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Use of uninitialized value $preseq in substr at ...TranscriptVariationAllele.pm line 2187 #1457

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Stikus opened this issue Jul 21, 2023 · 6 comments
Closed

Use of uninitialized value $preseq in substr at ...TranscriptVariationAllele.pm line 2187 #1457

Stikus opened this issue Jul 21, 2023 · 6 comments
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@nakib103

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@Stikus
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Stikus commented Jul 21, 2023

Describe the issue

After 110 VEP release we start catching a lot of warnings we haven't catch before:

Use of uninitialized value in subtraction (-) at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 24.
Use of uninitialized value $preseq in substr at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 24.

Additional information

Looks like the reason is behind these new lines in TranscriptVariationAllele.pm:
diff link

$preseq somehow left uninitialized.

      ### re-set as dup not delins
      my $prev_str = substr($preseq, length($preseq) - length($check_alt));
      if($check_alt eq $prev_str) {
        $hgvs_notation->{type} = "dup";
        $hgvs_notation->{start} -= length($check_alt);
      }

System

  • VEP version: 110.0
  • VEP Cache version: 110
  • Perl version: 5.26.1
  • OS: Ubuntu 18.04
  • tabix installed : yes

Full VEP command line

/soft/ensembl-vep-110.0/vep --fork 32 --input_file /inputs/input.2.vcf --format vcf --cache --dir_cache /ref/.vep --dir_plugins /soft/ensembl-vep-110.0/Plugins --assembly GRCh37 --offline --output_file /outputs/test1.annot-vep.vcf --vcf --force_overwrite --symbol --check_existing --terms SO --tsl --hgvs --hgvsg --transcript_version  --plugin Frameshift --plugin Wildtype   --shift_hgvs 0 --no_stats --plugin ProteinSeqs,/outputs/test1.annot-vep.reference.fa,/outputs/test1.annot-vep.mutated.fa

Full error message

Smartmatch is experimental at /soft/ensembl-vep-110.0/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm line 472.
WARNING: Plugin ProteinSeqs is disabling forking
Use of uninitialized value in subtraction (-) at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 24.
Use of uninitialized value $preseq in substr at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 24.
Use of uninitialized value in subtraction (-) at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 24.
Use of uninitialized value $preseq in substr at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 24.
Use of uninitialized value in subtraction (-) at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 24.
Use of uninitialized value $preseq in substr at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 24.
Use of uninitialized value in subtraction (-) at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 25.
Use of uninitialized value $preseq in substr at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 25.
Use of uninitialized value in subtraction (-) at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 25.
Use of uninitialized value $preseq in substr at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 25.
Use of uninitialized value in subtraction (-) at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 25.
Use of uninitialized value $preseq in substr at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 25.
Use of uninitialized value in subtraction (-) at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 25.
Use of uninitialized value $preseq in substr at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 25.
Use of uninitialized value in subtraction (-) at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 25.
Use of uninitialized value $preseq in substr at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 25.
Use of uninitialized value in subtraction (-) at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 25.
Use of uninitialized value $preseq in substr at /soft/ensembl-vep-110.0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 2187, <__ANONIO__> line 25.
2023-07-21 11:39:39 - INFO: --shift_hgvs has been set to zero, setting shift_3prime to 0

