[ensembl-dev] Perl errors running VEP v95

[Andrew Parton]

Hi Jessica,

Thanks for this, could you please provide the input file you’re using and I can take a look?

Kind Regards,
Andrew 

> On 23 Jan 2019, at 22:55, Jessica X. Chong <jxchong at uw.edu> wrote:
> 
> We previously were running v89 without problems and are trying to update to v95(.1). When I run v95, I get a lot of script errors although it seems to produce an output VCF ok (but very very slowly likely because of all the warning print statements). 
> 
> The errors look like this. I couldn't debug further because I don't know what the number 8852 is for -- it's not the line number (I am providing a 1000-line toy VCF as input) and it's not the chromosomal position because 8852 doesn't exist in my VCF.
> 
> 
> WARNING: 8852 : substr outside of string at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 519.
> Use of uninitialized value $ref_allele in string eq at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 522.
> Use of uninitialized value in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1595.
> Use of uninitialized value $len in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1621.
> Use of uninitialized value $check_ref in numeric eq (==) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1649.
> Use of uninitialized value $check_ref in numeric ge (>=) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1652.
> substr outside of string at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 519.
> Use of uninitialized value $ref_allele in string eq at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 522.
> Use of uninitialized value in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1595.
> Use of uninitialized value $len in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1621.
> Use of uninitialized value $check_ref in numeric eq (==) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1649.
> Use of uninitialized value $check_ref in numeric ge (>=) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1652.
> substr outside of string at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 519.
> Use of uninitialized value $ref_allele in string eq at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 522.
> Use of uninitialized value in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1595.
> Use of uninitialized value $len in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1621.
> Use of uninitialized value $check_ref in numeric eq (==) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1649.
> Use of uninitialized value $check_ref in numeric ge (>=) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1652.
> substr outside of string at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 519.
> Use of uninitialized value $ref_allele in string eq at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 522.
> Use of uninitialized value in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1595.
> Use of uninitialized value $len in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1621.
> Use of uninitialized value $check_ref in numeric eq (==) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1649.
> Use of uninitialized value $check_ref in numeric ge (>=) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1652.
> substr outside of string at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 519.
> Use of uninitialized value $ref_allele in string eq at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 522.
> Use of uninitialized value in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1595.
> Use of uninitialized value $len in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1621.
> Use of uninitialized value $check_ref in numeric eq (==) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1649.
> Use of uninitialized value $check_ref in numeric ge (>=) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1652.
> substr outside of string at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 519.
> Use of uninitialized value $ref_allele in string eq at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 522.
> Use of uninitialized value in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1595.
> Use of uninitialized value $len in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1621.
> Use of uninitialized value $check_ref in numeric eq (==) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1649.
> Use of uninitialized value $check_ref in numeric ge (>=) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1652.
> substr outside of string at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 519.
> Use of uninitialized value $ref_allele in string eq at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 522.
> Use of uninitialized value in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1595.
> Use of uninitialized value $len in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1621.
> Use of uninitialized value $check_ref in numeric eq (==) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1649.
> Use of uninitialized value $check_ref in numeric ge (>=) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1652.
> substr outside of string at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 519.
> Use of uninitialized value $ref_allele in string eq at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 522.
> Use of uninitialized value in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1595.
> Use of uninitialized value $len in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1621.
> Use of uninitialized value $check_ref in numeric eq (==) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1649.
> Use of uninitialized value $check_ref in numeric ge (>=) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1652.
> substr outside of string at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 519.
> Use of uninitialized value $ref_allele in string eq at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 522.
> Use of uninitialized value in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1595.
> Use of uninitialized value $len in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1621.
> Use of uninitialized value $check_ref in numeric eq (==) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1649.
> Use of uninitialized value $check_ref in numeric ge (>=) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1652.
> substr outside of string at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 519.
> Use of uninitialized value $ref_allele in string eq at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 522.
> Use of uninitialized value in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1595.
> Use of uninitialized value $len in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1621.
> Use of uninitialized value $check_ref in numeric eq (==) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1649.
> Use of uninitialized value $check_ref in numeric ge (>=) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1652.
> substr outside of string at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 519.
> Use of uninitialized value $ref_allele in string eq at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 522.
> Use of uninitialized value in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1595.
> Use of uninitialized value $len in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1621.
> Use of uninitialized value $check_ref in numeric eq (==) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1649.
> Use of uninitialized value $check_ref in numeric ge (>=) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1652.
> substr outside of string at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1131.
> Use of uninitialized value $post_seq in substr at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1132.
> Use of uninitialized value in numeric eq (==) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1142.
> substr outside of string at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1131.
> Use of uninitialized value $post_seq in substr at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1132.
> Use of uninitialized value in numeric eq (==) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1142.
> substr outside of string at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 519.
> Use of uninitialized value $ref_allele in string eq at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 522.
> Use of uninitialized value in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1595.
> Use of uninitialized value $len in numeric lt (<) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1621.
> Use of uninitialized value $check_ref in numeric eq (==) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1649.
> Use of uninitialized value $check_ref in numeric ge (>=) at /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1652.
> [if file is larger/contains more variants, this will repeat]
> 
> 
> Here's the command I'm trying to use:
> 
> 
> perl vep \
> -i 1000lines.vcf.gz \
> -o 1000lines.VEP95.vcf.gz \
> --compress_output bgzip --exclude_predicted --domain --nearest symbol --vcf --offline \
> --cache --dir_cache /references/ENSEMBL_genesets/release95/ \
> --species homo_sapiens --assembly GRCh37 \
> --fasta /references/human/hg19/genome/assembly_bwa_0.7.10/hs37d5.fa \
> --fork 8 --force_overwrite --sift b --polyphen b --symbol --numbers \
> --biotype --total_length --canonical --ccds --hgvs --shift_hgvs 1 \
> --gene_phenotype --check_existing --regulatory \
> --fields Consequence,Codons,Amino_acids,Gene,SYMBOL,Feature,Feature_type,EXON,cDNA_position,CDS_position,Protein_position,Existing_variation,PolyPhen,SIFT,BIOTYPE,CANONICAL,CCDS,HGVSc,HGVSp,PHENO,GENE_PHENO,NEAREST,DOMAINS
> 
> 
> 
> Thanks!
> Jessica
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