Done.
-parsing GTF file: /tmp/nxf.U4x38NdZyT/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.U4x38NdZyT/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.U4x38NdZyT/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.U4x38NdZyT/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.U4x38NdZyT/fi_workdir/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.U4x38NdZyT/fi_workdir/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
11:27:29 : INFO : Done.
-parsing GTF file: /tmp/nxf.U4x38NdZyT/fi_workdir/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.U4x38NdZyT/fi_workdir/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
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[1180000] -done parsing /tmp/nxf.U4x38NdZyT/fi_workdir/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 18,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8,
'seq-similar region overlap' => 174,
' ** passed ** ' => 1786,
'per_id < 96' => 4219,
'small anchor length' => 14,
'low complexity anchor region' => 1,
'excessive soft clipping' => 7958,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 9,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 15,
'num genes matched < 2' => 33,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 120
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.U4x38NdZyT/fi_workdir/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[107000] -fusion SPANNING read extraction for scaff: ATXN2L--MBD3
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[17000] -fusion SPANNING read extraction for scaff: KLHL22--SMPD4P1
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[12000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[54000] -fusion SPANNING read extraction for scaff: PHKB--ITFG1
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[49000] -fusion SPANNING read extraction for scaff: RUNDC3A-AS1--SLC25A39
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[39000] -fusion SPANNING read extraction for scaff: SIM2--ASS1
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[79000] -fusion SPANNING read extraction for scaff: TEAD2--ZNF106
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[27000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[6000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[199000] -fusion SPANNING read extraction for scaff: TNS3--PKD1L1
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[22000] -fusion SPANNING read extraction for scaff: TTC39B--CCDC171
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[13000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
[1000]
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[3000] -fusion SPANNING read extraction for scaff: ZNF81--AL928596.1
[1000]
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[3000] -fusion SPANNING read extraction for scaff: ZNF81--AL807740.1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 104250,
'lacks exon overlap' => 7595
};
EM: Starting log likelihood: -2219.118104
EM: Round [1] log likelihood: -2218.981815
EM: Round [2] log likelihood: -2218.958300
EM: Round [3] log likelihood: -2218.936062
EM: Round [4] log likelihood: -2218.914623
EM: Round [5] log likelihood: -2218.893939
EM: Round [6] log likelihood: -2218.873976
EM: Round [7] log likelihood: -2218.854702
EM: Round [8] log likelihood: -2218.836088
EM: Round [9] log likelihood: -2218.818103
EM: Round [10] log likelihood: -2218.800723
EM: Round [11] log likelihood: -2218.783921
EM: Round [12] log likelihood: -2218.767675
EM: Round [13] log likelihood: -2218.751960
EM: Round [14] log likelihood: -2218.736756
EM: Round [15] log likelihood: -2218.722043
EM: Round [16] log likelihood: -2218.707801
EM: Round [17] log likelihood: -2218.694012
EM: Round [18] log likelihood: -2218.680659
EM: Round [19] log likelihood: -2218.667725
EM: Round [20] log likelihood: -2218.655194
EM: Round [21] log likelihood: -2218.643052
EM: Round [22] log likelihood: -2218.631284
EM: Round [23] log likelihood: -2218.619876
EM: Round [24] log likelihood: -2218.608816
EM: Round [25] log likelihood: -2218.598091
EM: Round [26] log likelihood: -2218.587689
EM: Round [27] log likelihood: -2218.577599
EM: Round [28] log likelihood: -2218.567810
EM: Round [29] log likelihood: -2218.558311
EM: Round [30] log likelihood: -2218.549093
EM: Round [31] log likelihood: -2218.540147
EM: Round [32] log likelihood: -2218.531462
EM: Round [33] log likelihood: -2218.523031
EM: Round [34] log likelihood: -2218.514845
EM: Round [35] log likelihood: -2218.506895
EM: Round [36] log likelihood: -2218.499175
EM: Round [37] log likelihood: -2218.491676
