Done.
-parsing GTF file: /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.Kj68ZgUQ3V/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.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00764_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00764_B23MVV7LT4_1.star.sortedByCoord.out.bam
10:54:15 : INFO : Done.
-parsing GTF file: /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[4030000] -done parsing /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
' ** passed ** ' => 26951,
'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 12,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 372,
'excessive soft clipping' => 25444,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 84,
'per_id < 96' => 11477,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 16,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 38,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 407,
'seq-similar region overlap' => 610,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'num genes matched < 2' => 119,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 44,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 29,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 38,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 12,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 340,
'small anchor length' => 103,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 75,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 3,
'low complexity anchor region' => 20
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[8000] -fusion SPANNING read extraction for scaff: AC245452.1--TXNRD2
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[256000] -fusion SPANNING read extraction for scaff: BMPR1A--ACTA2
[1000] -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2
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[40000] -fusion SPANNING read extraction for scaff: FNDC3A--AC098862.1
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[90000] -fusion SPANNING read extraction for scaff: FNDC3A--SLIT2
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[120000] -fusion SPANNING read extraction for scaff: MAPK1--TXNRD2
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[60000] -fusion SPANNING read extraction for scaff: NPHP3--ACAD11
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[38000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[44000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[45000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[25000] -fusion SPANNING read extraction for scaff: PCDHA2--PCDHAC2
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[32000] -fusion SPANNING read extraction for scaff: PCDHA2--PCDHAC1
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[33000] -fusion SPANNING read extraction for scaff: PCDHA2--PCDHA13
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[28000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2
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[34000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1
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[35000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13
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[22000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[28000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[29000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[40000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA8
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC4
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[56000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC3
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[31000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGC5
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[36000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA10
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[32000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGB6
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[45000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA11
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[33000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGB7
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[40000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA12
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[39000] -fusion SPANNING read extraction for scaff: PCDHGA1--PCDHGA9
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[22000] -fusion SPANNING read extraction for scaff: PMS2P8--CCDC146
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[194000] -fusion SPANNING read extraction for scaff: PPIL2--AC007326.5
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[189000] -fusion SPANNING read extraction for scaff: PPIL2--AL353807.5
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[187000] -fusion SPANNING read extraction for scaff: PPIL2--ERVK-28
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[187000] -fusion SPANNING read extraction for scaff: PPIL2--AC087354.1
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[185000] -fusion SPANNING read extraction for scaff: PPIL2--LHFPL3-AS1
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[39000] -fusion SPANNING read extraction for scaff: SEPTIN5--TXNRD2
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[51000] -fusion SPANNING read extraction for scaff: SLIT2--PSME2P2