Data files

  • The input file
##fileformat=VCFv4.0
##source=VarscanSomatic
##reference=ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/special_requests/GRCh37-lite.fa.gz
##phasing=none
##center=genome.wustl.edu
##FILTER=<ID=PASS,Description="Passed all filters">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth at this position in the sample">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Depth of reads supporting alleles 0/1/2/3...">
##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases">
##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality for reads supporting alleles">
##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown">
##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample genotype filter">
##FORMAT=<ID=DP2,Number=1,Type=Integer,Description="Read depth for tier2">
##FORMAT=<ID=TAR,Number=2,Type=Integer,Description="Reads strongly supporting alternate allele for tiers 1,2">
##FORMAT=<ID=TIR,Number=2,Type=Integer,Description="Reads strongly supporting indel allele for tiers 1,2">
##FORMAT=<ID=TOR,Number=2,Type=Integer,Description="Other reads (weak support or insufficient indel breakpoint overlap) for tiers 1,2">
##FORMAT=<ID=DP50,Number=1,Type=Float,Description="Average tier1 read depth within 50 bases">
##FORMAT=<ID=FDP50,Number=1,Type=Float,Description="Average tier1 number of basecalls filtered from original read depth within 50 bases">
##FORMAT=<ID=SUBDP50,Number=1,Type=Float,Description="Average number of reads below tier1 mapping quality threshold aligned across sites within 50 bases">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
2	217498305	.	T	TGCTGCC	.	.	.	GT:AD:BQ:SS:DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT	0/1:90:.:2:101:101:90,91:4,4:40,40:103.29:0.59:0:PASS
4	40434704	.	AGCGGCTGCGGCGGCTGCGGCC	A	.	.	.	GT:AD:BQ:SS:DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT	0/1:125:.:2:128:128:125,125:5,5:12,12:119.5:1.75:0:PASS
6	41754573	.	C	CCTT	.	.	.	GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT	0/1:76:13,9,28,26:36:2:12:78:12,12:55,55:12,12:80.52:1.92:0:PASS
6	43250725	.	GGAA	G	.	.	.	GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT	0/1:200:43,47,54,56:34:2:56:215:56,57:123,123:37,37:205.2:7.66:0:PASS
  • The output file
##fileformat=VCFv4.0
##source=VarscanSomatic
##reference=ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/special_requests/GRCh37-lite.fa.gz
##phasing=none
##center=genome.wustl.edu
##FILTER=<ID=PASS,Description="Passed all filters">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth at this position in the sample">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Depth of reads supporting alleles 0/1/2/3...">
##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases">
##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality for reads supporting alleles">
##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal,0=wildtype,1=germline,2=somatic,3=LOH,4=post-transcriptional modification,5=unknown">
##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample genotype filter">
##FORMAT=<ID=DP2,Number=1,Type=Integer,Description="Read depth for tier2">
##FORMAT=<ID=TAR,Number=2,Type=Integer,Description="Reads strongly supporting alternate allele for tiers 1,2">
##FORMAT=<ID=TIR,Number=2,Type=Integer,Description="Reads strongly supporting indel allele for tiers 1,2">
