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

[Rishi Nag]

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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