BUG: Downloading Pfam-A fails. Connection time out.

[darcyabjones]

Moved here from a different issue #40 raised by @paulamool.

Something may have changed at EBI
Received a connection error for ftp://ftp.ebi.ac.uk/

"--2021-10-15 00:47:57-- ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz
(try:20) => ‘Pfam-A.hmm.dat.gz’
Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:21... failed: Connection timed out.
Giving up."

I changed url in nextflow.config from ftp to http and it seemed okay for a few runs (4) but getting the same error again.

pfam_hmm_url = "http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz"
pfam_dat_url = "http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz"

[darcyabjones]

thanks @paulamool

It looks like Pfam has been having issues for the last few days, which might be cause of second issue. https://twitter.com/PfamDB/status/1448580277899612162
They might also have finally migrated away from the FTP sites given that Chrome & Firefox finally ditched it.
So could be a few things.

I'll update the default download URL.

For future posterity (i'll add something like this to the FAQs too).
Predector also has command line options for this reason, so no need to go editing the configs unless you really want to.

You can download the pfam HMMs and .dat files separately and provide them yourself e.g. --pfam_hmm Pfam-A.hmm.gz --pfam_dat Pfam-A.hmm.dat.gz. (https://github.com/ccdmb/predector/wiki#command-line-parameters)

You can also change the URLs to download from at the command line as well.
e.g. --pfam_hmm_url "http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz".

[paulamool]

Great, thanks

[darcyabjones]

The default download location should now be fixed with release 1.1.1.
Thanks again.