##FORMAT=<ID=TOR,Number=2,Type=Integer,Description="Other reads (weak support or insufficient indel breakpoint overlap) for tiers 1,2">
##FORMAT=<ID=DP50,Number=1,Type=Float,Description="Average tier1 read depth within 50 bases">
##FORMAT=<ID=FDP50,Number=1,Type=Float,Description="Average tier1 number of basecalls filtered from original read depth within 50 bases">
##FORMAT=<ID=SUBDP50,Number=1,Type=Float,Description="Average number of reads below tier1 mapping quality threshold aligned across sites within 50 bases">
##VEP="v110" time="2023-07-21 11:39:39" cache="/ref/.vep/homo_sapiens/110_GRCh37" ensembl=110.584a8f3 ensembl-io=110.b1a0d57 ensembl-variation=110.2fc4a6a ensembl-funcgen=110.24e6da6 1000genomes="phase3" COSMIC="92" ClinVar="202012" HGMD-PUBLIC="20204" assembly="GRCh37.p13" dbSNP="154" gencode="GENCODE 19" genebuild="2011-04" gnomADe="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|TSL|HGVS_OFFSET|HGVSg|CLIN_SIG|SOMATIC|PHENO|FrameshiftSequence|WildtypeProtein">
##FrameshiftSequence=Predicted sequence for frameshift mutations
##WildtypeProtein=The normal, non-mutated protein sequence
##VEP-command-line='vep --assembly GRCh37 --cache --cache_version 110 --check_existing --database 0 --dir_cache [PATH]/.vep --dir_plugins [PATH]/Plugins --force_overwrite --fork 32 --format vcf --hgvs --hgvsg --input_file [PATH]/input.2.vcf --no_stats --offline --output_file [PATH]/test1.annot-vep.vcf --plugin [PATH]/test1.annot-vep.mutated.fa --shift_hgvs 0 --symbol --transcript_version --tsl --vcf'
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	H_NJ-HCC1395-HCC1395
2	217498305	.	T	TGCTGCC	.	.	CSQ=GCTGCC|inframe_insertion|MODERATE|IGFBP2|ENSG00000115457|Transcript|ENST00000233809.4|protein_coding|1/4||ENST00000233809.4:c.59_60insGCTGCC|ENSP00000233809.4:p.Leu21_Leu22insProLeu|188-189|59-60|20|L/LLP|ctg/ctGCTGCCg|rs1461501999||1||HGNC|5471|||2:g.217498305_217498306insGCTGCC|||||MLPRVGCPALPLPPPPLLPLLLLLLGASGGGGGARAEVLFRCPPCTPERLAACGPPPVAPPAAVAAVAGGARMPCAELVREPGCGCCSVCARLEGEACGVYTPRCGQGLRCYPHPGSELPLQALVMGEGTCEKRRDAEYGASPEQVADNGDDHSEGGLVENHVDSTMNMLGGGGSAGRKPLKSGMKELAVFREKVTEQHRQMGKGGKHHLGLEEPKKLRPPPARTPCQQELDQVLERISTMRLPDERGPLEHLYSLHIPNCDKHGLYNLKQCKMSLNGQRGECWCVNPNTGKLIQGAPTIRGDPECHLFYNEQQEARGVHTQRMQ,GCTGCC|intron_variant|MODIFIER|IGFBP2|ENSG00000115457|Transcript|ENST00000434997.1|protein_coding||1/2|ENST00000434997.1:c.-57+568_-57+569insGCTGCC|||||||rs1461501999||1|cds_end_NF|HGNC|5471|||2:g.217498305_217498306insGCTGCC|||||MNMLGGGGSAGRKPLKSGMKELAVFREKVTEQHRQMGKGGKHHLGLEEPKKLRPPPARTPCQQELDQVLERISTMRLP,GCTGCC|non_coding_transcript_exon_variant|MODIFIER|IGFBP2|ENSG00000115457|Transcript|ENST00000490362.1|retained_intron|1/2||ENST00000490362.1:n.154_155insGCTGCC||154-155|||||rs1461501999||1||HGNC|5471|||2:g.217498305_217498306insGCTGCC|||||	GT:AD:BQ:SS:DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT	0/1:90:.:2:101:101:90,91:4,4:40,40:103.29:0.59:0:PASS
4	40434704	.	AGCGGCTGCGGCGGCTGCGGCC	A	.	.	CSQ=-|inframe_deletion|MODERATE|RBM47|ENSG00000163694|Transcript|ENST00000295971.7|protein_coding|6/7||ENST00000295971.7:c.1485_1505del|ENSP00000295971.7:p.Ala496_Ala502del|2193-2213|1485-1505|495-502|AAAAAAAA/A|gcGGCCGCAGCCGCCGCAGCCGCt/gct|rs564837143||-1||HGNC|30358|||4:g.40434705_40434725del|||||MTAEDSTAAMSSDSAAGSSAKVPEGVAGAPNEAALLALMERTGYSMVQENGQRKYGGPPPGWEGPHPQRGCEVFVGKIPRDVYEDELVPVFEAVGRIYELRLMMDFDGKNRGYAFVMYCHKHEAKRAVRELNNYEIRPGRLLGVCCSVDNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVKILYVRNLMIETTEDTIKKSFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELEGSCLEVTLAKPVDKEQYSRYQKAARGGGAAEAAQQPSYVYSCDPYTLAYYGYPYNALIGPNRDYFVKAGSIRGRGRGAAGNRAPGPRGSYLGGYSAGRGIYSRYHEGKGKQQEKGYELVPNLEIPTVNPVAIKPGTVAIPAIGAQYSMFPAAPAPKMIEDGKIHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPTVSTPPPFQGRPITPVYTVAPNVQRIPTAGIYGASYVPFAAPATATIATLQKNAAAAAAMYGGYAGYIPQAFPAAAIQVPIPDVYQTY,-|inframe_deletion|MODERATE|RBM47|ENSG00000163694|Transcript|ENST00000319592.4|protein_coding|5/6||ENST00000319592.4:c.1278_1298del|ENSP00000320108.4:p.Ala427_Ala433del|1988-2008|1278-1298|426-433|AAAAAAAA/A|gcGGCCGCAGCCGCCGCAGCCGCt/gct|rs564837143||-1||HGNC|30358|||4:g.40434705_40434725del|||||MTAEDSTAAMSSDSAAGSSAKVPEGVAGAPNEAALLALMERTGYSMVQENGQRKYGGPPPGWEGPHPQRGCEVFVGKIPRDVYEDELVPVFEAVGRIYELRLMMDFDGKNRGYAFVMYCHKHEAKRAVRELNNYEIRPGRLLGVCCSVDNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVKILYVRNLMIETTEDTIKKSFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELEGSCLEVTLAKPVDKEQYSRYQKAARGGGAAEAAQQPSYVYSCDPYTLAYYGYPYNALIGPNRDYFVKVAIPAIGAQYSMFPAAPAPKMIEDGKIHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPTVSTPPPFQGRPITPVYTVAPNVQRIPTAGIYGASYVPFAAPATATIATLQKNAAAAAAMYGGYAGYIPQAFPAAAIQVPIPDVYQTY,-|inframe_deletion|MODERATE|RBM47|ENSG00000163694|Transcript|ENST00000381793.2|protein_coding|5/6||ENST00000381793.2:c.1485_1505del|ENSP00000371212.2:p.Ala496_Ala502del|1882-1902|1485-1505|495-502|AAAAAAAA/A|gcGGCCGCAGCCGCCGCAGCCGCt/gct|rs564837143||-1||HGNC|30358|||4:g.40434705_40434725del|||||MTAEDSTAAMSSDSAAGSSAKVPEGVAGAPNEAALLALMERTGYSMVQENGQRKYGGPPPGWEGPHPQRGCEVFVGKIPRDVYEDELVPVFEAVGRIYELRLMMDFDGKNRGYAFVMYCHKHEAKRAVRELNNYEIRPGRLLGVCCSVDNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVKILYVRNLMIETTEDTIKKSFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELEGSCLEVTLAKPVDKEQYSRYQKAARGGGAAEAAQQPSYVYSCDPYTLAYYGYPYNALIGPNRDYFVKAGSIRGRGRGAAGNRAPGPRGSYLGGYSAGRGIYSRYHEGKGKQQEKGYELVPNLEIPTVNPVAIKPGTVAIPAIGAQYSMFPAAPAPKMIEDGKIHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPTVSTPPPFQGRPITPVYTVAPNVQRIPTAGIYGASYVPFAAPATATIATLQKNAAAAAAMYGGYAGYIPQAFPAAAIQVPIPDVYQTY,-|inframe_deletion|MODERATE|RBM47|ENSG00000163694|Transcript|ENST00000381795.6|protein_coding|4/5||ENST00000381795.6:c.1278_1298del|ENSP00000371214.6:p.Ala427_Ala433del|1539-1559|1278-1298|426-433|AAAAAAAA/A|gcGGCCGCAGCCGCCGCAGCCGCt/gct|rs564837143||-1||HGNC|30358|||4:g.40434705_40434725del|||||MTAEDSTAAMSSDSAAGSSAKVPEGVAGAPNEAALLALMERTGYSMVQENGQRKYGGPPPGWEGPHPQRGCEVFVGKIPRDVYEDELVPVFEAVGRIYELRLMMDFDGKNRGYAFVMYCHKHEAKRAVRELNNYEIRPGRLLGVCCSVDNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVKILYVRNLMIETTEDTIKKSFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELEGSCLEVTLAKPVDKEQYSRYQKAARGGGAAEAAQQPSYVYSCDPYTLAYYGYPYNALIGPNRDYFVKVAIPAIGAQYSMFPAAPAPKMIEDGKIHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPTVSTPPPFQGRPITPVYTVAPNVQRIPTAGIYGASYVPFAAPATATIATLQKNAAAAAAMYGGYAGYIPQAFPAAAIQVPIPDVYQTY,-|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|RBM47|ENSG00000163694|Transcript|ENST00000510871.1|nonsense_mediated_decay|6/7||ENST00000510871.1:c.