[ensembl-dev] Perl errors running VEP v95

Fri Jan 25 10:32:39 GMT 2019

Hi Jessica,

I’ve had a look this morning, and it looks like something has gone wrong with your installation process - when I use your input file and command on a clean 95.1 install then it works as expected at my end.

Could you please attempt a clean reinstall of VEP and see if that resolves your issue? Failing that, could you please run VEP in verbose mode (add the ‘—v’ flag to your query) and report the output?

Kind Regards,
Andrew

> On 24 Jan 2019, at 17:26, Jessica X. Chong <jxchong at uw.edu> wrote:
> 
> I emailed it separately to you (Andrew). Thanks.
> 
> By the way, I left the process running overnight and the process eventually died -- the output VCF was truncated after the #CHROM POS [...] header line (no actual data/variant lines).
> 
> Here's the error after the process died.
> 
> 
> -------------------- EXCEPTION --------------------
> MSG:
> ERROR: Forked process PID 22369 was killed
> 
> STACK Bio::EnsEMBL::VEP::Runner::_forked_buffer_to_output /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/modules/Bio/EnsEMBL/VEP/Runner.pm:563
> STACK Bio::EnsEMBL::VEP::Runner::next_output_line /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/modules/Bio/EnsEMBL/VEP/Runner.pm:360
> STACK Bio::EnsEMBL::VEP::Runner::run /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/modules/Bio/EnsEMBL/VEP/Runner.pm:202
> STACK toplevel /net/gs/vol3/software/modules-sw/ensembl-vep/95.1/Linux/RHEL6/x86_64/vep:225
> Date (localtime)    = Thu Jan 24 03:32:44 2019
> Ensembl API version = 95
> ---------------------------------------------------
> 
> Thanks,
> Jessica
> 
> 
>> On Jan 24, 2019, at 2:25 AM, Andrew Parton <aparton at ebi.ac.uk> wrote:
>> 
>> 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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>> 
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