[ensembl-dev] Fwd: Ensembl VEP: FASTA gzip to bgzip conversion failed

[Platon workaccount]

VEP's install script was invoked by command perl INSTALL.pl

вт, 22 мар. 2016 г. в 15:32, Rishi Nag <rishi at ebi.ac.uk>:

>
> Hi
>
> Thanks for raising this issue. Can you provide details on how the install
> script was invoked please?
>
> Regards
>
> Rishi
>
> On 22/03/2016 12:04, Platon workaccount wrote:
> >
> >
> > ---------- Forwarded message ---------
> > From: Platon workaccount <platon.work at gmail.com <mailto:
> platon.work at gmail.com>>
> > Date: вт, 22 мар. 2016 г. в 14:58
> > Subject: Ensembl VEP: FASTA gzip to bgzip conversion failed
> > To: <dev at ensembl.org <mailto:dev at ensembl.org>>
> >
> >
> > Hello.
> >
> > Full API end dependencies are installed (bioperl-live, ensembl,
> ensembl-compara, ensembl-variation, ensembl-funcgen; tabix; DBI,
> DBD::mysql);
> > environment is set up
> > my $API_VERSION = 84
> > ubuntu-15.10-desktop-amd64
> >
> > Error of converting sequence data:
> >
> > ? 28
> > - downloading Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
> > - converting sequence data to bgzip format
> > Going to run:
> > ./biodbhts/scripts/convert_gz_2_bgz.sh
> /home/pl/.vep/homo_sapiens/84_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
> ./htslib/bgzip
> > This may take some time and will be removed when files are provided in
> bgzip format
> > /bin/bash: ./biodbhts/scripts/convert_gz_2_bgz.sh: No such file or
> directory
> > FASTA gzip to bgzip conversion failed:
> >
> >
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> >
>
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