blast+ and GnuTLS errors on Mac

Question

[larvalanobium]

Hi there

I'm having essentially a similar error output to the original asker in this thread (https://www.biostars.org/p/229783/#260571), but mine has something to with GnuTLS, so my output starts with:

Warning: [blastn] Unavailable feature GNUTLS

Critical: [blastn] Unavailable feature GNUTLS

Error: (303.7) [blastn] [URL_Connect; https://www.ncbi.nlm.nih.gov:443/Service/dispd.cgi?service=blast4&address=10.1.153.186&platform=x86_64-apple-darwin15.6.0] Failed to connect: Not supported

... etc.

My input line is:

blastn -db nt -query $FILE -out theten -entrez_query "$EQ" -outfmt 17 -max_target_seqs 10 -remote

I've used brew to double check the the most recent versions of blast+, GnuTLS (and its dependencies; GMP and nettle) are up to date.

Does anyone have any ideas where I'm going wrong?

Thanks and kind regards

Crystal

[GenoMax]

Are you using the latest blast+ executable for Mac? Are there more than one blast versions on your Mac?

[larvalanobium]

Yes, lastest blastn: Nucleotide-Nucleotide BLAST 2.6.0+

And no, just that copy.

[GenoMax]

Can you try and build GnuTLS outside of brew?

[larvalanobium]

Hi there, I ended just asking them to install the software on our local cluster at work and got it to work. I think there might have been an issue with our proxy. but thanks for your help!

[sacha.lau]

Hello,

I am bumping this thread because I'm having the exact same problem.

Blast 2.6 on Linux.

When I run blastn -remote -db nr with bioconda or a docker container of blast 2.6 I get

Warning: [blastn] Unavailable feature GNUTLS Critical: [blastn] Unavailable feature GNUTLS Error: (303.7) [blastn] [URL_Connect; https://www.ncbi.nlm.nih.gov:443/Service/dispd.cgi?service=blast4&address=HOS41488(127.0.1.1)&platform=x86_64-unknown-linux-gnu] Failed to connect: Not supported Error: (302.131) [blastn] SSOCK#2000[?]: [SOCK::Connect] Failed to initialize secure session

etc etc

However when I setup a server version of 17.04 using kvm on my computer, the command works.

I am in contact with an IT guy from my place and he tells me that everything runs fine on his end with blast 2.6 (plus he can't really offer a lot of support for this kind of tools).

I really don't understand what is going on, if someone has an idea where this could come from.

Thank you very much,

EDIT : Sorry I understand now where the problem comes from. Nevermind my post, it was a problem on the package distributed by bioconda.

Answer 1

[Alex Reynolds]

On a Mac. install Homebrew, then run brew install libgnutls. On CentOS 7, you could run sudo yum install gnutls-devel. If this is a dependency issue, either of these will install the GnuTLS library.