Done.
-parsing GTF file: /tmp/nxf.0CheZ9eDPk/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.0CheZ9eDPk/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.0CheZ9eDPk/659_bQZ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.0CheZ9eDPk/659_bQZ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.0CheZ9eDPk/fi_workdir/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.0CheZ9eDPk/fi_workdir/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bQZ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
11:05:00 : INFO : Done.
-parsing GTF file: /tmp/nxf.0CheZ9eDPk/fi_workdir/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.0CheZ9eDPk/fi_workdir/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[490000] -done parsing /tmp/nxf.0CheZ9eDPk/fi_workdir/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
' ** passed ** ' => 2197,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 24,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 28,
'small anchor length' => 2,
'seq-similar region overlap' => 19,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1,
'num genes matched < 2' => 4,
'per_id < 96' => 2080,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 26,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1,
'excessive soft clipping' => 3642,
'low complexity anchor region' => 6,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 181,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 8
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.0CheZ9eDPk/fi_workdir/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[124000] -fusion SPANNING read extraction for scaff: AGAP3--BRAF
-fusion SPANNING read extraction for scaff: GUCY1B2--NKAIN2
-fusion SPANNING read extraction for scaff: LINC00381--NKAIN2
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[5000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[4000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[4000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[16000] -fusion SPANNING read extraction for scaff: REXO5--TMX1
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[34000] -fusion SPANNING read extraction for scaff: SMARCD3--MGAM
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[229000] -fusion SPANNING read extraction for scaff: SYNE2--MTHFD1
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[22000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[24000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[24000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 4213,
'seq similar region alignment' => 2511
};
EM: Starting log likelihood: -2153.609352
EM: Round [1] log likelihood: -2148.994435
EM: Round [2] log likelihood: -2148.506681
EM: Round [3] log likelihood: -2148.457975
EM: Round [4] log likelihood: -2148.445891
EM: Round [5] log likelihood: -2148.436379
EM: Round [6] log likelihood: -2148.427349
EM: Round [7] log likelihood: -2148.418676
EM: Round [8] log likelihood: -2148.410338
EM: Round [9] log likelihood: -2148.402324
EM: Round [10] log likelihood: -2148.394620
EM: Round [11] log likelihood: -2148.387214
EM: Round [12] log likelihood: -2148.380094
EM: Round [13] log likelihood: -2148.373249
EM: Round [14] log likelihood: -2148.366669
EM: Round [15] log likelihood: -2148.360343
EM: Round [16] log likelihood: -2148.354261
EM: Round [17] log likelihood: -2148.348413
EM: Round [18] log likelihood: -2148.342791
EM: Round [19] log likelihood: -2148.337384
EM: Round [20] log likelihood: -2148.332185
EM: Round [21] log likelihood: -2148.327186
EM: Round [22] log likelihood: -2148.322379
EM: Round [23] log likelihood: -2148.317756
EM: Round [24] log likelihood: -2148.313310
EM: Round [25] log likelihood: -2148.309034
EM: Round [26] log likelihood: -2148.304922
EM: Round [27] log likelihood: -2148.300967
EM: Round [28] log likelihood: -2148.297162
EM: Round [29] log likelihood: -2148.293503
EM: Round [30] log likelihood: -2148.289983
EM: Round [31] log likelihood: -2148.286597
EM: Round [32] log likelihood: -2148.283340
EM: Round [33] log likelihood: -2148.280206
EM: Round [34] log likelihood: -2148.277191
EM: Round [35] log likelihood: -2148.274291
EM: Round [36] log likelihood: -2148.271501
EM: Round [37] log likelihood: -2148.268817
EM: Round [38] log likelihood: -2148.266234
EM: Round [39] log likelihood: -2148.263748
EM: Round [40] log likelihood: -2148.261357
EM: Round [41] log likelihood: -2148.259056
EM: Round [42] log likelihood: -2148.256842
EM: Round [43] log likelihood: -2148.254711
EM: Round [44] log likelihood: -2148.252661
EM: Round [45] log likelihood: -2148.250688
EM: Round [46] log likelihood: -2148.248790
EM: Round [47] log likelihood: -2148.246962
EM: Round [48] log likelihood: -2148.245204
EM: Round [49] log likelihood: -2148.243511
EM: Round [50] log likelihood: -2148.241883
EM: Round [51] log likelihood: -2148.240315
EM: Round [52] log likelihood: -2148.238806
