fastax FTP issue

[Tao2020yes]

I tried to populate the taxon database using "fastax populate". It gives a message saying "fastax: FTP InvalidResponse: Expected code [227], got response: 501 PASV: Operation not permitted". Such that, the database was not successfully cloned. Could you give suggestions to address the issue? Thanks.

[Picani]

Hi

Thanks for pointing this out!

Could you post the output of fastax --debug populate please?

Moreover, are you behind a proxy? If yes, it might be it blocking the FTP...

Thanks!

[Tao2020yes]

I don't use a proxy. Thank you for your reponse.

[Picani]

The PASV: Operation not permitted means that, for some reason, you cannot use the passive mode of FTP.

Could you try with a regular FTP client? Just to test if the problem is from fastax or from your network.

If the ftp command is available, you can try

ftp -p ftp.ncbi.nih.gov/pub/taxonomy

Then, once you're connected, type the following in the prompt

get taxdmp.zip

If the ftp command is not available, but the lftp command is available, you can try

lftp ftp.ncbi.nih.gov/pub/taxonomy/

Then, once you're connected, type the following in the prompt

set ftp:passive-mode true
get taxdmp.zip

In the meantime, I'll try to update the ftp library to a more up-to-date one.

[Picani]

Hi

I'm in the process of modernizing the database layer.

When done, it will be possible to populate the local database from a file or to let fastax downloads it from the NCBI servers. This should fix the current problem.

I'll close this issue at that time.

[Picani]

Fixed in v1.5.0