Done.
-parsing GTF file: /tmp/nxf.tSIygJLDqS/tih_rna_sample_00681_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.tSIygJLDqS/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.tSIygJLDqS/tih_rna_sample_00681_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.tSIygJLDqS/tih_rna_sample_00681_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.tSIygJLDqS/fi_workdir/tih_rna_sample_00681_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.tSIygJLDqS/fi_workdir/tih_rna_sample_00681_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00681_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00681_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:14:57 : INFO : Done.
-parsing GTF file: /tmp/nxf.tSIygJLDqS/fi_workdir/tih_rna_sample_00681_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.tSIygJLDqS/fi_workdir/tih_rna_sample_00681_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[1390000] -done parsing /tmp/nxf.tSIygJLDqS/fi_workdir/tih_rna_sample_00681_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'seq-similar region overlap' => 155,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 16,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 289,
'excessive soft clipping' => 7266,
'num genes matched < 2' => 20,
' ** passed ** ' => 11751,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 17,
'small anchor length' => 43,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 21,
'low complexity anchor region' => 18,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 28,
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 16,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 16,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 34,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 5,
'per_id < 96' => 7282,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.tSIygJLDqS/fi_workdir/tih_rna_sample_00681_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[87000] -fusion SPANNING read extraction for scaff: EIF3E--TMEM71
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[24000] -fusion SPANNING read extraction for scaff: EPHA4--LINC02832
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
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[9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[51000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
[1000]
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[23000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
[1000]
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[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000]
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[14000]
[15000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
[10000] -fusion SPANNING read extraction for scaff: PMS2P8--CCDC146
[1000]
[2000]
[3000]
[4000]
[5000]
[6000]
[7000]
[8000]
[9000]
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[12000] -fusion SPANNING read extraction for scaff: SLC39A9--TMEM229B
[1000]
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[5000]
[6000]
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[58000]
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[64000]
[65000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
[1000]
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[24000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
[1000]
[2000]
[3000]
[4000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
[1000]
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[80000]
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[87000] -fusion SPANNING read extraction for scaff: TMEM71--EIF3E
[1000]
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[18000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
[1000]
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[121000] -fusion SPANNING read extraction for scaff: XKR6--DLC1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 32501,
'lacks exon overlap' => 3769
};
EM: Starting log likelihood: -6118.148385
EM: Round [1] log likelihood: -6115.041560
EM: Round [2] log likelihood: -6113.562847
EM: Round [3] log likelihood: -6112.299997
EM: Round [4] log likelihood: -6111.199936
EM: Round [5] log likelihood: -6110.231682
