Diamond database creation

Question

[stu111392]

Hello,

I just installed the Diamond Protein Alignment Algorithm (http://ab.inf.uni-tuebingen.de/software/diamond/) yesterday and the first step before the alignment is to set up a database. The input for generating a database should be a FASTA file containing protein sequences. I created a db-File from a FSTA file containing multiple Protein sequences and it worked out (meaning Diamond did the job without any errors). But after that if I want to start aligning samples to the databse I always get the error: incompatible database version. Has anyone of you expirience with this program?

[stu111392]

I think is solved the problem. At the moment it is running. I'll have a look at the results but I'm optimistic now :)

[maubarsom]

How did you solve it? I am havin the same problem as well. I downloaded nr from the NCBI blast ftp site.

[maubarsom]

Nevermind, the message appears if there is any kind of error regarding the name of the database file, including non-existent database files,wrong path etc. Just remember to not include the ".dmnd" extension in the invocation

[stu111392]

Yep, that's also the way I made it working. Just cut off the library data extension and it worked.

Answer 1

[henning.og]

In the description it is written "DIAMOND is a new high-throughput program for aligning a file of short reads against a protein reference database such as NR".

But I fail to make my NR database compatible for DIAMOND. I have NR downloaded locally that I use for blast. But how to fix NR so I can run DIAMOND as well? I do not include .dmnd in the command.

The command I run:

diamond blastx -p 28 -q /path/fasta.fasta -o /path/output.fasta -d /path/to/database/nr

Which leads to the error:

Error: function Input_stream::Input_stream(const string&, bool) line 74. Error opening file /path/to/database/nr.dmnd

[5heikki]

Do you have the blast formatted nr db in that path or have you downloaded the nr fasta file and created a diamond database from that? You have to do the latter.

[henning.og]

It works now! Hehe realized I made a lot of beginners mistakes. Went to ftp://ftp.ncbi.nlm.nih.gov and fixed the file I needed to format.