Done.
-parsing GTF file: /tmp/nxf.yetIuoqVgK/tih_rna_sample_00622_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.yetIuoqVgK/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.yetIuoqVgK/tih_rna_sample_00622_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.yetIuoqVgK/tih_rna_sample_00622_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.yetIuoqVgK/fi_workdir/tih_rna_sample_00622_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.yetIuoqVgK/fi_workdir/tih_rna_sample_00622_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00622_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00622_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:59:59 : INFO : Done.
-parsing GTF file: /tmp/nxf.yetIuoqVgK/fi_workdir/tih_rna_sample_00622_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.yetIuoqVgK/fi_workdir/tih_rna_sample_00622_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[1440000] -done parsing /tmp/nxf.yetIuoqVgK/fi_workdir/tih_rna_sample_00622_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
' ** passed ** ' => 4640,
'exons hit < 2' => 2,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 6,
'per_id < 96' => 5623,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 304,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 42,
'seq-similar region overlap' => 201,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
'num genes matched < 2' => 41,
'low complexity anchor region' => 1,
'small anchor length' => 1,
'excessive soft clipping' => 7322
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.yetIuoqVgK/fi_workdir/tih_rna_sample_00622_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[123000] -fusion SPANNING read extraction for scaff: AP2A2--AC132217.2
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[107000] -fusion SPANNING read extraction for scaff: CLSTN2--AC046134.2
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[38000] -fusion SPANNING read extraction for scaff: FARSB--KCNE4
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[63000] -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1
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[64000] -fusion SPANNING read extraction for scaff: NPHP3--ACAD11
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[17000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[18000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[16000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[22000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[22000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[20000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12
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[55000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3
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[17000] -fusion SPANNING read extraction for scaff: PMS2P6--CCDC146
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[123000] -fusion SPANNING read extraction for scaff: RALGDS--RAPGEF1
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[29000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[22000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 29664,
'seq similar region alignment' => 15136
};
EM: Starting log likelihood: -4234.123288
EM: Round [1] log likelihood: -4233.453300
EM: Round [2] log likelihood: -4233.177155
EM: Round [3] log likelihood: -4232.958116
EM: Round [4] log likelihood: -4232.780338
EM: Round [5] log likelihood: -4232.635524
EM: Round [6] log likelihood: -4232.517184
EM: Round [7] log likelihood: -4232.420169
EM: Round [8] log likelihood: -4232.340373
EM: Round [9] log likelihood: -4232.274509
EM: Round [10] log likelihood: -4232.219938
EM: Round [11] log likelihood: -4232.174535
EM: Round [12] log likelihood: -4232.136585
EM: Round [13] log likelihood: -4232.104704
EM: Round [14] log likelihood: -4232.077770
