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

Michael Yourshaw myourshaw at gmail.com
Sat Feb 17 00:07:29 GMT 2018


My apologies if this is a duplicate. My other email program seems not to
have liked the "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

ॐ
Michael Yourshaw
myourshaw at gmail.com <myourshaw at ucla.edu>

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