*541_*561del||2431-2451|||||rs564837143||-1||HGNC|30358|||4:g.40434705_40434725del|||||MTAEDSTAAMSSDSAAGSSAKVPEGVAGAPNEAALLALMERTGYSMVQENGQRKYGGPPPGWEGPHPQRGCEVFVGKIPRDVYEDELVPVFEAVGRIYELRLMMDFDGKNRGYAFVMYCHKHEAKRAVRELNNYEIRPGRLLGVCCSVDNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVKILYVRNLMIETTEDTIKKSFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELEGSCLEVTLAKPVDKEQYSRYQKAARGGGAAEAAQQPSYVYSCDPYTLAYYGYPYNALIGPNRDYFVKDTILETHPASLPLVLRRHA,-|inframe_deletion|MODERATE|RBM47|ENSG00000163694|Transcript|ENST00000514014.1|protein_coding|5/6||ENST00000514014.1:c.1371_1391del|ENSP00000423243.1:p.Ala458_Ala464del|1630-1650|1371-1391|457-464|AAAAAAAA/A|gcGGCCGCAGCCGCCGCAGCCGCt/gct|rs564837143||-1||HGNC|30358|||4:g.40434705_40434725del|||||MERTGYSMVQENGQRKYGGPPPGWEGPHPQRGCEVFVGKIPRDVYEDELVPVFEAVGRIYELRLMMDFDGKNRGYAFVMYCHKHEAKRAVRELNNYEIRPGRLLGVCCSVDNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVKILYVRNLMIETTEDTIKKSFGQFNPGCVERVKKIRDYAFVHFTSREDAVHAMNNLNGTELEGSCLEVTLAKPVDKEQYSRYQKAARGGGAAEAAQQPSYVYSCDPYTLAYYGYPYNALIGPNRDYFVKAGSIRGRGRGAAGNRAPGPRGSYLGGYSAGRGIYSRYHEGKGKQQEKGYELVPNLEIPTVNPVAIKPGTVAIPAIGAQYSMFPAAPAPKMIEDGKIHTVEHMISPIAVQPDPASAAAAAAAAAAAAAAVIPTVSTPPPFQGRPITPVYTVAPNVQRIPTAGIYGASYVPFAAPATATIATLQKNAAAAAAMYGGYAGYIPQAFPAAAIQVPIPDVYQTY,-|non_coding_transcript_exon_variant|MODIFIER|RBM47|ENSG00000163694|Transcript|ENST00000515809.1|processed_transcript|2/2||||224-?|||||rs564837143||-1||HGNC|30358|||4:g.40434705_40434725del|||||	GT:AD:BQ:SS:DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT	0/1:125:.:2:128:128:125,125:5,5:12,12:119.5:1.75:0:PASS
6	41754573	.	C	CCTT	.	.	CSQ=CTT|inframe_insertion&NMD_transcript_variant|MODERATE|PRICKLE4|ENSG00000124593|Transcript|ENST00000335515.6|nonsense_mediated_decay|7/9||ENST00000335515.6:c.861_862insCTT|ENSP00000335185.6:p.Leu288dup|1448-1449|861-862|287-288|-/L|-/CTT|rs140326303||1||HGNC|16805|||6:g.41754573_41754574insCTT|||||MSVQNSGWPHQEDSPKPQDPGPPANSDSDSGHLPGEDPEDTHAQGPAVLSLGSLCLDTNQAPNWTGLQTLLQQLPPQDIDERYCLALGEEERAELQLFCARRKQEALGQGVARLVLPKLEGHTCEKCRELLKPGEYGVFAARAGEQRCWHQPCFACQACGQALINLIYFYHDGQLYCGRHHAELLRPRCPACDQLIFSWRCTEAEGQRWHENHFCCQDCAGPLGGGRYALPGGSPCCPSCFENRYSDAGSSWAGALEGQAFLGETGLDRTEGRDQTSVNSATLSRTLLAAAGGSSLQTQRGLPGSSPQQENRPGDKAEAPKGQEQCRLETIRDPKDTPFSTCSSSSDSEPEGFFLGERLPQSWKTPGSLQAEDSNASKTHCTMC,CTT|downstream_gene_variant|MODIFIER|PRICKLE4|ENSG00000124593|Transcript|ENST00000359201.5|protein_coding||||||||||rs140326303|124|1||HGNC|16805|||6:g.41754573_41754574insCTT|||||MSVQNSGWPHQEDSPKPQDPGPPANSDSDSGHLPGEDPEDTHAQGPAVLSLGSLCLDTNQAPNWTGLQTLLQQLPPQDIDERYCLALGEEERAELQLFCARRKQEALGQGVARLVLPKLEGHTCEKCRELLKPGEYGVFAARAGEQRCWHQPCFACQACGQALINLIYFYHDGQLYCGRHHAELLRPRCPACDQLIFSWRCTEAEGQRWHENHFCCQDCAGPLGGGRYALPGGSPCCPSCFENRYSDAGSSWAGALEGQAFLGAPPPHPPDPSLGARSSHRASLAGAFQGPPEPTPRRGRGCGARLPPRRGRRTPSGGGGGPWRGLSAAAAARTAQGLGGAGGWASPPLAAV,CTT|downstream_gene_variant|MODIFIER|USP49|ENSG00000164663|Transcript|ENST00000394253.3|protein_coding||||||||||rs140326303|3060|-1||HGNC|20078|||6:g.41754573_41754574insCTT|||||MDRCKHVGRLRLAQDHSILNPQKWCCLECATTESVWACLKCSHVACGRYIEDHALKHFEETGHPLAMEVRDLYVFCYLCKDYVLNDNPEGDLKLLRSSLLAVRGQKQDTPVRRGRTLRSMASGEDVVLPQRAPQGQPQMLTALWYRRQRLLARTLRLWFEKSSRGQAKLEQRRQEEALERKKEEARRRRREVKRRLLEELASTPPRKSARLLLHTPRDAGPAASRPAALPTSRRVPAATLKLRRQPAMAPGVTGLRNLGNTCYMNSILQVLSHLQKFRECFLNLDPSKTEHLFPKATNGKTQLSGKPTNSSATELSLRNDRAEACEREGFCWNGRASISRSLELIQNKEPSSKHISLCRELHTLFRVMWSGKWALVSPFAMLHSVWSLIPAFRGYDQQDAQEFLCELLHKVQQELESEGTTRRILIPFSQRKLTKQVLKVVNTIFHGQLLSQVTCISCNYKSNTIEPFWDLSLEFPERYHCIEKGFVPLNQTECLLTEMLAKFTETEALEGRIYACDQCNSKRRKSNPKPLVLSEARKQLMIYRLPQVLRLHLKRFRWSGRNHREKIGVHVVFDQVLTMEPYCCRDMLSSLDKETFAYDLSAVVMHHGKGFGSGHYTAYCYNTEGGFWVHCNDSKLNVCSVEEVCKTQAYILFYTQRTVQGNARISETHLQAQVQSSNNDEGRPQTFS,CTT|downstream_gene_variant|MODIFIER|PRICKLE4|ENSG00000124593|Transcript|ENST00000394259.1|protein_coding||||||||||rs140326303|124|1||HGNC|16805|||6:g.41754573_41754574insCTT|||||MSPQGPAVLSLGSLCLDTNQAPNWTGLQTLLQQLPPQDIDERYCLALGEEERAELQLFCARRKQEALGQGVARLVLPKLEGHTCEKCRELLKPGEYGVFAARAGEQRCWHQPCFACQACGQALINLIYFYHDGQLYCGRHHAELLRPRCPACDQLIFSWRCTEAEGQRWHENHFCCQDCAGPLGGGRYALPGGSPCCPSCFENRYSDAGSSWAGALEGQAFLGAPPPHPPDPSLGARSSHRASLAGAFQGPPEPTPRRGRGCGARLPPRRGRRTPSGGGGGPWRGLSAAAAARTAQGLGGAGGWASPPLAAV,CTT|inframe_insertion|MODERATE|PRICKLE4|ENSG00000124593|Transcript|ENST00000394260.1|protein_coding|5/5||ENST00000394260.1:c.741_742insCTT|ENSP00000377803.1:p.Leu248dup|741-742|741-742|247-248|-/L|-/CTT|rs140326303||1||HGNC|16805|||6:g.41754573_41754574insCTT|||||MSPQGPAVLSLGSLCLDTNQAPNWTGLQTLLQQLPPQDIDERYCLALGEEERAELQLFCARRKQEALGQGVARLVLPKLEGHTCEKCRELLKPGEYGVFAARAGEQRCWHQPCFACQACGQALINLIYFYHDGQLYCGRHHAELLRPRCPACDQLIFSWRCTEAEGQRWHENHFCCQDCAGPLGGGRYALPGGSPCCPSCFENRYSDAGSSWAGALEGQAFLGETGLDRTEGRDQTSVNSATLSRTLLAAAGGSSLQTQRGLPGSSPQQENRPGDKAEAPKGQEQCRLETIRDPKDTPFSTCSSSSDSEPEGFFLGERLPQSWKTPGSLQAEDSNASKTHCTMC,CTT|inframe_insertion|MODERATE|PRICKLE4|ENSG00000124593|Transcript|ENST00000394263.1|protein_coding|6/6||ENST00000394263.1:c.861_862insCTT|ENSP00000377806.1:p.Leu288dup|861-862|861-862|287-288|-/L|-/CTT|rs140326303||1||HGNC|16805|||6:g.41754573_41754574insCTT|||||MSVQNSGWPHQEDSPKPQDPGPPANSDSDSGHLPGEDPEDTHAQGPAVLSLGSLCLDTNQAPNWTGLQTLLQQLPPQDIDERYCLALGEEERAELQLFCARRKQEALGQGVARLVLPKLEGHTCEKCRELLKPGEYGVFAARAGEQRCWHQPCFACQACGQALINLIYFYHDGQLYCGRHHAELLRPRCPACDQLIFSWRCTEAEGQRWHENHFCCQDCAGPLGGGRYALPGGSPCCPSCFENRYSDAGSSWAGALEGQAFLGETGLDRTEGRDQTSVNSATLSRTLLAAAGGSSLQTQRGLPGSSPQQENRPGDKAEAPKGQEQCRLETIRDPKDTPFSTCSSSSDSEPEGFFLGERLPQSWKTPGSLQAEDSNASKTHCTMC,CTT|upstream_gene_variant|MODIFIER|TOMM6|ENSG00000214736|Transcript|ENST00000398881.3|protein_coding||||||||||rs140326303|829|1||HGNC|34528|||6:g.41754573_41754574insCTT|||||MASSTVPVSAAGSANETPEIPDNVGDWLRGVYRFATDRNDFRRNLILNLGLFAAGVWLARNLSDIDLMAPQPGV,CTT|upstream_gene_variant|MODIFIER|TOMM6|ENSG00000214736|Transcript|ENST00000398884.3|protein_coding||||||||||rs140326303|826|1||HGNC|34528|||6:g.41754573_41754574insCTT|||||MASSTVPVSAAGSANETPEIPDNVGDWLRGVYRFATDRNDFRRNLILNLGLFAAGVWLARNLSDIDLMAPQPGV,CTT|upstream_gene_variant|MODIFIER|FRS3|ENSG00000137218|Transcript|ENST00000422888.1|protein_coding||||||||||rs140326303|293|-1|cds_end_NF|HGNC|16970|||6:g.41754573_41754574insCTT|||||MGSCCSCLNRDSVPDNHPTKFKVTNVDDEGVELGSG,CTT|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|PRICKLE4|ENSG00000124593|Transcript|ENST00000456057.1|nonsense_mediated_decay|8/10||ENST00000456057.1:c.