Question: blast+ and GnuTLS errors on Mac
0
gravatar for larvalanobium
3.6 years ago by
larvalanobium30 wrote:

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

blast gnutls • 1.8k views
ADD COMMENTlink modified 3.4 years ago by Alex Reynolds31k • written 3.6 years ago by larvalanobium30

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

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by GenoMax95k

Yes, lastest blastn: Nucleotide-Nucleotide BLAST 2.6.0+

And no, just that copy.

ADD REPLYlink written 3.6 years ago by larvalanobium30

Can you try and build GnuTLS outside of brew?

ADD REPLYlink written 3.6 years ago by GenoMax95k

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!

ADD REPLYlink written 3.5 years ago by larvalanobium30

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.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by sacha.lau0
0
gravatar for Alex Reynolds
3.4 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

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.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Alex Reynolds31k
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