EM: Round [6] log likelihood: -6109.372987
EM: Round [7] log likelihood: -6108.607231
EM: Round [8] log likelihood: -6107.921530
EM: Round [9] log likelihood: -6107.305563
EM: Round [10] log likelihood: -6106.750833
EM: Round [11] log likelihood: -6106.250185
EM: Round [12] log likelihood: -6105.797495
EM: Round [13] log likelihood: -6105.387458
EM: Round [14] log likelihood: -6105.015437
EM: Round [15] log likelihood: -6104.677360
EM: Round [16] log likelihood: -6104.369631
EM: Round [17] log likelihood: -6104.089073
EM: Round [18] log likelihood: -6103.832870
EM: Round [19] log likelihood: -6103.598524
EM: Round [20] log likelihood: -6103.383819
EM: Round [21] log likelihood: -6103.186790
EM: Round [22] log likelihood: -6103.005686
EM: Round [23] log likelihood: -6102.838955
EM: Round [24] log likelihood: -6102.685216
EM: Round [25] log likelihood: -6102.543238
EM: Round [26] log likelihood: -6102.411926
EM: Round [27] log likelihood: -6102.290304
EM: Round [28] log likelihood: -6102.177500
EM: Round [29] log likelihood: -6102.072736
EM: Round [30] log likelihood: -6101.975315
EM: Round [31] log likelihood: -6101.884614
EM: Round [32] log likelihood: -6101.800071
EM: Round [33] log likelihood: -6101.721183
EM: Round [34] log likelihood: -6101.647496
EM: Round [35] log likelihood: -6101.578603
EM: Round [36] log likelihood: -6101.514132
EM: Round [37] log likelihood: -6101.453749
EM: Round [38] log likelihood: -6101.397151
EM: Round [39] log likelihood: -6101.344061
EM: Round [40] log likelihood: -6101.294227
EM: Round [41] log likelihood: -6101.247421
EM: Round [42] log likelihood: -6101.203432
EM: Round [43] log likelihood: -6101.162068
EM: Round [44] log likelihood: -6101.123152
EM: Round [45] log likelihood: -6101.086523
EM: Round [46] log likelihood: -6101.052030
EM: Round [47] log likelihood: -6101.019537
EM: Round [48] log likelihood: -6100.988915
EM: Round [49] log likelihood: -6100.960047
EM: Round [50] log likelihood: -6100.932823
EM: Round [51] log likelihood: -6100.907143
EM: Round [52] log likelihood: -6100.882912
EM: Round [53] log likelihood: -6100.860042
EM: Round [54] log likelihood: -6100.838452
EM: Round [55] log likelihood: -6100.818066
EM: Round [56] log likelihood: -6100.798812
EM: Round [57] log likelihood: -6100.780624
EM: Round [58] log likelihood: -6100.763441
EM: Round [59] log likelihood: -6100.747203
EM: Round [60] log likelihood: -6100.731858
EM: Round [61] log likelihood: -6100.717352
EM: Round [62] log likelihood: -6100.703640
EM: Round [63] log likelihood: -6100.690675
EM: Round [64] log likelihood: -6100.678416
EM: Round [65] log likelihood: -6100.666823
EM: Round [66] log likelihood: -6100.655858
EM: Round [67] log likelihood: -6100.645488
EM: Round [68] log likelihood: -6100.635677
EM: Round [69] log likelihood: -6100.626397
EM: Round [70] log likelihood: -6100.617616
EM: Round [71] log likelihood: -6100.609309
EM: Round [72] log likelihood: -6100.601448
EM: Round [73] log likelihood: -6100.594009
EM: Round [74] log likelihood: -6100.586970
EM: Round [75] log likelihood: -6100.580308
EM: Round [76] log likelihood: -6100.574003
EM: Round [77] log likelihood: -6100.568035
EM: Round [78] log likelihood: -6100.562386
EM: Round [79] log likelihood: -6100.557039
EM: Round [80] log likelihood: -6100.551978
EM: Round [81] log likelihood: -6100.547186
EM: Round [82] log likelihood: -6100.542651
EM: Round [83] log likelihood: -6100.538356
EM: Round [84] log likelihood: -6100.534291
EM: Round [85] log likelihood: -6100.530442
EM: Round [86] log likelihood: -6100.526798
EM: Round [87] log likelihood: -6100.523347
EM: Round [88] log likelihood: -6100.520080
EM: Round [89] log likelihood: -6100.516986
EM: Round [90] log likelihood: -6100.514057
EM: Round [91] log likelihood: -6100.511284
EM: Round [92] log likelihood: -6100.508657
EM: Round [93] log likelihood: -6100.506170
EM: Round [94] log likelihood: -6100.503815
EM: Round [95] log likelihood: -6100.501584
EM: Round [96] log likelihood: -6100.499472
EM: Round [97] log likelihood: -6100.497472
EM: Round [98] log likelihood: -6100.495578
EM: Round [99] log likelihood: -6100.493784
EM: Round [100] log likelihood: -6100.492085