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[49000] -fusion SPANNING read extraction for scaff: SLIT2--AL161421.1
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[25000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[60000] -fusion SPANNING read extraction for scaff: TMCO3--TP53
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[53000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[12000] -fusion SPANNING read extraction for scaff: UBE2Q2P1--GOLGA6L10
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 13335,
'seq similar region alignment' => 148580
};
EM: Starting log likelihood: -14485.101537
EM: Round [1] log likelihood: -14110.147082
EM: Round [2] log likelihood: -13951.152027
EM: Round [3] log likelihood: -13872.878025
EM: Round [4] log likelihood: -13830.828361
EM: Round [5] log likelihood: -13806.453411
EM: Round [6] log likelihood: -13791.393481
EM: Round [7] log likelihood: -13781.552986
EM: Round [8] log likelihood: -13774.810392
EM: Round [9] log likelihood: -13770.029702
EM: Round [10] log likelihood: -13766.567568
EM: Round [11] log likelihood: -13764.027877
EM: Round [12] log likelihood: -13762.147880
EM: Round [13] log likelihood: -13760.745130
EM: Round [14] log likelihood: -13759.689951
EM: Round [15] log likelihood: -13758.889111
EM: Round [16] log likelihood: -13758.275161
EM: Round [17] log likelihood: -13757.799116
EM: Round [18] log likelihood: -13757.425295
EM: Round [19] log likelihood: -13757.127637
EM: Round [20] log likelihood: -13756.887062
EM: Round [21] log likelihood: -13756.689557
EM: Round [22] log likelihood: -13756.524805
EM: Round [23] log likelihood: -13756.385179
EM: Round [24] log likelihood: -13756.265021
EM: Round [25] log likelihood: -13756.160118
EM: Round [26] log likelihood: -13756.067312
EM: Round [27] log likelihood: -13755.984228
EM: Round [28] log likelihood: -13755.909063
EM: Round [29] log likelihood: -13755.840442
EM: Round [30] log likelihood: -13755.777307
EM: Round [31] log likelihood: -13755.718837
EM: Round [32] log likelihood: -13755.664386
EM: Round [33] log likelihood: -13755.613444
EM: Round [34] log likelihood: -13755.565602
EM: Round [35] log likelihood: -13755.520527
EM: Round [36] log likelihood: -13755.477946
EM: Round [37] log likelihood: -13755.437633
EM: Round [38] log likelihood: -13755.399397
EM: Round [39] log likelihood: -13755.363075
EM: Round [40] log likelihood: -13755.328527
EM: Round [41] log likelihood: -13755.295630
EM: Round [42] log likelihood: -13755.264277
EM: Round [43] log likelihood: -13755.234372
EM: Round [44] log likelihood: -13755.205829
EM: Round [45] log likelihood: -13755.178572
EM: Round [46] log likelihood: -13755.152528
EM: Round [47] log likelihood: -13755.127633
EM: Round [48] log likelihood: -13755.103828
EM: Round [49] log likelihood: -13755.081058
EM: Round [50] log likelihood: -13755.059271
EM: Round [51] log likelihood: -13755.038420
EM: Round [52] log likelihood: -13755.018461
EM: Round [53] log likelihood: -13754.999350
EM: Round [54] log likelihood: -13754.981050
EM: Round [55] log likelihood: -13754.963522
EM: Round [56] log likelihood: -13754.946732
EM: Round [57] log likelihood: -13754.930647
EM: Round [58] log likelihood: -13754.915235
EM: Round [59] log likelihood: -13754.900467
EM: Round [60] log likelihood: -13754.886314
EM: Round [61] log likelihood: -13754.872749
EM: Round [62] log likelihood: -13754.859748
EM: Round [63] log likelihood: -13754.847285
EM: Round [64] log likelihood: -13754.835338
EM: Round [65] log likelihood: -13754.823884
EM: Round [66] log likelihood: -13754.812902
EM: Round [67] log likelihood: -13754.802373
EM: Round [68] log likelihood: -13754.792277
EM: Round [69] log likelihood: -13754.782596
EM: Round [70] log likelihood: -13754.773313
EM: Round [71] log likelihood: -13754.764410
EM: Round [72] log likelihood: -13754.755872
EM: Round [73] log likelihood: -13754.747684
EM: Round [74] log likelihood: -13754.739830
EM: Round [75] log likelihood: -13754.732298
EM: Round [76] log likelihood: -13754.725073
EM: Round [77] log likelihood: -13754.718144
EM: Round [78] log likelihood: -13754.711497
EM: Round [79] log likelihood: -13754.705121
EM: Round [80] log likelihood: -13754.699004
EM: Round [81] log likelihood: -13754.693137
EM: Round [82] log likelihood: -13754.687508
EM: Round [83] log likelihood: -13754.682109
EM: Round [84] log likelihood: -13754.676929
EM: Round [85] log likelihood: -13754.671959
EM: Round [86] log likelihood: -13754.667192
EM: Round [87] log likelihood: -13754.662617
EM: Round [88] log likelihood: -13754.658229
EM: Round [89] log likelihood: -13754.654019
EM: Round [90] log likelihood: -13754.649979
EM: Round [91] log likelihood: -13754.646103
EM: Round [92] log likelihood: -13754.642384
EM: Round [93] log likelihood: -13754.638816
EM: Round [94] log likelihood: -13754.635392
EM: Round [95] log likelihood: -13754.632107
EM: Round [96] log likelihood: -13754.628954
EM: Round [97] log likelihood: -13754.625930
EM: Round [98] log likelihood: -13754.623027
EM: Round [99] log likelihood: -13754.620242
EM: Round [100] log likelihood: -13754.617570
EM: Round [101] log likelihood: -13754.615005
EM: Round [102] log likelihood: -13754.612545
EM: Round [103] log likelihood: -13754.610183
EM: Round [104] log likelihood: -13754.607917
EM: Round [105] log likelihood: -13754.605742
EM: Round [106] log likelihood: -13754.603656