EM: Round [15] log likelihood: -4232.054875
EM: Round [16] log likelihood: -4232.035284
EM: Round [17] log likelihood: -4232.018397
EM: Round [18] log likelihood: -4232.003729
EM: Round [19] log likelihood: -4231.990886
EM: Round [20] log likelihood: -4231.979546
EM: Round [21] log likelihood: -4231.969448
EM: Round [22] log likelihood: -4231.960379
EM: Round [23] log likelihood: -4231.952165
EM: Round [24] log likelihood: -4231.944665
EM: Round [25] log likelihood: -4231.937764
EM: Round [26] log likelihood: -4231.931366
EM: Round [27] log likelihood: -4231.925395
EM: Round [28] log likelihood: -4231.919787
EM: Round [29] log likelihood: -4231.914491
EM: Round [30] log likelihood: -4231.909464
EM: Round [31] log likelihood: -4231.904672
EM: Round [32] log likelihood: -4231.900084
EM: Round [33] log likelihood: -4231.895679
EM: Round [34] log likelihood: -4231.891435
EM: Round [35] log likelihood: -4231.887337
EM: Round [36] log likelihood: -4231.883370
EM: Round [37] log likelihood: -4231.879524
EM: Round [38] log likelihood: -4231.875788
EM: Round [39] log likelihood: -4231.872155
EM: Round [40] log likelihood: -4231.868618
EM: Round [41] log likelihood: -4231.865171
EM: Round [42] log likelihood: -4231.861808
EM: Round [43] log likelihood: -4231.858526
EM: Round [44] log likelihood: -4231.855320
EM: Round [45] log likelihood: -4231.852187
EM: Round [46] log likelihood: -4231.849125
EM: Round [47] log likelihood: -4231.846129
EM: Round [48] log likelihood: -4231.843199
EM: Round [49] log likelihood: -4231.840331
EM: Round [50] log likelihood: -4231.837524
EM: Round [51] log likelihood: -4231.834776
EM: Round [52] log likelihood: -4231.832086
EM: Round [53] log likelihood: -4231.829450
EM: Round [54] log likelihood: -4231.826869
EM: Round [55] log likelihood: -4231.824341
EM: Round [56] log likelihood: -4231.821863
EM: Round [57] log likelihood: -4231.819436
EM: Round [58] log likelihood: -4231.817057
EM: Round [59] log likelihood: -4231.814727
EM: Round [60] log likelihood: -4231.812442
EM: Round [61] log likelihood: -4231.810203
EM: Round [62] log likelihood: -4231.808008
EM: Round [63] log likelihood: -4231.805857
EM: Round [64] log likelihood: -4231.803748
EM: Round [65] log likelihood: -4231.801681
EM: Round [66] log likelihood: -4231.799654
EM: Round [67] log likelihood: -4231.797666
EM: Round [68] log likelihood: -4231.795718
EM: Round [69] log likelihood: -4231.793807
EM: Round [70] log likelihood: -4231.791934
EM: Round [71] log likelihood: -4231.790096
EM: Round [72] log likelihood: -4231.788295
EM: Round [73] log likelihood: -4231.786528
EM: Round [74] log likelihood: -4231.784795
EM: Round [75] log likelihood: -4231.783095
EM: Round [76] log likelihood: -4231.781428
EM: Round [77] log likelihood: -4231.779794
EM: Round [78] log likelihood: -4231.778190
EM: Round [79] log likelihood: -4231.776617
EM: Round [80] log likelihood: -4231.775074
EM: Round [81] log likelihood: -4231.773560
EM: Round [82] log likelihood: -4231.772075
EM: Round [83] log likelihood: -4231.770619
EM: Round [84] log likelihood: -4231.769190
EM: Round [85] log likelihood: -4231.767788
EM: Round [86] log likelihood: -4231.766412
EM: Round [87] log likelihood: -4231.765063
EM: Round [88] log likelihood: -4231.763739
EM: Round [89] log likelihood: -4231.762440
EM: Round [90] log likelihood: -4231.761165
EM: Round [91] log likelihood: -4231.759915
EM: Round [92] log likelihood: -4231.758687
EM: Round [93] log likelihood: -4231.757483
EM: Round [94] log likelihood: -4231.756301
EM: Round [95] log likelihood: -4231.755142
EM: Round [96] log likelihood: -4231.754004
EM: Round [97] log likelihood: -4231.752887
EM: Round [98] log likelihood: -4231.751791
EM: Round [99] log likelihood: -4231.750715
EM: Round [100] log likelihood: -4231.749660
EM: Round [101] log likelihood: -4231.748624
