.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-4bcd26-R1_A23YTGFLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/18575a8128c21796bf6d29b776403b/.command.err
Size: 12.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (aih-tih-sc-4bcd26-R1_A23YTGFLT4_1)
Attempt
Content

Done.
-parsing GTF file: /tmp/nxf.sbHlT9MIaz/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.sbHlT9MIaz/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.sbHlT9MIaz/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.sbHlT9MIaz/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.sbHlT9MIaz/fi_workdir/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.sbHlT9MIaz/fi_workdir/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
09:56:30 : INFO : Done.
-parsing GTF file: /tmp/nxf.sbHlT9MIaz/fi_workdir/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.sbHlT9MIaz/fi_workdir/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[320000]   -done parsing /tmp/nxf.sbHlT9MIaz/fi_workdir/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 6,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 12,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 18,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 18,
          'seq-similar region overlap' => 113,
          ' ** passed ** ' => 2002,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 3,
          'per_id < 96' => 1745,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 85,
          'num genes matched < 2' => 79,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1,
          'excessive soft clipping' => 2618,
          'low complexity anchor region' => 2,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 16
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.sbHlT9MIaz/fi_workdir/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[10000]   -fusion SPANNING read extraction for scaff: AC100821.2--LYPLA1

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[12000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[12000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[14000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[12000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[12000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[13000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

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[94000]   -fusion SPANNING read extraction for scaff: PDXDC2P--PDPR

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[76000]   -fusion SPANNING read extraction for scaff: RBM14--RBM4B

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[19000]   -fusion SPANNING read extraction for scaff: TBP--ATXN3

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[29000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 9241,
          'lacks exon overlap' => 2458
        };
EM: Starting log likelihood: -2041.044448
EM: Round [1] log likelihood: -2040.018311
EM: Round [2] log likelihood: -2039.580083
EM: Round [3] log likelihood: -2039.272732
EM: Round [4] log likelihood: -2039.025066
EM: Round [5] log likelihood: -2038.819197
EM: Round [6] log likelihood: -2038.646516
EM: Round [7] log likelihood: -2038.501015
EM: Round [8] log likelihood: -2038.378020
EM: Round [9] log likelihood: -2038.273779
EM: Round [10] log likelihood: -2038.185241
EM: Round [11] log likelihood: -2038.109904
EM: Round [12] log likelihood: -2038.045704
EM: Round [13] log likelihood: -2037.990923
EM: Round [14] log likelihood: -2037.944129
EM: Round [15] log likelihood: -2037.904120
EM: Round [16] log likelihood: -2037.869885
EM: Round [17] log likelihood: -2037.840572
EM: Round [18] log likelihood: -2037.815458
EM: Round [19] log likelihood: -2037.793933
EM: Round [20] log likelihood: -2037.775474
EM: Round [21] log likelihood: -2037.759640
EM: Round [22] log likelihood: -2037.746054
EM: Round [23] log likelihood: -2037.734392
EM: Round [24] log likelihood: -2037.724381
EM: Round [25] log likelihood: -2037.715785
EM: Round [26] log likelihood: -2037.708403
EM: Round [27] log likelihood: -2037.702062
EM: Round [28] log likelihood: -2037.696616
EM: Round [29] log likelihood: -2037.691937
EM: Round [30] log likelihood: -2037.687916
EM: Round [31] log likelihood: -2037.684462
EM: Round [32] log likelihood: -2037.681493
EM: Round [33] log likelihood: -2037.678942
EM: Round [34] log likelihood: -2037.676750
EM: Round [35] log likelihood: -2037.674866
EM: Round [36] log likelihood: -2037.673247
EM: Round [37] log likelihood: -2037.671855
EM: Round [38] log likelihood: -2037.670659
EM: Round [39] log likelihood: -2037.669630
EM: Round [40] log likelihood: -2037.668747
EM: Round [41] log likelihood: -2037.667987
EM: Round [42] log likelihood: -2037.667334
EM: Round [43] log likelihood: -2037.666773
EM: Round [44] log likelihood: -2037.666290
EM: Round [45] log likelihood: -2037.665875
EM: Round [46] log likelihood: -2037.665519
EM: Round [47] log likelihood: -2037.665212
EM: Round [48] log likelihood: -2037.664949
EM: Round [49] log likelihood: -2037.664722
EM: Round [50] log likelihood: -2037.664528
EM: Round [51] log likelihood: -2037.664360
EM: Round [52] log likelihood: -2037.664217
EM: Round [53] log likelihood: -2037.664093
EM: Round [54] log likelihood: -2037.663987
EM: Round [55] log likelihood: -2037.663895
EM: Stopping iterations at round 55 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.sbHlT9MIaz/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.sbHlT9MIaz/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.sbHlT9MIaz/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.sbHlT9MIaz/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.sbHlT9MIaz/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.sbHlT9MIaz/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.sbHlT9MIaz/aih-tih-sc-4bcd26-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.sbHlT9MIaz/fi_workdir/aih-tih-sc-4bcd26-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.sbHlT9MIaz/fi_workdir/aih-tih-sc-4bcd26-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.sbHlT9MIaz/fi_workdir/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.sbHlT9MIaz/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.sbHlT9MIaz/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1664.608617
EM: Round [1] log likelihood: -1664.608617
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.sbHlT9MIaz/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 194210175
Warning - not locating file: /tmp/nxf.sbHlT9MIaz/aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000255185.6]
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 [ENSG00000260955.2]
ls: cannot access 'IGV_inputs': No such file or directory