[ensembl-dev] VEP Cannot index bgzipped FASTA file with Bio::DB::Fasta

[Laurent Gil]

Dear Michael,

It looks like the ensembl-variation library can't find the 
Bio::DB::HTS::Faidx module.

Are you sure that the ${INSTALL_DIR}/*biodbhts*directory is in your 
PERL5LIB variable ?

Do you have an other installation of BioPerl on your machine ?

Best regards,

Laurent
Ensembl Variation

On 17/02/2018 00:07, Michael Yourshaw wrote:
> My apologies if this is a duplicate. My other email program seems not 
> to have liked the "dev at ensembl.org <mailto:dev at ensembl.org>" address.
>
> I need to run the VEP perl script offline but dairly full-featured.
>
> I downloaded and installed the current (91) VEP with `perl INSTALL.pl 
> --DESTDIR ${INSTALL_DIR} --CACHEDIR ${INSTALL_DIR} --PLUGINS all;`
>
> No errors were reported,, and in particular installing Bio::DB::HTS 
> and htslib seemed to go well.
>
> PERL5LIB includes the DESTDIR for VEP and PATH includes the htslib 
> directory.
>
> Bio::DB::HTS::Faidx.pm exists under the Bio directory that the VEP 
> installer created in the DESTDIR.
>
> --fasta is set to 
> .../homo_sapiens/91_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz. The 
> .fai and .gzi files are also present.
>
> Nonetheless, when I run the VEP, I get the error "Cannot index 
> bgzipped FASTA file with Bio::DB::Fasta".
>
> It appears that 
> Bio::EnsEMBL::Variation::Utils::FastaSequence::setup_fasta is failing 
> the test `eval { require Bio::DB::HTS::Faidx; 1 }` and therefore 
> not setting $CAN_USE_FAIDX.
>
> The command and error are below.
>
> Thanks for your help.
>
> > /usr/local/bin/perl \
> > /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/vep \
> > -i /gpfs/share/cmoco_sys_dev/nfs/storage/cromwell/cromwell-executions/PairedEndSingleSampleWorkflow/ff81a90d-ea94-4f33-9405-98575fd8e0af/call-VariantEffectPredictor/inputs/gpfs/share/cmoco_sys_dev/nfs/storage/cromwell/cromwell-executions/PairedEndSingleSampleWorkflow/ff81a90d-ea94-4f33-9405-98575fd8e0af/call-MakeSitesOnlyVcf/execution/AI-HEP7.lValExome0019.downsampled.recalibrated.filtered.postCGP.GQfiltered.sites.vcf \
> > --offline \
> > --cache \
> > --fasta 
> /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/homo_sapiens/91_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz 
> \
> > --merged \
> > --dir /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91 \
> > --output_file AI-HEP7.lValExome0019.downsampled.json \
> > --force_overwrite \
> > --json \
> > --everything \
> > -v
> 2018-02-16 16:03:21 - INFO: BAM-edited cache detected, enabling 
> --use_transcript_ref; use --use_given_ref to override this
>
> -------------------- EXCEPTION --------------------
> MSG: ERROR: Cannot index bgzipped FASTA file with Bio::DB::Fasta
>
> STACK Bio::EnsEMBL::Variation::Utils::FastaSequence::setup_fasta 
> /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm:210
> STACK Bio::EnsEMBL::VEP::BaseVEP::fasta_db 
> /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:477
> STACK Bio::EnsEMBL::VEP::Runner::init 
> /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:129
> STACK Bio::EnsEMBL::VEP::Runner::run 
> /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194
> STACK toplevel 
> /gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/vep:222
> Date (localtime)    = Fri Feb 16 16:03:22 2018
> Ensembl API version = 91
> ---------------------------------------------------
>
>
> Michael Yourshaw, JD, PhD
> Bioinformatician
> Colorado Center for Personalized Medicine
> Colorado Molecular Correlates
> michael.yourshaw at ucdenver.edu <mailto:michael.yourshaw at ucdenver.edu>
>
> ॐ
> Michael Yourshaw
> myourshaw at gmail.com <mailto:myourshaw at ucla.edu>
>
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