Unaccepted characters after Rfam-database-check

[Tim15-tech]

I encountered the error "assert (np.all(msa<=31))" when running the program sometimes. It seems that after checking the Rfam-database some annotations contain like an R, which is unknown within the RoseTTAFold2NA-RNAalphabet. I circumvent this problem by writing characters to an N. The code is in my forked repository in case someone encounters the same problem.

Thanks for the model!

[anar-rzayev]

First of all, thank you for your commits in the forked repo, they were quite helpful at least to get rid of the bad characters. I was wondering if there is any way to resolve the FASTA-Reader: Ignoring invalid residues at position(s) as I still get these issues when running your scripts.

Meanwhile, by any chance, have you encountered problems with downloading update_blastdb.pl --decompress n as it seems there are so many disconnections happening to NCBI, even with timeout 3600, passive FTP, and verbose outputs, I have hard time to download this 151GB dataset. Do you have any possible approaches to solve it I wanted to ask

[Tim15-tech]

Sadly, I don't know. I'm not familiar with this kind of issue, however it might simply be due to the fasta-files? If the error is in the origin, then I assume it's fine for running the program - however, I finally don't know. I remember this message - if not wrongly remembered - and I think I simply ignored it.

However, regarding the second question: I think sadly the best is to have fast internet. In example, with poor internet git clone can be a horror. In case there are disconnections from NCBI-side maybe wait some days or a week. However, in the end a stable and fast connection is required. I downloaded it a my university on a server over days using screen, which allowed me to let the command run and detach my terminal to allow shutdown of my local PC.

[anar-rzayev]

Actually, you are right. As long as the bad characters are gone, it shouldn't be a big deal to have those FASTA invalid warnings. About the second point, in fact, I also run the tmux session as running nohup on the background didn't help initially:

/home/intern/protein/.conda/envs/RF2NA/bin/perl /home/intern/protein/.conda/envs/RF2NA/bin/update_blastdb.pl --decompress --passive --timeout 3600 --force --verbose --verbose nt > nt_download_log.txt 2>&1

It is so strange that even with timeout of 1 hour, running the attached session disconnects after 1-2 hours. The output keeps telling that

Downloading nt.000.tar.gz...Net::FTP=GLOB(0x55b3acd21cf8)>>> PASV
Net::FTP=GLOB(0x55b3acd21cf8)<<< 227 Entering Passive Mode (130,14,250,12,196,235).
Net::FTP=GLOB(0x55b3acd21cf8)>>> RETR nt.000.tar.gz
Net::FTP=GLOB(0x55b3acd21cf8)<<< 150 Opening BINARY mode data connection for nt.000.tar.gz (4721879742 bytes)
Net::FTP: Net::Cmd::getline(): unexpected EOF on command channel:  at /home/intern/protein/.conda/envs/RF2NA/lib/perl5/core_perl/Net/FTP/dataconn.pm line 82.
Unable to close datastream at /home/intern/protein/.conda/envs/RF2NA/bin/update_blastdb.pl line 202.
Net::FTP: Net::Cmd::_is_closed(): unexpected EOF on command channel:  at /home/intern/protein/.conda/envs/RF2NA/bin/update_blastdb.pl line 203.
Net::FTP: Net::Cmd::_is_closed(): unexpected EOF on command channel:  at /home/intern/protein/.conda/envs/RF2NA/bin/update_blastdb.pl line 203.
Failed to download nt.000.tar.gz.md5!
Net::FTP: Net::Cmd::_is_closed(): unexpected EOF on command channel:  at /home/intern/protein/.conda/envs/RF2NA/bin/update_blastdb.pl line 101.
Net::FTP: Net::Cmd::_is_closed(): unexpected EOF on command channel:  at /home/intern/protein/.conda/envs/RF2NA/bin/update_blastdb.pl line 101.

Did you have any specific installations by any chance or running this perl script after maybe downloading MoreUtils or other library was sufficient?

[anar-rzayev]

Also, on top of the installations part, did you have any issues with downloading all the necessary packages for running RF2NA? Maybe any specific blast versions were necessary or any other specificity