Done.
-parsing GTF file: /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.jJbViTbJ8s/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.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00680_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00680_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:59:01 : INFO : Done.
-parsing GTF file: /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[3200000] -done parsing /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 24,
'num_hits: 9 != num_counted_on_fusion_contigs 8 ' => 160,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 395,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 84,
'num_hits: 9 != num_counted_on_fusion_contigs 1 ' => 11,
'num_hits: 7 != num_counted_on_fusion_contigs 1 ' => 18,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1285,
'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 4,
'num genes matched < 2' => 25,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 67,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 176,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 210,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 10 != num_counted_on_fusion_contigs 6 ' => 6,
'num_hits: 8 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 592,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 6,
'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 315,
' ** passed ** ' => 17371,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6,
'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 216,
'excessive soft clipping' => 20757,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 13,
'per_id < 96' => 18849,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 66,
'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 264,
'num_hits: 10 != num_counted_on_fusion_contigs 1 ' => 6,
'num_hits: 8 != num_counted_on_fusion_contigs 1 ' => 20,
'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 12,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 6,
'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 4,
'small anchor length' => 507,
'num_hits: 10 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 20,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 33,
'num_hits: 10 != num_counted_on_fusion_contigs 4 ' => 20,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 5,
'num_hits: 10 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 9 != num_counted_on_fusion_contigs 4 ' => 4,
'seq-similar region overlap' => 218
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[6000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
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[92000] -fusion SPANNING read extraction for scaff: GPATCH8--AL133464.1
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[92000] -fusion SPANNING read extraction for scaff: GPATCH8--LINC00261
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[119000] -fusion SPANNING read extraction for scaff: KATNIP--EPG5
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[49000] -fusion SPANNING read extraction for scaff: KIF3B--EFCAB8
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[429000] -fusion SPANNING read extraction for scaff: NPIPB12--AC009093.1
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[32000] -fusion SPANNING read extraction for scaff: PIK3C3--RIT2
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[91000] -fusion SPANNING read extraction for scaff: PRSS27--TPSB2
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[147000] -fusion SPANNING read extraction for scaff: RIOK3--AC016074.2
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[19000] -fusion SPANNING read extraction for scaff: SMURF2P1--LRRC37B
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[85000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[46000] -fusion SPANNING read extraction for scaff: STX4--C16orf96
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[37000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[40000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[7000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[77000] -fusion SPANNING read extraction for scaff: TMEM123--MMP20
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[26000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[78000] -fusion SPANNING read extraction for scaff: USP22--C21orf62
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[10000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF610
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[15000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF880
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 22010,
'seq similar region alignment' => 62798
};
EM: Starting log likelihood: -7717.778134
EM: Round [1] log likelihood: -7717.189182
EM: Round [2] log likelihood: -7716.888387
EM: Round [3] log likelihood: -7716.624805
EM: Round [4] log likelihood: -7716.392920
EM: Round [5] log likelihood: -7716.188303
EM: Round [6] log likelihood: -7716.007244
EM: Round [7] log likelihood: -7715.846616
EM: Round [8] log likelihood: -7715.703769
EM: Round [9] log likelihood: -7715.576444
EM: Round [10] log likelihood: -7715.462705
EM: Round [11] log likelihood: -7715.360889
EM: Round [12] log likelihood: -7715.269561
EM: Round [13] log likelihood: -7715.187479
EM: Round [14] log likelihood: -7715.113565
EM: Round [15] log likelihood: -7715.046882
EM: Round [16] log likelihood: -7714.986609
EM: Round [17] log likelihood: -7714.932033
EM: Round [18] log likelihood: -7714.882526
EM: Round [19] log likelihood: -7714.837538
EM: Round [20] log likelihood: -7714.796585
EM: Round [21] log likelihood: -7714.759242