EM: Round [102] log likelihood: -4231.747607
EM: Round [103] log likelihood: -4231.746609
EM: Round [104] log likelihood: -4231.745630
EM: Round [105] log likelihood: -4231.744669
EM: Round [106] log likelihood: -4231.743725
EM: Round [107] log likelihood: -4231.742799
EM: Round [108] log likelihood: -4231.741890
EM: Round [109] log likelihood: -4231.740998
EM: Round [110] log likelihood: -4231.740122
EM: Round [111] log likelihood: -4231.739262
EM: Round [112] log likelihood: -4231.738418
EM: Round [113] log likelihood: -4231.737590
EM: Round [114] log likelihood: -4231.736777
EM: Round [115] log likelihood: -4231.735978
EM: Round [116] log likelihood: -4231.735194
EM: Round [117] log likelihood: -4231.734425
EM: Round [118] log likelihood: -4231.733670
EM: Round [119] log likelihood: -4231.732928
EM: Round [120] log likelihood: -4231.732200
EM: Round [121] log likelihood: -4231.731486
EM: Round [122] log likelihood: -4231.730784
EM: Round [123] log likelihood: -4231.730095
EM: Round [124] log likelihood: -4231.729419
EM: Round [125] log likelihood: -4231.728755
EM: Round [126] log likelihood: -4231.728103
EM: Round [127] log likelihood: -4231.727463
EM: Round [128] log likelihood: -4231.726835
EM: Round [129] log likelihood: -4231.726218
EM: Round [130] log likelihood: -4231.725612
EM: Round [131] log likelihood: -4231.725017
EM: Round [132] log likelihood: -4231.724433
EM: Round [133] log likelihood: -4231.723860
EM: Round [134] log likelihood: -4231.723297
EM: Round [135] log likelihood: -4231.722744
EM: Round [136] log likelihood: -4231.722201
EM: Round [137] log likelihood: -4231.721668
EM: Round [138] log likelihood: -4231.721144
EM: Round [139] log likelihood: -4231.720630
EM: Round [140] log likelihood: -4231.720126
EM: Round [141] log likelihood: -4231.719630
EM: Round [142] log likelihood: -4231.719143
EM: Round [143] log likelihood: -4231.718665
EM: Round [144] log likelihood: -4231.718196
EM: Round [145] log likelihood: -4231.717735
EM: Round [146] log likelihood: -4231.717283
EM: Round [147] log likelihood: -4231.716838
EM: Round [148] log likelihood: -4231.716402
EM: Round [149] log likelihood: -4231.715973
EM: Round [150] log likelihood: -4231.715552
EM: Round [151] log likelihood: -4231.715139
EM: Round [152] log likelihood: -4231.714733
EM: Round [153] log likelihood: -4231.714334
EM: Round [154] log likelihood: -4231.713943
EM: Round [155] log likelihood: -4231.713558
EM: Round [156] log likelihood: -4231.713181
EM: Round [157] log likelihood: -4231.712810
EM: Round [158] log likelihood: -4231.712446
EM: Round [159] log likelihood: -4231.712088
EM: Round [160] log likelihood: -4231.711737
EM: Round [161] log likelihood: -4231.711392
EM: Round [162] log likelihood: -4231.711053
EM: Round [163] log likelihood: -4231.710720
EM: Round [164] log likelihood: -4231.710393
EM: Round [165] log likelihood: -4231.710072
EM: Round [166] log likelihood: -4231.709757
EM: Round [167] log likelihood: -4231.709447
EM: Round [168] log likelihood: -4231.709143
EM: Round [169] log likelihood: -4231.708845
EM: Round [170] log likelihood: -4231.708551
EM: Round [171] log likelihood: -4231.708263
EM: Round [172] log likelihood: -4231.707980
EM: Round [173] log likelihood: -4231.707702
EM: Round [174] log likelihood: -4231.707429
EM: Round [175] log likelihood: -4231.707161
EM: Round [176] log likelihood: -4231.706898
EM: Round [177] log likelihood: -4231.706639
EM: Round [178] log likelihood: -4231.706385
EM: Round [179] log likelihood: -4231.706136
EM: Round [180] log likelihood: -4231.705890
EM: Round [181] log likelihood: -4231.705650
EM: Round [182] log likelihood: -4231.705413
EM: Round [183] log likelihood: -4231.705181
EM: Round [184] log likelihood: -4231.704953
EM: Round [185] log likelihood: -4231.704729
EM: Round [186] log likelihood: -4231.704509