*1367_*1368insCTT||2241-2242|||||rs140326303||1||HGNC|16805|||6:g.41754573_41754574insCTT|||||MSVQNSGWPHQEDSPKPQDPGPPANSDSDSGHLPGEDPEDTHAQEFLSLHLLRTWGFDFKLIHMSIHYLS,CTT|inframe_insertion|MODERATE|PRICKLE4|ENSG00000124593|Transcript|ENST00000458694.1|protein_coding|8/8||ENST00000458694.1:c.861_862insCTT|ENSP00000404911.1:p.Leu288dup|1109-1110|861-862|287-288|-/L|-/CTT|rs140326303||1||HGNC|16805|||6:g.41754573_41754574insCTT|||||MSVQNSGWPHQEDSPKPQDPGPPANSDSDSGHLPGEDPEDTHAQGPAVLSLGSLCLDTNQAPNWTGLQTLLQQLPPQDIDERYCLALGEEERAELQLFCARRKQEALGQGVARLVLPKLEGHTCEKCRELLKPGEYGVFAARAGEQRCWHQPCFACQACGQALINLIYFYHDGQLYCGRHHAELLRPRCPACDQLIFSWRCTEAEGQRWHENHFCCQDCAGPLGGGRYALPGGSPCCPSCFENRYSDAGSSWAGALEGQAFLGETGLDRTEGRDQTSVNSATLSRTLLAAAGGSSLQTQRGLPGSSPQQENRPGDKAEAPKGQEQCRLETIRDPKDTPFSTCSSSSDSEPEGFFLGERLPQSWKTPGSLQAEDSNASKTHCTMC,CTT|downstream_gene_variant|MODIFIER|PRICKLE4|ENSG00000124593|Transcript|ENST00000463606.1|processed_transcript||||||||||rs140326303|1414|1||HGNC|16805|||6:g.41754573_41754574insCTT|||||,CTT|downstream_gene_variant|MODIFIER|PRICKLE4|ENSG00000124593|Transcript|ENST00000483200.1|retained_intron||||||||||rs140326303|99|1||HGNC|16805|||6:g.41754573_41754574insCTT|||||,CTT|non_coding_transcript_exon_variant|MODIFIER|PRICKLE4|ENSG00000124593|Transcript|ENST00000487182.1|retained_intron|7/9||ENST00000487182.1:n.1624_1625insCTT||1624-1625|||||rs140326303||1||HGNC|16805|||6:g.41754573_41754574insCTT|||||,CTT|upstream_gene_variant|MODIFIER|RP11-298J23.9|ENSG00000268745|Transcript|ENST00000594586.1|antisense||||||||||rs140326303|4574|1||Clone_based_vega_gene||||6:g.41754573_41754574insCTT|||||	GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT	0/1:76:13,9,28,26:36:2:12:78:12,12:55,55:12,12:80.52:1.92:0:PASS
6	43250725	.	GGAA	G	.	.	CSQ=-|inframe_deletion|MODERATE|TTBK1|ENSG00000146216|Transcript|ENST00000259750.4|protein_coding|14/15||ENST00000259750.4:c.2248_2250del|ENSP00000259750.4:p.Glu771del|2331-2333|2248-2250|750|E/-|GAA/-|rs113160341||1||HGNC|19140|||6:g.43250726_43250728del|||||MQCLAAALKDETNMSGGGEQADILPANYVVKDRWKVLKKIGGGGFGEIYEAMDLLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNEKFNYVVMQLQGRNLADLRRSQPRGTFTLSTTLRLGKQILESIEAIHSVGFLHRDIKPSNFAMGRLPSTYRKCYMLDFGLARQYTNTTGDVRPPRNVAGFRGTVRYASVNAHKNREMGRHDDLWSLFYMLVEFAVGQLPWRKIKDKEQVGMIKEKYEHRMLLKHMPSEFHLFLDHIASLDYFTKPDYQLIMSVFENSMKERGIAENEAFDWEKAGTDALLSTSTSTPPQQNTRQTAAMFGVVNVTPVPGDLLRENTEDVLQGEHLSDQENAPPILPGRPSEGLGPSPHLVPHPGGPEAEVWEETDVNRNKLRINIGKSPCVEEEQSRGMGVPSSPVRAPPDSPTTPVRSLRYRRVNSPESERLSTADGRVELPERRSRMDLPGSPSRQACSSQPAQMLSVDTGHADRQASGRMDVSASVEQEALSNAFRSVPLAEEEDFDSKEWVIIDKETELKDFPPGAEPSTSGTTDEEPEELRPLPEEGEERRRLGAEPTVRPRGRSMQALAEEDLQHLPPQPLPPQLSQGDGRSETSQPPTPGSPSHSPLHSGPRPRRRESDPTGPQRQVFSVAPPFEVNGLPRAVPLSLPYQDFKRDLSDYRERARLLNRVRRVGFSHMLLTTPQVPLAPVQPQANGKEEEEEEEEDEEEEEEDEEEEEEEEEEEEEEEEEEEEEEEAAAAVALGEVLGPRSGSSSEGSERSTDRSQEGAPSTLLADDQKESRGRASMADGDLEPEEGSKTLVLVSPGDMKKSPVTAELAPDPDLGTLAALTPQHERPQPTGSQLDVSEPGTLSSVLKSEPKPPGPGAGLGAGTVTTGVGGVAVTSSPFTKVERTFVHIAEKTHLNVMSSGGQALRSEEFSAGGELGLELASDGGAVEEGARAPLENGLALSGLNGAEIEGSALSGAPRETPSEMATNSLPNGPALADGPAPVSPLEPSPEKVATISPRRHAMPGSRPRSRIPVLLSEEDTGSEPSGSLSAKERWSKRARPQQDLARLVMEKRQGRLLLRLASGASSSSSEEQRRASETLSGTGSEEDTPASEPAAALPRKSGRAAATRSRIPRPIGLRMPMPVAAQQPASRSHGAAPALDTAITSRLQLQTPPGSATAADLRPKQPPGRGLGPGRAQAGARPPAPRSPRLPASTSAARNASASPRSQSLSRRESPSPSHQARPGVPPPRGVPPARAQPDGTPSPGGSKKGPRGKLQAQRATTKGRAGGAEGRAGAR	GT:DP:DP4:BQ:SS:AD:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50:FT	0/1:200:43,47,54,56:34:2:56:215:56,57:123,123:37,37:205.2:7.66:0:PASS
@serge2016
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Same here. Is it possible to fix this "spam"? Or what is the reason for such messages?

