Done.
-parsing GTF file: /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.bbugZeEaKv/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.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
22:20:44 : INFO : Done.
-parsing GTF file: /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam
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[2260000] -done parsing /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
' ** passed ** ' => 15696,
'small anchor length' => 99,
'low complexity anchor region' => 12,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 10,
'per_id < 96' => 6545,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 13,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 45,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 12,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 24,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 23,
'seq-similar region overlap' => 772,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 63,
'excessive soft clipping' => 9581,
'num genes matched < 2' => 1,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 84
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[14000] -fusion SPANNING read extraction for scaff: C1QTNF3--AMACR
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[27000] -fusion SPANNING read extraction for scaff: CREBRF--AL137786.2
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[27000] -fusion SPANNING read extraction for scaff: CREBRF--LINC02299
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[10000] -fusion SPANNING read extraction for scaff: MTCYBP4--EYA4
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[49000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[38000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[88000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6
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[110000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10
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[59000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7
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[97000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11
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[103000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12
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[54000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3
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[36000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4
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[44000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
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[151000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[88000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
[1000]
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[110000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[59000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[97000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[54000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
[1000]
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[35000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[43000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[102000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[79000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[15000] -fusion SPANNING read extraction for scaff: PMS2P8--CCDC146
[1000]
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[5000] -fusion SPANNING read extraction for scaff: RNU6-138P--KCNH8
[1000]
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[48000] -fusion SPANNING read extraction for scaff: SBF2--PPIAP86
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[48000] -fusion SPANNING read extraction for scaff: SBF2--LINC01299
[1000]
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[47000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[14000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[101000]
[102000]
[103000]
[104000]
[105000]
[106000]
[107000]
[108000]
[109000] -fusion SPANNING read extraction for scaff: UBE2O--ZIC1
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 320602,
'lacks exon overlap' => 5199
};
EM: Starting log likelihood: -6778.137456
EM: Round [1] log likelihood: -6739.644749
EM: Round [2] log likelihood: -6728.827591
EM: Round [3] log likelihood: -6725.615996
EM: Round [4] log likelihood: -6724.452836
EM: Round [5] log likelihood: -6723.818725
EM: Round [6] log likelihood: -6723.337296
EM: Round [7] log likelihood: -6722.921730