EM: Round [38] log likelihood: -2218.484391
EM: Round [39] log likelihood: -2218.477314
EM: Round [40] log likelihood: -2218.470438
EM: Round [41] log likelihood: -2218.463757
EM: Round [42] log likelihood: -2218.457264
EM: Round [43] log likelihood: -2218.450953
EM: Round [44] log likelihood: -2218.444820
EM: Round [45] log likelihood: -2218.438858
EM: Round [46] log likelihood: -2218.433062
EM: Round [47] log likelihood: -2218.427427
EM: Round [48] log likelihood: -2218.421948
EM: Round [49] log likelihood: -2218.416620
EM: Round [50] log likelihood: -2218.411440
EM: Round [51] log likelihood: -2218.406401
EM: Round [52] log likelihood: -2218.401501
EM: Round [53] log likelihood: -2218.396735
EM: Round [54] log likelihood: -2218.392099
EM: Round [55] log likelihood: -2218.387589
EM: Round [56] log likelihood: -2218.383202
EM: Round [57] log likelihood: -2218.378934
EM: Round [58] log likelihood: -2218.374781
EM: Round [59] log likelihood: -2218.370740
EM: Round [60] log likelihood: -2218.366808
EM: Round [61] log likelihood: -2218.362982
EM: Round [62] log likelihood: -2218.359258
EM: Round [63] log likelihood: -2218.355634
EM: Round [64] log likelihood: -2218.352108
EM: Round [65] log likelihood: -2218.348675
EM: Round [66] log likelihood: -2218.345334
EM: Round [67] log likelihood: -2218.342081
EM: Round [68] log likelihood: -2218.338915
EM: Round [69] log likelihood: -2218.335833
EM: Round [70] log likelihood: -2218.332833
EM: Round [71] log likelihood: -2218.329912
EM: Round [72] log likelihood: -2218.327068
EM: Round [73] log likelihood: -2218.324299
EM: Round [74] log likelihood: -2218.321603
EM: Round [75] log likelihood: -2218.318978
EM: Round [76] log likelihood: -2218.316422
EM: Round [77] log likelihood: -2218.313933
EM: Round [78] log likelihood: -2218.311509
EM: Round [79] log likelihood: -2218.309148
EM: Round [80] log likelihood: -2218.306850
EM: Round [81] log likelihood: -2218.304611
EM: Round [82] log likelihood: -2218.302430
EM: Round [83] log likelihood: -2218.300307
EM: Round [84] log likelihood: -2218.298238
EM: Round [85] log likelihood: -2218.296224
EM: Round [86] log likelihood: -2218.294262
EM: Round [87] log likelihood: -2218.292350
EM: Round [88] log likelihood: -2218.290488
EM: Round [89] log likelihood: -2218.288675
EM: Round [90] log likelihood: -2218.286908
EM: Round [91] log likelihood: -2218.285187
EM: Round [92] log likelihood: -2218.283511
EM: Round [93] log likelihood: -2218.281877
EM: Round [94] log likelihood: -2218.280286
EM: Round [95] log likelihood: -2218.278736
EM: Round [96] log likelihood: -2218.277226
EM: Round [97] log likelihood: -2218.275754
EM: Round [98] log likelihood: -2218.274321
EM: Round [99] log likelihood: -2218.272924
EM: Round [100] log likelihood: -2218.271563
EM: Round [101] log likelihood: -2218.270237
EM: Round [102] log likelihood: -2218.268945
EM: Round [103] log likelihood: -2218.267686
EM: Round [104] log likelihood: -2218.266459
EM: Round [105] log likelihood: -2218.265264
EM: Round [106] log likelihood: -2218.264099
EM: Round [107] log likelihood: -2218.262964
EM: Round [108] log likelihood: -2218.261858
EM: Round [109] log likelihood: -2218.260781
EM: Round [110] log likelihood: -2218.259731
EM: Round [111] log likelihood: -2218.258707
EM: Round [112] log likelihood: -2218.257710
EM: Round [113] log likelihood: -2218.256738
EM: Round [114] log likelihood: -2218.255791
EM: Round [115] log likelihood: -2218.254868
EM: Round [116] log likelihood: -2218.253968
EM: Round [117] log likelihood: -2218.253091
EM: Round [118] log likelihood: -2218.252237
EM: Round [119] log likelihood: -2218.251404
EM: Round [120] log likelihood: -2218.250593
EM: Round [121] log likelihood: -2218.249802
EM: Round [122] log likelihood: -2218.249031
EM: Round [123] log likelihood: -2218.248280
EM: Round [124] log likelihood: -2218.247547
EM: Round [125] log likelihood: -2218.246834
EM: Round [126] log likelihood: -2218.246138
EM: Round [127] log likelihood: -2218.245460
EM: Round [128] log likelihood: -2218.244799
EM: Round [129] log likelihood: -2218.244155
EM: Round [130] log likelihood: -2218.243528
EM: Round [131] log likelihood: -2218.242916
EM: Round [132] log likelihood: -2218.242319
EM: Round [133] log likelihood: -2218.241738
EM: Round [134] log likelihood: -2218.241171
EM: Round [135] log likelihood: -2218.240619
EM: Round [136] log likelihood: -2218.240081
EM: Round [137] log likelihood: -2218.239556
EM: Round [138] log likelihood: -2218.239044
EM: Round [139] log likelihood: -2218.238546
EM: Round [140] log likelihood: -2218.238060
EM: Round [141] log likelihood: -2218.237586
