Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error in prepareDatabase('accessionTaxa.sql'), change in url? #66

Closed
mgpapadaki opened this issue Mar 14, 2024 · 3 comments
Closed

Error in prepareDatabase('accessionTaxa.sql'), change in url? #66

mgpapadaki opened this issue Mar 14, 2024 · 3 comments

Comments

@mgpapadaki
Copy link

Hello,

I've been trying to follow the instructions to set up the database using the prepareDatabase('accessionTaxa.sql') command. I encounter the following issue:

> prepareDatabase('accessionTaxa.sql')
Downloading names and nodes with getNamesAndNodes()
Download status: 1 done; 0 in progress. Total size: 0 b ... done!             
Error in resumableDownload(url, tarFile, resume = resume) : 
  Download failed with error: "Could not resolve host: ftp.ncbi.nih.gov".

I have tried manually checking the ftp url and it seems like it has changed to ftp.ncbi.nlm.nih.gov. The older url seems hard coded into the prepareDatabase function and I was wondering if you could help me solve this issue.

Thank you very much in advance!

@sherrillmix
Copy link
Owner

Both http://ftp.ncbi.nih.gov/ or ftp://ftp.ncbi.nih.gov seem to work fine for me. And the url isn't hardcoded but is accessible with the url= argument. Perhaps a transient problem with NCBI or some funny internet connections?

@sherrillmix
Copy link
Owner

Closing but let me know if problem persists/pops up again.

@mgpapadaki
Copy link
Author

Thank you very much for your reply. I was able to make it work for me by using the following:
prepareDatabase('accessionTaxa.sql',url= 'https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz')

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants