[ensembl-dev] Ensembl release 108 is out

Thu Nov 10 02:25:41 GMT 2022

Hi,

It looks like installation for 108_GRCh37 is broken:

$ perl INSTALL.pl -a c -s homo_sapiens -y GRCh37 -c /data/vep --NO_HTSLIB --NO_TEST
 - getting list of available cache files
 - downloading https://ftp.ensembl.org/pub/release-108/variation/indexed_vep_cache/homo_sapiens_vep_108_GRCh37.tar.gz<https://urldefense.proofpoint.com/v2/url?u=https-3A__ftp.ensembl.org_pub_release-2D108_variation_indexed-5Fvep-5Fcache_homo-5Fsapiens-5Fvep-5F108-5FGRCh37.tar.gz&d=DwMGaQ&c=WO-RGvefibhHBZq3fL85hQ&r=fpFYsQD9efuj6qk0TjK1MbUTPI07tTdDii-uM88QGpo&m=uEeAtmcBVmdX_pYTuAZvb2qERdaRosoAWop6hummx2YX5fU9PHe2Eg2QxKw-9-aA&s=aJ4A-kNCHvqTdpd3zD-IdHQPMtNEscAdIhnVin8ADK4&e=>
 - unpacking homo_sapiens_vep_108_GRCh37.tar.gz
 - converting cache, this may take some time but will allow VEP to look up variants and frequency data much faster
 - use CTRL-C to cancel if you do not wish to convert this cache now (you may run convert_cache.pl later)
ERROR: Version 108_GRCh37 not found
WARNING: Failed to run convert script

All done

For some reason, it attempts to run indexing script and fails, even though the caches downloaded were already indexed. Caches are in fact downloaded & installed successfully, or at least it looks like they did. I have not run actual tests yet.

Update: In fact, caches are successfully downloaded, checked and uncompressed into the tmp directory but then deleted for no apparent reason, hence installation failed completely. Probably triggered by  the "ERROR: Version 108_GRCh37 not found", see above but what it means is unclear.

Also, there is no way to install FASTA sequence since it will first remove all cache files installed previously. And if I try the other way round it refuses to download caches *after* FASTA sequence has been downloaded because cache directory already exists.

$ perl INSTALL.pl -a f -s homo_sapiens -y GRCh37 -c /data/vep --NO_HTSLIB --NO_TEST

WARNING: Changing URL for GRCh37
 - downloading Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz
 - extracting data
 - attempting to index
Indexing failed - VEP will attempt to index the file the first time you use it

The FASTA file should be automatically detected by the VEP when using --cache or --offline.
If it is not, use "--fasta /data/vep/homo_sapiens/108_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa"

All done

$ perl INSTALL.pl -a c -s homo_sapiens -y GRCh37 -c /data/vep --NO_HTSLIB --NO_TEST
 - getting list of available cache files

WARNING: It looks like you already have the cache for homo_sapiens GRCh37 (v108) installed.

Delete the folder /data/vep/homo_sapiens/108_GRCh37 and re-run INSTALL.pl if you want to re-install
 - skipping homo_sapiens

All done

I had to first move .fa file out of the 108_GRCh37 folder, delete empty folder, re-install caches and then move .fa file back and index it manually. Not a big deal but it took me some time to figure out what's going on. Does not seems to be an intended behavior, so I assume this is due to some bug(s) in INSTALL.pl script.

Thanks,

Ivan

On 10/20/22 06:08, Louisse Paola Mirabueno wrote:
Hi all,

We are pleased to announce that the latest Ensembl and Ensembl Genomes updates have been released!

Highlights of this release include:

  *   Changes in the human default tracks
  *   New genomes added in Ensembl Plants and Ensembl Metazoa
  *   Addition of mitochondrial annotation for Tasmanian devil
  *   New and additional data reported by VEP

The release blog post with all news can be viewed here.

For the latest news from the Ensembl project visit our blog. Thank you all!

All the best,

Louisse (on behalf of the Ensembl team)

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