Question: Diamond database creation
2
gravatar for stu111392
3.5 years ago by
stu11139230
Germany/Kiel
stu11139230 wrote:

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?

blast sequence next-gen alignment • 3.9k views
ADD COMMENTlink modified 3.4 years ago by henning.og0 • written 3.5 years ago by stu11139230

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

ADD REPLYlink written 3.5 years ago by maubarsom0

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

 

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by maubarsom0

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

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by stu11139230
0
gravatar for stu111392
3.5 years ago by
stu11139230
Germany/Kiel
stu11139230 wrote:

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

ADD COMMENTlink written 3.5 years ago by stu11139230
0
gravatar for henning.og
3.4 years ago by
henning.og0
Sweden
henning.og0 wrote:

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

ADD COMMENTlink written 3.4 years ago by henning.og0

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.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by 5heikki7.3k

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.

ADD REPLYlink written 3.4 years ago by henning.og0
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