EM: Round [53] log likelihood: -2148.237354
EM: Round [54] log likelihood: -2148.235956
EM: Round [55] log likelihood: -2148.234611
EM: Round [56] log likelihood: -2148.233316
EM: Round [57] log likelihood: -2148.232070
EM: Round [58] log likelihood: -2148.230870
EM: Round [59] log likelihood: -2148.229715
EM: Round [60] log likelihood: -2148.228604
EM: Round [61] log likelihood: -2148.227534
EM: Round [62] log likelihood: -2148.226504
EM: Round [63] log likelihood: -2148.225512
EM: Round [64] log likelihood: -2148.224558
EM: Round [65] log likelihood: -2148.223639
EM: Round [66] log likelihood: -2148.222755
EM: Round [67] log likelihood: -2148.221903
EM: Round [68] log likelihood: -2148.221083
EM: Round [69] log likelihood: -2148.220294
EM: Round [70] log likelihood: -2148.219535
EM: Round [71] log likelihood: -2148.218803
EM: Round [72] log likelihood: -2148.218099
EM: Round [73] log likelihood: -2148.217421
EM: Round [74] log likelihood: -2148.216769
EM: Round [75] log likelihood: -2148.216140
EM: Round [76] log likelihood: -2148.215535
EM: Round [77] log likelihood: -2148.214953
EM: Round [78] log likelihood: -2148.214392
EM: Round [79] log likelihood: -2148.213853
EM: Round [80] log likelihood: -2148.213333
EM: Round [81] log likelihood: -2148.212833
EM: Round [82] log likelihood: -2148.212351
EM: Round [83] log likelihood: -2148.211887
EM: Round [84] log likelihood: -2148.211440
EM: Round [85] log likelihood: -2148.211010
EM: Round [86] log likelihood: -2148.210596
EM: Round [87] log likelihood: -2148.210198
EM: Round [88] log likelihood: -2148.209814
EM: Round [89] log likelihood: -2148.209445
EM: Round [90] log likelihood: -2148.209089
EM: Round [91] log likelihood: -2148.208746
EM: Round [92] log likelihood: -2148.208416
EM: Round [93] log likelihood: -2148.208099
EM: Round [94] log likelihood: -2148.207793
EM: Round [95] log likelihood: -2148.207499
EM: Round [96] log likelihood: -2148.207215
EM: Round [97] log likelihood: -2148.206942
EM: Round [98] log likelihood: -2148.206679
EM: Round [99] log likelihood: -2148.206426
EM: Round [100] log likelihood: -2148.206183
EM: Round [101] log likelihood: -2148.205948
EM: Round [102] log likelihood: -2148.205722
EM: Round [103] log likelihood: -2148.205505
EM: Round [104] log likelihood: -2148.205295
EM: Round [105] log likelihood: -2148.205093
EM: Round [106] log likelihood: -2148.204899
EM: Round [107] log likelihood: -2148.204712
EM: Round [108] log likelihood: -2148.204532
EM: Round [109] log likelihood: -2148.204359
EM: Round [110] log likelihood: -2148.204192
EM: Round [111] log likelihood: -2148.204031
EM: Round [112] log likelihood: -2148.203876
EM: Round [113] log likelihood: -2148.203727
EM: Round [114] log likelihood: -2148.203584
EM: Round [115] log likelihood: -2148.203445
EM: Round [116] log likelihood: -2148.203312
EM: Round [117] log likelihood: -2148.203184
EM: Round [118] log likelihood: -2148.203061
EM: Round [119] log likelihood: -2148.202942
EM: Round [120] log likelihood: -2148.202828
EM: Round [121] log likelihood: -2148.202717
EM: Round [122] log likelihood: -2148.202611
EM: Round [123] log likelihood: -2148.202509
EM: Round [124] log likelihood: -2148.202411
EM: Stopping iterations at round 124 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.0CheZ9eDPk/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.0CheZ9eDPk/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.0CheZ9eDPk/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.0CheZ9eDPk/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.0CheZ9eDPk/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.0CheZ9eDPk/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.0CheZ9eDPk/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.0CheZ9eDPk/fi_workdir/659_bQZ-T1-TRNA-1_B23MHV2LT4_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.0CheZ9eDPk/fi_workdir/659_bQZ-T1-TRNA-1_B23MHV2LT4_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.0CheZ9eDPk/fi_workdir/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.0CheZ9eDPk/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.0CheZ9eDPk/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2043.897367
EM: Round [1] log likelihood: -2039.826456
EM: Round [2] log likelihood: -2039.349067
EM: Round [3] log likelihood: -2039.310517
EM: Round [4] log likelihood: -2039.308197
EM: Round [5] log likelihood: -2039.308072
EM: Round [6] log likelihood: -2039.308065
EM: Stopping iterations at round 6 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.0CheZ9eDPk/659_bQZ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295955895
Warning - not locating file: /tmp/nxf.0CheZ9eDPk/659_bQZ-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226240.2]
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 [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
ls: cannot access 'IGV_inputs': No such file or directory