Vcf2maf error message: Cannot index bgzipped fasta file

Question

[Winson]

Hi

I get the error message while running the vcf2maf test samples. I have installed the latest ensembl-vep (v105), vcf2maf, and download GRCh37 cache and fasta file from VEP installer.

perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf --ref-fasta /home/robunken/.vep/homo_sapiens/105_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz --vep-path /home/robunken/Downloads/stuffs/ensembl-vep-release-105
STATUS: Running VEP and writing to: tests/test.vep.vcf

-------------------- EXCEPTION --------------------
MSG: ERROR: Cannot index bgzipped FASTA file with Bio::DB::Fasta

STACK Bio::EnsEMBL::Variation::Utils::FastaSequence::setup_fasta /home/robunken/Downloads/stuffs/ensembl-vep-release-105/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm:210
STACK Bio::EnsEMBL::VEP::BaseVEP::fasta_db /home/robunken/Downloads/stuffs/ensembl-vep-release-105/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:477
STACK Bio::EnsEMBL::VEP::Runner::init /home/robunken/Downloads/stuffs/ensembl-vep-release-105/modules/Bio/EnsEMBL/VEP/Runner.pm:134
STACK Bio::EnsEMBL::VEP::Runner::run /home/robunken/Downloads/stuffs/ensembl-vep-release-105/modules/Bio/EnsEMBL/VEP/Runner.pm:199
STACK toplevel /home/robunken/Downloads/stuffs/ensembl-vep-release-105/vep:232
Date (localtime)    = Mon Jan 17 20:45:54 2022
Ensembl API version = 105
---------------------------------------------------

ERROR: Failed to run the VEP annotator! Command: /home/robunken/miniconda3/bin/perl /home/robunken/Downloads/stuffs/ensembl-vep-release-105/vep --species homo_sapiens --assembly GRCh37 --no_progress --no_stats --buffer_size 5000 --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --vcf --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --dir /home/robunken/.vep --fasta /home/robunken/.vep/homo_sapiens/105_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz --format vcf --input_file tests/test.vcf --output_file tests/test.vep.vcf --offline --pubmed --fork 4 --polyphen b --af --af_1kg --af_esp --af_gnomad --regulatory

Any help would be appreciated.

Thanks in advance

Answer 1

[Pierre Lindenbaum]

try to de-zip your fasta sequence.

gunzip  /home/robunken/.vep/homo_sapiens/105_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz 

and then

(...) --fasta /home/robunken/.vep/homo_sapiens/105_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa  (...)

[Winson]

It works! Thanks a lot.

[Ram]

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