EM: Round [8] log likelihood: -6722.550258
EM: Round [9] log likelihood: -6722.214967
EM: Round [10] log likelihood: -6721.911178
EM: Round [11] log likelihood: -6721.635280
EM: Round [12] log likelihood: -6721.384234
EM: Round [13] log likelihood: -6721.155419
EM: Round [14] log likelihood: -6720.946546
EM: Round [15] log likelihood: -6720.755606
EM: Round [16] log likelihood: -6720.580829
EM: Round [17] log likelihood: -6720.420645
EM: Round [18] log likelihood: -6720.273658
EM: Round [19] log likelihood: -6720.138627
EM: Round [20] log likelihood: -6720.014440
EM: Round [21] log likelihood: -6719.900101
EM: Round [22] log likelihood: -6719.794717
EM: Round [23] log likelihood: -6719.697486
EM: Round [24] log likelihood: -6719.607684
EM: Round [25] log likelihood: -6719.524658
EM: Round [26] log likelihood: -6719.447820
EM: Round [27] log likelihood: -6719.376637
EM: Round [28] log likelihood: -6719.310628
EM: Round [29] log likelihood: -6719.249355
EM: Round [30] log likelihood: -6719.192424
EM: Round [31] log likelihood: -6719.139473
EM: Round [32] log likelihood: -6719.090177
EM: Round [33] log likelihood: -6719.044240
EM: Round [34] log likelihood: -6719.001389
EM: Round [35] log likelihood: -6718.961381
EM: Round [36] log likelihood: -6718.923990
EM: Round [37] log likelihood: -6718.889012
EM: Round [38] log likelihood: -6718.856260
EM: Round [39] log likelihood: -6718.825564
EM: Round [40] log likelihood: -6718.796768
EM: Round [41] log likelihood: -6718.769730
EM: Round [42] log likelihood: -6718.744319
EM: Round [43] log likelihood: -6718.720416
EM: Round [44] log likelihood: -6718.697912
EM: Round [45] log likelihood: -6718.676705
EM: Round [46] log likelihood: -6718.656705
EM: Round [47] log likelihood: -6718.637825
EM: Round [48] log likelihood: -6718.619990
EM: Round [49] log likelihood: -6718.603127
EM: Round [50] log likelihood: -6718.587170
EM: Round [51] log likelihood: -6718.572059
EM: Round [52] log likelihood: -6718.557739
EM: Round [53] log likelihood: -6718.544157
EM: Round [54] log likelihood: -6718.531266
EM: Round [55] log likelihood: -6718.519022
EM: Round [56] log likelihood: -6718.507385
EM: Round [57] log likelihood: -6718.496317
EM: Round [58] log likelihood: -6718.485783
EM: Round [59] log likelihood: -6718.475752
EM: Round [60] log likelihood: -6718.466193
EM: Round [61] log likelihood: -6718.457079
EM: Round [62] log likelihood: -6718.448383
EM: Round [63] log likelihood: -6718.440083
EM: Round [64] log likelihood: -6718.432155
EM: Round [65] log likelihood: -6718.424580
EM: Round [66] log likelihood: -6718.417337
EM: Round [67] log likelihood: -6718.410409
EM: Round [68] log likelihood: -6718.403779
EM: Round [69] log likelihood: -6718.397432
EM: Round [70] log likelihood: -6718.391352
EM: Round [71] log likelihood: -6718.385526
EM: Round [72] log likelihood: -6718.379941
EM: Round [73] log likelihood: -6718.374586
EM: Round [74] log likelihood: -6718.369448
EM: Round [75] log likelihood: -6718.364517
EM: Round [76] log likelihood: -6718.359783
EM: Round [77] log likelihood: -6718.355237
EM: Round [78] log likelihood: -6718.350871
EM: Round [79] log likelihood: -6718.346675
EM: Round [80] log likelihood: -6718.342641
EM: Round [81] log likelihood: -6718.338764
EM: Round [82] log likelihood: -6718.335035
EM: Round [83] log likelihood: -6718.331447
EM: Round [84] log likelihood: -6718.327996
EM: Round [85] log likelihood: -6718.324674
EM: Round [86] log likelihood: -6718.321477
EM: Round [87] log likelihood: -6718.318398
EM: Round [88] log likelihood: -6718.315433
EM: Round [89] log likelihood: -6718.312578
EM: Round [90] log likelihood: -6718.309827
EM: Round [91] log likelihood: -6718.307177
EM: Round [92] log likelihood: -6718.304622
EM: Round [93] log likelihood: -6718.302161
EM: Round [94] log likelihood: -6718.299788
EM: Round [95] log likelihood: -6718.297500
EM: Round [96] log likelihood: -6718.295293
EM: Round [97] log likelihood: -6718.293166
EM: Round [98] log likelihood: -6718.291114
EM: Round [99] log likelihood: -6718.289134
EM: Round [100] log likelihood: -6718.287225
EM: Round [101] log likelihood: -6718.285383
EM: Round [102] log likelihood: -6718.283605
EM: Round [103] log likelihood: -6718.281889
EM: Round [104] log likelihood: -6718.280234
EM: Round [105] log likelihood: -6718.278636
EM: Round [106] log likelihood: -6718.277093
EM: Round [107] log likelihood: -6718.275604
EM: Round [108] log likelihood: -6718.274167
EM: Round [109] log likelihood: -6718.272779
EM: Round [110] log likelihood: -6718.271438
EM: Round [111] log likelihood: -6718.270144
EM: Round [112] log likelihood: -6718.268895
