[ensembl-dev] Perl errors running VEP v95

[Jessica X. Chong]

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