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

[Rishi Nag]

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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