.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-96d0f6-R1_A23YTGFLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/7ce28938a0d11a6c29a7dda4d89229/.command.err
Size: 10.8 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-96d0f6-R1_A23YTGFLT4_1)
Attempt
Content

Done.
-parsing GTF file: /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.nPMYJDuozx/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.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
22:38:55 : INFO : Done.
-parsing GTF file: /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[80000]   -done parsing /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'excessive soft clipping' => 733,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 10,
          'seq-similar region overlap' => 19,
          ' ** passed ** ' => 671,
          'per_id < 96' => 347,
          'num genes matched < 2' => 2,
          'exons hit < 2' => 2
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[7000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[5000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[6000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[6000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[30000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[28000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 691,
          'seq similar region alignment' => 3815
        };
EM: Starting log likelihood: -701.559623
EM: Round [1] log likelihood: -701.489914
EM: Round [2] log likelihood: -701.471009
EM: Round [3] log likelihood: -701.453260
EM: Round [4] log likelihood: -701.436573
EM: Round [5] log likelihood: -701.420867
EM: Round [6] log likelihood: -701.406072
EM: Round [7] log likelihood: -701.392122
EM: Round [8] log likelihood: -701.378958
EM: Round [9] log likelihood: -701.366527
EM: Round [10] log likelihood: -701.354779
EM: Round [11] log likelihood: -701.343669
EM: Round [12] log likelihood: -701.333157
EM: Round [13] log likelihood: -701.323204
EM: Round [14] log likelihood: -701.313776
EM: Round [15] log likelihood: -701.304840
EM: Round [16] log likelihood: -701.296367
EM: Round [17] log likelihood: -701.288328
EM: Round [18] log likelihood: -701.280699
EM: Round [19] log likelihood: -701.273456
EM: Round [20] log likelihood: -701.266577
EM: Round [21] log likelihood: -701.260041
EM: Round [22] log likelihood: -701.253828
EM: Round [23] log likelihood: -701.247922
EM: Round [24] log likelihood: -701.242305
EM: Round [25] log likelihood: -701.236961
EM: Round [26] log likelihood: -701.231877
EM: Round [27] log likelihood: -701.227037
EM: Round [28] log likelihood: -701.222430
EM: Round [29] log likelihood: -701.218043
EM: Round [30] log likelihood: -701.213864
EM: Round [31] log likelihood: -701.209884
EM: Round [32] log likelihood: -701.206091
EM: Round [33] log likelihood: -701.202476
EM: Round [34] log likelihood: -701.199031
EM: Round [35] log likelihood: -701.195747
EM: Round [36] log likelihood: -701.192616
EM: Round [37] log likelihood: -701.189630
EM: Round [38] log likelihood: -701.186782
EM: Round [39] log likelihood: -701.184065
EM: Round [40] log likelihood: -701.181474
EM: Round [41] log likelihood: -701.179001
EM: Round [42] log likelihood: -701.176642
EM: Round [43] log likelihood: -701.174390
EM: Round [44] log likelihood: -701.172241
EM: Round [45] log likelihood: -701.170190
EM: Round [46] log likelihood: -701.168232
EM: Round [47] log likelihood: -701.166362
EM: Round [48] log likelihood: -701.164577
EM: Round [49] log likelihood: -701.162873
EM: Round [50] log likelihood: -701.161246
EM: Round [51] log likelihood: -701.159692
EM: Round [52] log likelihood: -701.158207
EM: Round [53] log likelihood: -701.156789
EM: Round [54] log likelihood: -701.155435
EM: Round [55] log likelihood: -701.154141
EM: Round [56] log likelihood: -701.152905
EM: Round [57] log likelihood: -701.151725
EM: Round [58] log likelihood: -701.150597
EM: Round [59] log likelihood: -701.149519
EM: Round [60] log likelihood: -701.148489
EM: Round [61] log likelihood: -701.147505
EM: Round [62] log likelihood: -701.146564
EM: Round [63] log likelihood: -701.145666
EM: Round [64] log likelihood: -701.144807
EM: Round [65] log likelihood: -701.143986
EM: Round [66] log likelihood: -701.143201
EM: Round [67] log likelihood: -701.142452
EM: Round [68] log likelihood: -701.141735
EM: Round [69] log likelihood: -701.141050
EM: Round [70] log likelihood: -701.140395
EM: Round [71] log likelihood: -701.139769
EM: Round [72] log likelihood: -701.139171
EM: Round [73] log likelihood: -701.138599
EM: Round [74] log likelihood: -701.138052
EM: Round [75] log likelihood: -701.137529
EM: Round [76] log likelihood: -701.137029
EM: Round [77] log likelihood: -701.136551
EM: Round [78] log likelihood: -701.136094
EM: Round [79] log likelihood: -701.135657
EM: Round [80] log likelihood: -701.135240
EM: Round [81] log likelihood: -701.134841
EM: Round [82] log likelihood: -701.134459
EM: Round [83] log likelihood: -701.134094
EM: Round [84] log likelihood: -701.133745
EM: Round [85] log likelihood: -701.133411
EM: Round [86] log likelihood: -701.133092
EM: Round [87] log likelihood: -701.132786
EM: Round [88] log likelihood: -701.132495
EM: Round [89] log likelihood: -701.132216
EM: Round [90] log likelihood: -701.131949
EM: Round [91] log likelihood: -701.131693
EM: Round [92] log likelihood: -701.131449
EM: Round [93] log likelihood: -701.131216
EM: Round [94] log likelihood: -701.130993
EM: Round [95] log likelihood: -701.130779
EM: Round [96] log likelihood: -701.130575
EM: Round [97] log likelihood: -701.130380
EM: Round [98] log likelihood: -701.130194
EM: Round [99] log likelihood: -701.130015
EM: Round [100] log likelihood: -701.129844
EM: Round [101] log likelihood: -701.129681
EM: Round [102] log likelihood: -701.129525
EM: Round [103] log likelihood: -701.129376
EM: Round [104] log likelihood: -701.129233
EM: Round [105] log likelihood: -701.129096
EM: Round [106] log likelihood: -701.128965
EM: Round [107] log likelihood: -701.128841
EM: Round [108] log likelihood: -701.128721
EM: Round [109] log likelihood: -701.128607
EM: Round [110] log likelihood: -701.128497
EM: Round [111] log likelihood: -701.128393
EM: Round [112] log likelihood: -701.128293
EM: Stopping iterations at round 112 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-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.nPMYJDuozx/fi_workdir/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -656.365350
EM: Round [1] log likelihood: -656.315789
EM: Round [2] log likelihood: -656.315782
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296375716
Warning - not locating file: /tmp/nxf.nPMYJDuozx/aih-tih-sc-96d0f6-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
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 [ENSG00000280136.2]
ls: cannot access 'IGV_inputs': No such file or directory