Error running blastn on Linux: Critical [blastn] External MBEDTLS version mismatch: 2.16.2 headers vs. 2.16.3 runtime

Question

[2jackcummins]

I am running blastn (blast+) version 2.9.0 on Ubuntu. My command is this blastn -task megablast -db nt -query blast.fasta -out blast_results.tsv -evalue 0.001 -outfmt "6 qseqid sseqid pident qstart qend sstart send evalue qlen slen staxids sscinames scommnames sblastnames sskingdoms" -remote. When I run this I get the error "Critical [blastn] External MBEDTLS version mismatch: 2.16.2 headers vs. 2.16.3 runtime" Can anybody help? Thanks, Jack

[GenoMax]

Are you using pre-compiled version of blast? Did you get it from NCBI?

[2jackcummins]

I got blast using these instructions https://ngsprimer.wordpress.com/.

Answer 1

[GenoMax]

Install the latest blast+ binary and see if that works.

[2jackcummins]

I couldn't download the latest blast binary. I got this error:

Selecting previously unselected package ncbi-blast. (Reading database ... 39918 files and directories currently installed.) Preparing to unpack ncbi-blast_2.10.1+-2_amd64.deb ... Unpacking ncbi-blast (2.10.1+-2) ... dpkg: error processing archive ncbi-blast_2.10.1+-2_amd64.deb (--install): trying to overwrite '/usr/bin/blast_formatter', which is also in package ncbi-blast+ 2.9.0-2 dpkg-deb: error: paste subprocess was killed by signal (Broken pipe) Errors were encountered while processing: ncbi-blast_2.10.1+-2_amd64.deb Unable to install at /usr/share/perl5/Alien/Package/Deb.pm line 97, <getperms> line 24. find ncbi-blast-2.10.1+ -type d -exec chmod 755 {} ; rm -rf ncbi-blast-2.10.1+

[2jackcummins]

Wait, I was able to download the newest blast+. I will keep you updated on whether it works.

[2jackcummins]

It's working! Thank you so much!

[Octavius]

Could you explain how you installed it? I'm in taking bio stats and ran into the exact problem you did but unfortunately for me I don't know how to install the blast+ binary update.

[GenoMax]

You can simply download a pre-compiled blast version for your OS from blast ftp site. No installation should be needed. Make sure the directory you put these files in is available in your $PATH after you un-compress the tar archive.