@nakib103 nakib103 self-assigned this Jul 21, 2023
@nakib103
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Thanks @Stikus @serge2016 for reporting this issue!

This is a warning and does not effect output. It is generated during calculation of HGVS notation when there is no extraneous matching sequence between ref and alt alleles - which is actually the common case.

It is quite a misleading message. We will put a fix in place and let you know.

Best regards,
Nakib

@Stikus
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Stikus commented Jul 21, 2023

@nakib103 Thanks for fast answer, we'll wait for fix.

Btw - someone forgot to mark 110 release as latest:
image

And I cannot reopen #1350 (comment) this issue, but we still have problem with fasta changes - should I open separate issue about it? All conversation will be lost.

@nakib103
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Thanks @Stikus, the tag has been placed.
It is also better to create a new issue instead of re-opening already closed one. You can tag the previous issue if needed.

Best regards,
Nakib

@Stikus Stikus mentioned this issue Jul 24, 2023
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@nakib103
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Hello @Stikus @serge2016 ,

A new version of VEP 110.1 is available with the fix. Please upgrade your VEP installation to this version and let us know if that fixes your issue.

If you are using docker image you can just pull the latest image and it will contain the fix.

docker pull ensemblorg/ensembl-vep:latest

If you have installed VEP from the command line make sure you also update the API when updating VEP to latest version.

git checkout release/110.1
perl INSTALL.pl --AUTO a

Best regards,
Nakib

@Stikus
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Stikus commented Jul 25, 2023

All good now, thx:

  Command: '/soft/ensembl-vep-110.1/vep --fork 32 --input_file /inputs/input.vcf --format vcf --cache --dir_cache /ref/.vep --dir_plugins /soft/ensembl-vep-110.1/Plugins --assembly GRCh37 --offline --output_file /outputs/test1.annot-vep.vcf --vcf --force_overwrite --symbol --check_existing --terms SO --tsl --hgvs --hgvsg --transcript_version  --plugin Frameshift --plugin Wildtype   --shift_hgvs 0 --no_stats --plugin ProteinSeqs,/outputs/test1.annot-vep.reference.fa,/outputs/test1.annot-vep.mutated.fa'.
  PID=194 (last job)
Smartmatch is experimental at /soft/ensembl-vep-110.1/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm line 472.
WARNING: Plugin ProteinSeqs is disabling forking
2023-07-24 14:57:06 - INFO: --shift_hgvs has been set to zero, setting shift_3prime to 0

@Stikus Stikus closed this as completed Jul 25, 2023
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