EM: Round [187] log likelihood: -4231.704292
EM: Round [188] log likelihood: -4231.704080
EM: Round [189] log likelihood: -4231.703872
EM: Round [190] log likelihood: -4231.703667
EM: Round [191] log likelihood: -4231.703465
EM: Round [192] log likelihood: -4231.703268
EM: Round [193] log likelihood: -4231.703074
EM: Round [194] log likelihood: -4231.702883
EM: Round [195] log likelihood: -4231.702695
EM: Round [196] log likelihood: -4231.702511
EM: Round [197] log likelihood: -4231.702331
EM: Round [198] log likelihood: -4231.702153
EM: Round [199] log likelihood: -4231.701979
EM: Round [200] log likelihood: -4231.701807
EM: Round [201] log likelihood: -4231.701639
EM: Round [202] log likelihood: -4231.701474
EM: Round [203] log likelihood: -4231.701311
EM: Round [204] log likelihood: -4231.701152
EM: Round [205] log likelihood: -4231.700995
EM: Round [206] log likelihood: -4231.700841
EM: Round [207] log likelihood: -4231.700690
EM: Round [208] log likelihood: -4231.700542
EM: Round [209] log likelihood: -4231.700396
EM: Round [210] log likelihood: -4231.700252
EM: Round [211] log likelihood: -4231.700112
EM: Round [212] log likelihood: -4231.699973
EM: Round [213] log likelihood: -4231.699837
EM: Round [214] log likelihood: -4231.699704
EM: Round [215] log likelihood: -4231.699573
EM: Round [216] log likelihood: -4231.699444
EM: Round [217] log likelihood: -4231.699318
EM: Round [218] log likelihood: -4231.699193
EM: Round [219] log likelihood: -4231.699071
EM: Round [220] log likelihood: -4231.698951
EM: Round [221] log likelihood: -4231.698834
EM: Round [222] log likelihood: -4231.698718
EM: Round [223] log likelihood: -4231.698604
EM: Round [224] log likelihood: -4231.698493
EM: Round [225] log likelihood: -4231.698383
EM: Round [226] log likelihood: -4231.698275
EM: Round [227] log likelihood: -4231.698169
EM: Round [228] log likelihood: -4231.698065
EM: Round [229] log likelihood: -4231.697963
EM: Round [230] log likelihood: -4231.697863
EM: Round [231] log likelihood: -4231.697764
EM: Stopping iterations at round 231 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.yetIuoqVgK/tih_rna_sample_00622_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.yetIuoqVgK/tih_rna_sample_00622_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.yetIuoqVgK/tih_rna_sample_00622_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.yetIuoqVgK/tih_rna_sample_00622_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.yetIuoqVgK/tih_rna_sample_00622_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.yetIuoqVgK/tih_rna_sample_00622_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.yetIuoqVgK/tih_rna_sample_00622_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.yetIuoqVgK/fi_workdir/tih_rna_sample_00622_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.yetIuoqVgK/fi_workdir/tih_rna_sample_00622_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.yetIuoqVgK/fi_workdir/tih_rna_sample_00622_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.yetIuoqVgK/tih_rna_sample_00622_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.yetIuoqVgK/tih_rna_sample_00622_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3605.379055
EM: Round [1] log likelihood: -3605.286165
EM: Round [2] log likelihood: -3605.285037
EM: Round [3] log likelihood: -3605.285023
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.yetIuoqVgK/tih_rna_sample_00622_B23MVV7LT4_1_1.fastp.fastq.gz: 295576441
Warning - not locating file: /tmp/nxf.yetIuoqVgK/tih_rna_sample_00622_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
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 [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000248932.6]
WARNING, no entry stored in dbm for [ENSG00000248932.6]
ls: cannot access 'IGV_inputs': No such file or directory