EM: Round [107] log likelihood: -13754.601653
EM: Round [108] log likelihood: -13754.599731
EM: Round [109] log likelihood: -13754.597887
EM: Round [110] log likelihood: -13754.596117
EM: Round [111] log likelihood: -13754.594419
EM: Round [112] log likelihood: -13754.592788
EM: Round [113] log likelihood: -13754.591224
EM: Round [114] log likelihood: -13754.589723
EM: Round [115] log likelihood: -13754.588282
EM: Round [116] log likelihood: -13754.586899
EM: Round [117] log likelihood: -13754.585572
EM: Round [118] log likelihood: -13754.584298
EM: Round [119] log likelihood: -13754.583076
EM: Round [120] log likelihood: -13754.581903
EM: Round [121] log likelihood: -13754.580777
EM: Round [122] log likelihood: -13754.579696
EM: Round [123] log likelihood: -13754.578659
EM: Round [124] log likelihood: -13754.577664
EM: Round [125] log likelihood: -13754.576708
EM: Round [126] log likelihood: -13754.575791
EM: Round [127] log likelihood: -13754.574911
EM: Round [128] log likelihood: -13754.574066
EM: Round [129] log likelihood: -13754.573255
EM: Round [130] log likelihood: -13754.572477
EM: Round [131] log likelihood: -13754.571730
EM: Round [132] log likelihood: -13754.571013
EM: Round [133] log likelihood: -13754.570325
EM: Round [134] log likelihood: -13754.569664
EM: Round [135] log likelihood: -13754.569030
EM: Round [136] log likelihood: -13754.568422
EM: Round [137] log likelihood: -13754.567838
EM: Round [138] log likelihood: -13754.567277
EM: Round [139] log likelihood: -13754.566739
EM: Round [140] log likelihood: -13754.566222
EM: Round [141] log likelihood: -13754.565726
EM: Round [142] log likelihood: -13754.565250
EM: Round [143] log likelihood: -13754.564793
EM: Round [144] log likelihood: -13754.564355
EM: Round [145] log likelihood: -13754.563934
EM: Round [146] log likelihood: -13754.563529
EM: Round [147] log likelihood: -13754.563141
EM: Round [148] log likelihood: -13754.562769
EM: Round [149] log likelihood: -13754.562411
EM: Round [150] log likelihood: -13754.562068
EM: Round [151] log likelihood: -13754.561738
EM: Round [152] log likelihood: -13754.561422
EM: Round [153] log likelihood: -13754.561118
EM: Round [154] log likelihood: -13754.560827
EM: Round [155] log likelihood: -13754.560547
EM: Round [156] log likelihood: -13754.560278
EM: Round [157] log likelihood: -13754.560020
EM: Round [158] log likelihood: -13754.559772
EM: Round [159] log likelihood: -13754.559535
EM: Round [160] log likelihood: -13754.559306
EM: Round [161] log likelihood: -13754.559087
EM: Round [162] log likelihood: -13754.558877
EM: Round [163] log likelihood: -13754.558675
EM: Round [164] log likelihood: -13754.558480
EM: Round [165] log likelihood: -13754.558294
EM: Round [166] log likelihood: -13754.558115
EM: Round [167] log likelihood: -13754.557944
EM: Round [168] log likelihood: -13754.557779
EM: Round [169] log likelihood: -13754.557620
EM: Round [170] log likelihood: -13754.557468
EM: Round [171] log likelihood: -13754.557322
EM: Round [172] log likelihood: -13754.557182
EM: Round [173] log likelihood: -13754.557047
EM: Round [174] log likelihood: -13754.556918
EM: Round [175] log likelihood: -13754.556794
EM: Round [176] log likelihood: -13754.556674
EM: Round [177] log likelihood: -13754.556560
EM: Round [178] log likelihood: -13754.556450
EM: Round [179] log likelihood: -13754.556344
EM: Round [180] log likelihood: -13754.556242
EM: Round [181] log likelihood: -13754.556145
EM: Stopping iterations at round 181 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_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.Kj68ZgUQ3V/fi_workdir/tih_rna_sample_00764_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -10626.427294
EM: Round [1] log likelihood: -10312.127402
EM: Round [2] log likelihood: -10198.158187
EM: Round [3] log likelihood: -10151.444663
EM: Round [4] log likelihood: -10131.785965
EM: Round [5] log likelihood: -10123.431502
EM: Round [6] log likelihood: -10119.951869
EM: Round [7] log likelihood: -10118.580416
EM: Round [8] log likelihood: -10118.074945
EM: Round [9] log likelihood: -10117.899255
EM: Round [10] log likelihood: -10117.840754
EM: Round [11] log likelihood: -10117.821815
EM: Round [12] log likelihood: -10117.815789
EM: Round [13] log likelihood: -10117.813891
EM: Round [14] log likelihood: -10117.813297
EM: Round [15] log likelihood: -10117.813112
EM: Round [16] log likelihood: -10117.813054
EM: Stopping iterations at round 16 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1_1.fastp.fastq.gz: 245131577
Warning - not locating file: /tmp/nxf.Kj68ZgUQ3V/tih_rna_sample_00764_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000284294.1]
WARNING, no entry stored in dbm for [ENSG00000284294.1]
WARNING, no entry stored in dbm for [ENSG00000284294.1]
WARNING, no entry stored in dbm for [ENSG00000267696.6]
WARNING, no entry stored in dbm for [ENSG00000286699.1]
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 [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 [ENSG00000226869.6]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000287700.1]
WARNING, no entry stored in dbm for [ENSG00000287700.1]
WARNING, no entry stored in dbm for [ENSG00000287700.1]
WARNING, no entry stored in dbm for [ENSG00000287700.1]
WARNING, no entry stored in dbm for [ENSG00000232849.2]
WARNING, no entry stored in dbm for [ENSG00000232849.2]
ls: cannot access 'IGV_inputs': No such file or directory