EM: Round [101] log likelihood: -6100.490476
EM: Round [102] log likelihood: -6100.488952
EM: Round [103] log likelihood: -6100.487509
EM: Round [104] log likelihood: -6100.486142
EM: Round [105] log likelihood: -6100.484848
EM: Round [106] log likelihood: -6100.483621
EM: Round [107] log likelihood: -6100.482460
EM: Round [108] log likelihood: -6100.481360
EM: Round [109] log likelihood: -6100.480319
EM: Round [110] log likelihood: -6100.479332
EM: Round [111] log likelihood: -6100.478398
EM: Round [112] log likelihood: -6100.477513
EM: Round [113] log likelihood: -6100.476674
EM: Round [114] log likelihood: -6100.475880
EM: Round [115] log likelihood: -6100.475128
EM: Round [116] log likelihood: -6100.474416
EM: Round [117] log likelihood: -6100.473741
EM: Round [118] log likelihood: -6100.473102
EM: Round [119] log likelihood: -6100.472497
EM: Round [120] log likelihood: -6100.471923
EM: Round [121] log likelihood: -6100.471380
EM: Round [122] log likelihood: -6100.470866
EM: Round [123] log likelihood: -6100.470379
EM: Round [124] log likelihood: -6100.469917
EM: Round [125] log likelihood: -6100.469480
EM: Round [126] log likelihood: -6100.469066
EM: Round [127] log likelihood: -6100.468674
EM: Round [128] log likelihood: -6100.468302
EM: Round [129] log likelihood: -6100.467950
EM: Round [130] log likelihood: -6100.467617
EM: Round [131] log likelihood: -6100.467301
EM: Round [132] log likelihood: -6100.467002
EM: Round [133] log likelihood: -6100.466719
EM: Round [134] log likelihood: -6100.466450
EM: Round [135] log likelihood: -6100.466196
EM: Round [136] log likelihood: -6100.465956
EM: Round [137] log likelihood: -6100.465727
EM: Round [138] log likelihood: -6100.465511
EM: Round [139] log likelihood: -6100.465307
EM: Round [140] log likelihood: -6100.465113
EM: Round [141] log likelihood: -6100.464929
EM: Round [142] log likelihood: -6100.464755
EM: Round [143] log likelihood: -6100.464591
EM: Round [144] log likelihood: -6100.464435
EM: Round [145] log likelihood: -6100.464287
EM: Round [146] log likelihood: -6100.464147
EM: Round [147] log likelihood: -6100.464014
EM: Round [148] log likelihood: -6100.463888
EM: Round [149] log likelihood: -6100.463769
EM: Round [150] log likelihood: -6100.463657
EM: Round [151] log likelihood: -6100.463550
EM: Round [152] log likelihood: -6100.463449
EM: Round [153] log likelihood: -6100.463353
EM: Stopping iterations at round 153 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.tSIygJLDqS/tih_rna_sample_00681_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.tSIygJLDqS/tih_rna_sample_00681_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.tSIygJLDqS/tih_rna_sample_00681_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.tSIygJLDqS/tih_rna_sample_00681_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.tSIygJLDqS/tih_rna_sample_00681_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.tSIygJLDqS/tih_rna_sample_00681_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.tSIygJLDqS/tih_rna_sample_00681_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.tSIygJLDqS/fi_workdir/tih_rna_sample_00681_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.tSIygJLDqS/fi_workdir/tih_rna_sample_00681_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.tSIygJLDqS/fi_workdir/tih_rna_sample_00681_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.tSIygJLDqS/tih_rna_sample_00681_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.tSIygJLDqS/tih_rna_sample_00681_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -4553.200955
EM: Round [1] log likelihood: -4553.179438
EM: Round [2] log likelihood: -4553.179431
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.tSIygJLDqS/tih_rna_sample_00681_B23MVV7LT4_1_1.fastp.fastq.gz: 296336988
Warning - not locating file: /tmp/nxf.tSIygJLDqS/tih_rna_sample_00681_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
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 [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 [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 [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
ls: cannot access 'IGV_inputs': No such file or directory