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

[Platon workaccount]

Thanks! "Converted FASTA gzip file to bgzip successfully", but this time
"Indexing failed - VEP will attempt to index the file the first time you
use it". Is it a critical error?

ср, 23 мар. 2016 г. в 12:02, Rishi Nag <rishi at ebi.ac.uk>:

>
> Thanks.
>
> Change into the same directory as INSTALL.pl
>
> First check for a htslib directory being present with the ls command. If
> not then download and compile this:
> git clone -b master --depth=1 https://github.com/samtools/htslib.git
> cd htslib
> make
> cd ..
>
> git clone https://github.com/Ensembl/Bio-HTS.git biodbhts
> You should then be able to re-run the install commands to download the
> sequence from this directory.
>
> Regards
>
> Rishi
>
>
> On 22/03/2016 18:17, Platon workaccount wrote:
> > 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 <mailto:
> 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> <mailto: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> <mailto:
> 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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