EM: Round [22] log likelihood: -7714.725132
EM: Round [23] log likelihood: -7714.693925
EM: Round [24] log likelihood: -7714.665325
EM: Round [25] log likelihood: -7714.639074
EM: Round [26] log likelihood: -7714.614941
EM: Round [27] log likelihood: -7714.592719
EM: Round [28] log likelihood: -7714.572228
EM: Round [29] log likelihood: -7714.553305
EM: Round [30] log likelihood: -7714.535803
EM: Round [31] log likelihood: -7714.519595
EM: Round [32] log likelihood: -7714.504564
EM: Round [33] log likelihood: -7714.490607
EM: Round [34] log likelihood: -7714.477630
EM: Round [35] log likelihood: -7714.465550
EM: Round [36] log likelihood: -7714.454292
EM: Round [37] log likelihood: -7714.443788
EM: Round [38] log likelihood: -7714.433976
EM: Round [39] log likelihood: -7714.424802
EM: Round [40] log likelihood: -7714.416216
EM: Round [41] log likelihood: -7714.408172
EM: Round [42] log likelihood: -7714.400629
EM: Round [43] log likelihood: -7714.393551
EM: Round [44] log likelihood: -7714.386903
EM: Round [45] log likelihood: -7714.380653
EM: Round [46] log likelihood: -7714.374775
EM: Round [47] log likelihood: -7714.369241
EM: Round [48] log likelihood: -7714.364028
EM: Round [49] log likelihood: -7714.359116
EM: Round [50] log likelihood: -7714.354482
EM: Round [51] log likelihood: -7714.350110
EM: Round [52] log likelihood: -7714.345983
EM: Round [53] log likelihood: -7714.342084
EM: Round [54] log likelihood: -7714.338399
EM: Round [55] log likelihood: -7714.334916
EM: Round [56] log likelihood: -7714.331621
EM: Round [57] log likelihood: -7714.328504
EM: Round [58] log likelihood: -7714.325553
EM: Round [59] log likelihood: -7714.322759
EM: Round [60] log likelihood: -7714.320113
EM: Round [61] log likelihood: -7714.317606
EM: Round [62] log likelihood: -7714.315230
EM: Round [63] log likelihood: -7714.312978
EM: Round [64] log likelihood: -7714.310842
EM: Round [65] log likelihood: -7714.308817
EM: Round [66] log likelihood: -7714.306896
EM: Round [67] log likelihood: -7714.305073
EM: Round [68] log likelihood: -7714.303343
EM: Round [69] log likelihood: -7714.301701
EM: Round [70] log likelihood: -7714.300142
EM: Round [71] log likelihood: -7714.298662
EM: Round [72] log likelihood: -7714.297257
EM: Round [73] log likelihood: -7714.295923
EM: Round [74] log likelihood: -7714.294655
EM: Round [75] log likelihood: -7714.293451
EM: Round [76] log likelihood: -7714.292307
EM: Round [77] log likelihood: -7714.291219
EM: Round [78] log likelihood: -7714.290187
EM: Round [79] log likelihood: -7714.289205
EM: Round [80] log likelihood: -7714.288272
EM: Round [81] log likelihood: -7714.287385
EM: Round [82] log likelihood: -7714.286542
EM: Round [83] log likelihood: -7714.285741
EM: Round [84] log likelihood: -7714.284979
EM: Round [85] log likelihood: -7714.284255
EM: Round [86] log likelihood: -7714.283566
EM: Round [87] log likelihood: -7714.282911
EM: Round [88] log likelihood: -7714.282288
EM: Round [89] log likelihood: -7714.281696
EM: Round [90] log likelihood: -7714.281133
EM: Round [91] log likelihood: -7714.280598
EM: Round [92] log likelihood: -7714.280088
EM: Round [93] log likelihood: -7714.279604
EM: Round [94] log likelihood: -7714.279143
EM: Round [95] log likelihood: -7714.278705
EM: Round [96] log likelihood: -7714.278288
EM: Round [97] log likelihood: -7714.277891
EM: Round [98] log likelihood: -7714.277514
EM: Round [99] log likelihood: -7714.277156
EM: Round [100] log likelihood: -7714.276814
EM: Round [101] log likelihood: -7714.276489
EM: Round [102] log likelihood: -7714.276181
EM: Round [103] log likelihood: -7714.275887
EM: Round [104] log likelihood: -7714.275607
EM: Round [105] log likelihood: -7714.275341
EM: Round [106] log likelihood: -7714.275088
EM: Round [107] log likelihood: -7714.274847
EM: Round [108] log likelihood: -7714.274618
EM: Round [109] log likelihood: -7714.274400
EM: Round [110] log likelihood: -7714.274193
EM: Round [111] log likelihood: -7714.273996
EM: Round [112] log likelihood: -7714.273808
EM: Round [113] log likelihood: -7714.273630
EM: Round [114] log likelihood: -7714.273460
EM: Round [115] log likelihood: -7714.273298
EM: Round [116] log likelihood: -7714.273144
EM: Round [117] log likelihood: -7714.272998
EM: Round [118] log likelihood: -7714.272859
EM: Round [119] log likelihood: -7714.272726
EM: Round [120] log likelihood: -7714.272600
EM: Round [121] log likelihood: -7714.272480
EM: Round [122] log likelihood: -7714.272366
EM: Round [123] log likelihood: -7714.272257
EM: Round [124] log likelihood: -7714.272154
EM: Round [125] log likelihood: -7714.272055
EM: Stopping iterations at round 125 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_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.jJbViTbJ8s/fi_workdir/tih_rna_sample_00680_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -6772.601260
EM: Round [1] log likelihood: -6772.403710
EM: Round [2] log likelihood: -6772.403416
EM: Round [3] log likelihood: -6772.403414
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1_1.fastp.fastq.gz: 296091919
Warning - not locating file: /tmp/nxf.jJbViTbJ8s/tih_rna_sample_00680_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000286122.1]
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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000259929.5]
WARNING, no entry stored in dbm for [ENSG00000259929.5]
WARNING, no entry stored in dbm for [ENSG00000259807.2]
WARNING, no entry stored in dbm for [ENSG00000259807.2]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
ls: cannot access 'IGV_inputs': No such file or directory