [79] log likelihood: -3143.844661
EM: Round [80] log likelihood: -3143.842922
EM: Round [81] log likelihood: -3143.841287
EM: Round [82] log likelihood: -3143.839750
EM: Round [83] log likelihood: -3143.838304
EM: Round [84] log likelihood: -3143.836946
EM: Round [85] log likelihood: -3143.835668
EM: Round [86] log likelihood: -3143.834467
EM: Round [87] log likelihood: -3143.833337
EM: Round [88] log likelihood: -3143.832276
EM: Round [89] log likelihood: -3143.831277
EM: Round [90] log likelihood: -3143.830339
EM: Round [91] log likelihood: -3143.829456
EM: Round [92] log likelihood: -3143.828626
EM: Round [93] log likelihood: -3143.827846
EM: Round [94] log likelihood: -3143.827112
EM: Round [95] log likelihood: -3143.826423
EM: Round [96] log likelihood: -3143.825774
EM: Round [97] log likelihood: -3143.825164
EM: Round [98] log likelihood: -3143.824591
EM: Round [99] log likelihood: -3143.824052
EM: Round [100] log likelihood: -3143.823545
EM: Round [101] log likelihood: -3143.823068
EM: Round [102] log likelihood: -3143.822620
EM: Round [103] log likelihood: -3143.822199
EM: Round [104] log likelihood: -3143.821803
EM: Round [105] log likelihood: -3143.821430
EM: Round [106] log likelihood: -3143.821080
EM: Round [107] log likelihood: -3143.820750
EM: Round [108] log likelihood: -3143.820441
EM: Round [109] log likelihood: -3143.820150
EM: Round [110] log likelihood: -3143.819876
EM: Round [111] log likelihood: -3143.819618
EM: Round [112] log likelihood: -3143.819376
EM: Round [113] log likelihood: -3143.819149
EM: Round [114] log likelihood: -3143.818935
EM: Round [115] log likelihood: -3143.818733
EM: Round [116] log likelihood: -3143.818544
EM: Round [117] log likelihood: -3143.818366
EM: Round [118] log likelihood: -3143.818199
EM: Round [119] log likelihood: -3143.818042
EM: Round [120] log likelihood: -3143.817894
EM: Round [121] log likelihood: -3143.817755
EM: Round [122] log likelihood: -3143.817624
EM: Round [123] log likelihood: -3143.817501
EM: Round [124] log likelihood: -3143.817385
EM: Round [125] log likelihood: -3143.817276
EM: Round [126] log likelihood: -3143.817174
EM: Round [127] log likelihood: -3143.817078
EM: Stopping iterations at round 127 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.YkRoeD1bYA/tih_rna_sample_00736_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.YkRoeD1bYA/tih_rna_sample_00736_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.YkRoeD1bYA/tih_rna_sample_00736_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.YkRoeD1bYA/tih_rna_sample_00736_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.YkRoeD1bYA/tih_rna_sample_00736_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.YkRoeD1bYA/tih_rna_sample_00736_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.YkRoeD1bYA/tih_rna_sample_00736_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.YkRoeD1bYA/fi_workdir/tih_rna_sample_00736_B23MVV7LT4_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.YkRoeD1bYA/fi_workdir/tih_rna_sample_00736_B23MVV7LT4_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.YkRoeD1bYA/fi_workdir/tih_rna_sample_00736_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.YkRoeD1bYA/tih_rna_sample_00736_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.YkRoeD1bYA/tih_rna_sample_00736_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3072.332737
EM: Round [1] log likelihood: -3072.320340
EM: Round [2] log likelihood: -3072.320220
EM: Round [3] log likelihood: -3072.320218
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.YkRoeD1bYA/tih_rna_sample_00736_B23MVV7LT4_1_1.fastp.fastq.gz: 296000167
Warning - not locating file: /tmp/nxf.YkRoeD1bYA/tih_rna_sample_00736_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
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 [IGH.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000260126.2]
WARNING, no entry stored in dbm for [ENSG00000254681.6]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
ls: cannot access 'IGV_inputs': No such file or directory