EM: Round [113] log likelihood: -6718.267688
EM: Round [114] log likelihood: -6718.266522
EM: Round [115] log likelihood: -6718.265397
EM: Round [116] log likelihood: -6718.264309
EM: Round [117] log likelihood: -6718.263259
EM: Round [118] log likelihood: -6718.262244
EM: Round [119] log likelihood: -6718.261264
EM: Round [120] log likelihood: -6718.260318
EM: Round [121] log likelihood: -6718.259403
EM: Round [122] log likelihood: -6718.258519
EM: Round [123] log likelihood: -6718.257665
EM: Round [124] log likelihood: -6718.256840
EM: Round [125] log likelihood: -6718.256043
EM: Round [126] log likelihood: -6718.255272
EM: Round [127] log likelihood: -6718.254528
EM: Round [128] log likelihood: -6718.253809
EM: Round [129] log likelihood: -6718.253114
EM: Round [130] log likelihood: -6718.252442
EM: Round [131] log likelihood: -6718.251793
EM: Round [132] log likelihood: -6718.251165
EM: Round [133] log likelihood: -6718.250559
EM: Round [134] log likelihood: -6718.249973
EM: Round [135] log likelihood: -6718.249407
EM: Round [136] log likelihood: -6718.248859
EM: Round [137] log likelihood: -6718.248330
EM: Round [138] log likelihood: -6718.247819
EM: Round [139] log likelihood: -6718.247325
EM: Round [140] log likelihood: -6718.246847
EM: Round [141] log likelihood: -6718.246385
EM: Round [142] log likelihood: -6718.245939
EM: Round [143] log likelihood: -6718.245507
EM: Round [144] log likelihood: -6718.245090
EM: Round [145] log likelihood: -6718.244687
EM: Round [146] log likelihood: -6718.244297
EM: Round [147] log likelihood: -6718.243920
EM: Round [148] log likelihood: -6718.243556
EM: Round [149] log likelihood: -6718.243204
EM: Round [150] log likelihood: -6718.242864
EM: Round [151] log likelihood: -6718.242535
EM: Round [152] log likelihood: -6718.242217
EM: Round [153] log likelihood: -6718.241909
EM: Round [154] log likelihood: -6718.241612
EM: Round [155] log likelihood: -6718.241325
EM: Round [156] log likelihood: -6718.241047
EM: Round [157] log likelihood: -6718.240778
EM: Round [158] log likelihood: -6718.240519
EM: Round [159] log likelihood: -6718.240268
EM: Round [160] log likelihood: -6718.240025
EM: Round [161] log likelihood: -6718.239791
EM: Round [162] log likelihood: -6718.239564
EM: Round [163] log likelihood: -6718.239344
EM: Round [164] log likelihood: -6718.239133
EM: Round [165] log likelihood: -6718.238928
EM: Round [166] log likelihood: -6718.238729
EM: Round [167] log likelihood: -6718.238538
EM: Round [168] log likelihood: -6718.238353
EM: Round [169] log likelihood: -6718.238174
EM: Round [170] log likelihood: -6718.238000
EM: Round [171] log likelihood: -6718.237833
EM: Round [172] log likelihood: -6718.237671
EM: Round [173] log likelihood: -6718.237515
EM: Round [174] log likelihood: -6718.237364
EM: Round [175] log likelihood: -6718.237217
EM: Round [176] log likelihood: -6718.237076
EM: Round [177] log likelihood: -6718.236939
EM: Round [178] log likelihood: -6718.236807
EM: Round [179] log likelihood: -6718.236679
EM: Round [180] log likelihood: -6718.236556
EM: Round [181] log likelihood: -6718.236436
EM: Round [182] log likelihood: -6718.236321
EM: Round [183] log likelihood: -6718.236209
EM: Round [184] log likelihood: -6718.236101
EM: Round [185] log likelihood: -6718.235997
EM: Round [186] log likelihood: -6718.235896
EM: Round [187] log likelihood: -6718.235798
EM: Stopping iterations at round 187 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_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.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_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.bbugZeEaKv/fi_workdir/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -6126.398363
EM: Round [1] log likelihood: -6088.747135
EM: Round [2] log likelihood: -6078.663716
EM: Round [3] log likelihood: -6076.097955
EM: Round [4] log likelihood: -6075.507332
EM: Round [5] log likelihood: -6075.383649
EM: Round [6] log likelihood: -6075.359357
EM: Round [7] log likelihood: -6075.354747
EM: Round [8] log likelihood: -6075.353886
EM: Round [9] log likelihood: -6075.353726
EM: Round [10] log likelihood: -6075.353696
EM: Stopping iterations at round 10 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296543195
Warning - not locating file: /tmp/nxf.bbugZeEaKv/aih-tih-sc-5519ab-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000226240.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
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 [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000223698.3]
ls: cannot access 'IGV_inputs': No such file or directory