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josuebarrera / GenEra

genEra is a fast and easy-to-use command-line tool that estimates the age of the last common ancestor of protein-coding gene families.
GNU General Public License v3.0
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Trouble with installation #1

Closed billadelonge closed 2 years ago

billadelonge commented 2 years ago

Hi, I would love to give this a but I am currently struggling with installation, this bit doesn't work for me, as the file gets somehow corrupted I think and cannot gunzip it

wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr{.gz,.gz.md5} && md5sum -c *.md5
gunzip nr.gz

Thanks! Laura

josuebarrera commented 2 years ago

Dear Laura, Thank you for your interest in using GenEra!

We just double-checked, and there was an error in the command, thanks for pointing it out. Could you please check if these commands work for you?

wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz.md5
md5sum -c *.md5
gunzip nr.gz

Best, Josué.

josuebarrera commented 2 years ago

Also, please bear in mind that the nr file is huge (~130GB). Could it be that the file got corrupted because you ran out of storage space?

billadelonge commented 2 years ago

Hi Jose, Thanks, that helped, I seem to have to use https:// instead of ftp:// (found something about this online). However now I seem to have the same problem with the prot.accession2taxid it keeps getting corrupted. I checked and I seem to have enough space. Any suggestions? Best, Laura

josuebarrera commented 2 years ago

Dear Laura,

My guess is that the solution should be very similar as with the NR, but I'm unable to test it right now, since I'm currently on vacations. Could you please contact my colleage Sodai? He will be able to help you out: jaruwatana.lotharukpong@tuebingen.mpg.de Otherwise, I'll be able to check the issue in a couple of weeks.

Best, Josué.

billadelonge commented 2 years ago

Okay! So this worked somehow wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid//prot.accession2taxid.gz

josuebarrera commented 2 years ago

Dear Laura, I'm glad you found a solution! I'll close the issue, but please feel free to contact us again if you come across any further issues. Best, Josué.