[ensembl-dev] Perl errors running VEP v95

Jessica X. Chong jxchong at uw.edu
Thu Jan 24 17:26:17 GMT 2019 

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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