ndaniel / fusioncatcher

Finder of Somatic Fusion Genes in RNA-seq data
GNU General Public License v3.0
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rattus_norvegicus download fails #195

Open hvelab opened 2 years ago

hvelab commented 2 years ago

Hi! I've tried several ways to download the genome of rattus_norvegicus, but it seems to always fail with a:

Downloading the genome of organism 'rattus_norvegicus' from Ensembl!
230 Login successful.
ERROR: Cannot find the genome and mitochondria files!
['Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa.gz']

Which I find weird because that file exists in the Ensembl FTP server: http://ftp.ensembl.org/pub/release-105/fasta/rattus_norvegicus/dna/

I've executed this command:

fusioncatcher-build -g rattus_norvegicus -o /<my-path>

Also tried it specifying python2.7, and/or the ensembl path:

python2.7 bin/fusioncatcher-build.py -g rattus_norvegicus -o /<path> --ftp-ensembl-path=/pub/release-105/

I think it might be something about the Ensembl release, because with "homo_sapiens" it works perfectly.

Also I tried it "the dirty way", downloading the data with a wget, decompressing everything and renaming it as I saw that you do in the script for getting the data. But seems to not work.

Any kind of help would be appreciated :)

Thanks in advance!

ndaniel commented 2 years ago

This will be fixed in the next official release.

hvelab commented 1 year ago

Thanks! Is there any date on that release? Is there any patch? I work for the User Support Team of a Supercomputing Research center and we have users interested in that genome.

Thank you very much again and best regards.