EM: Round [142] log likelihood: -2218.237124
EM: Round [143] log likelihood: -2218.236674
EM: Round [144] log likelihood: -2218.236235
EM: Round [145] log likelihood: -2218.235808
EM: Round [146] log likelihood: -2218.235391
EM: Round [147] log likelihood: -2218.234984
EM: Round [148] log likelihood: -2218.234588
EM: Round [149] log likelihood: -2218.234202
EM: Round [150] log likelihood: -2218.233825
EM: Round [151] log likelihood: -2218.233458
EM: Round [152] log likelihood: -2218.233101
EM: Round [153] log likelihood: -2218.232752
EM: Round [154] log likelihood: -2218.232412
EM: Round [155] log likelihood: -2218.232080
EM: Round [156] log likelihood: -2218.231757
EM: Round [157] log likelihood: -2218.231442
EM: Round [158] log likelihood: -2218.231135
EM: Round [159] log likelihood: -2218.230836
EM: Round [160] log likelihood: -2218.230544
EM: Round [161] log likelihood: -2218.230260
EM: Round [162] log likelihood: -2218.229982
EM: Round [163] log likelihood: -2218.229712
EM: Round [164] log likelihood: -2218.229448
EM: Round [165] log likelihood: -2218.229191
EM: Round [166] log likelihood: -2218.228941
EM: Round [167] log likelihood: -2218.228697
EM: Round [168] log likelihood: -2218.228459
EM: Round [169] log likelihood: -2218.228227
EM: Round [170] log likelihood: -2218.228000
EM: Round [171] log likelihood: -2218.227780
EM: Round [172] log likelihood: -2218.227565
EM: Round [173] log likelihood: -2218.227355
EM: Round [174] log likelihood: -2218.227151
EM: Round [175] log likelihood: -2218.226952
EM: Round [176] log likelihood: -2218.226757
EM: Round [177] log likelihood: -2218.226568
EM: Round [178] log likelihood: -2218.226383
EM: Round [179] log likelihood: -2218.226204
EM: Round [180] log likelihood: -2218.226028
EM: Round [181] log likelihood: -2218.225857
EM: Round [182] log likelihood: -2218.225690
EM: Round [183] log likelihood: -2218.225528
EM: Round [184] log likelihood: -2218.225369
EM: Round [185] log likelihood: -2218.225215
EM: Round [186] log likelihood: -2218.225064
EM: Round [187] log likelihood: -2218.224917
EM: Round [188] log likelihood: -2218.224774
EM: Round [189] log likelihood: -2218.224634
EM: Round [190] log likelihood: -2218.224498
EM: Round [191] log likelihood: -2218.224365
EM: Round [192] log likelihood: -2218.224236
EM: Round [193] log likelihood: -2218.224110
EM: Round [194] log likelihood: -2218.223987
EM: Round [195] log likelihood: -2218.223867
EM: Round [196] log likelihood: -2218.223750
EM: Round [197] log likelihood: -2218.223636
EM: Round [198] log likelihood: -2218.223525
EM: Round [199] log likelihood: -2218.223417
EM: Round [200] log likelihood: -2218.223311
EM: Round [201] log likelihood: -2218.223208
EM: Round [202] log likelihood: -2218.223108
EM: Round [203] log likelihood: -2218.223010
EM: Stopping iterations at round 203 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.U4x38NdZyT/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.U4x38NdZyT/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.U4x38NdZyT/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.U4x38NdZyT/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.U4x38NdZyT/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.U4x38NdZyT/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.U4x38NdZyT/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.U4x38NdZyT/fi_workdir/aih-tih-sc-a19eaa-R1_A23WJ53LT4_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.U4x38NdZyT/fi_workdir/aih-tih-sc-a19eaa-R1_A23WJ53LT4_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.U4x38NdZyT/fi_workdir/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.U4x38NdZyT/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.U4x38NdZyT/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2018.613743
EM: Round [1] log likelihood: -2018.589650
EM: Round [2] log likelihood: -2018.589226
EM: Round [3] log likelihood: -2018.589219
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.U4x38NdZyT/aih-tih-sc-a19eaa-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 296674443
Warning - not locating file: /tmp/nxf.U4x38NdZyT/aih-tih-sc-a19eaa-R1_A23WJ53LT4_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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000267750.6]
WARNING, no entry stored in dbm for [ENSG00000267750.6]
WARNING, no entry stored in dbm for [ENSG00000249383.2]
WARNING, no entry stored in dbm for [ENSG00000255158.1]
WARNING, no entry stored in dbm for [ENSG00000255158.1]
WARNING, no entry stored in dbm for [ENSG00000223553.6]
ls: cannot access 'IGV_inputs': No such file or directory