Issue with diamond makedb and the "taxonmap" parameter

Question

[Alessandro]

Hi all,

Apparently, I'm not able to build correctly the nr database for diamond. To build it I run the following line:

diamond makedb --in nr.gz -d nr --taxonmap prot.accession2taxid --taxonnodes nodes.dmp  --threads 20

The process works fine, but I think that something is missing. If I run diamond with the staxids included in the -outfmt flag it reports the follwing error:

diamond blastx -p SRR8217837_Trinity.fasta -p 16 -d /home/dbs/nr.dmnd -o SRR8217837_blastx_Trinity --outfmt 6 qseqid sseqid evalue bitscore pident staxids  stitle --max-target-seqs 5 --evalue 0.005

diamond v0.9.14.115 | by Benjamin Buchfink <[e-mail]>
Licensed under the GNU AGPL <https://www.gnu.org/licenses/agpl.txt>
Check http://github.com/bbuchfink/diamond for updates.


#CPU threads: 16
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Error: staxids output field requires setting the --taxonmap parameter.

I tried to rebuild the database many times, but I don't get why it tells me that --taxonmap is not set.

Thank you in advance,

Ale

[lieven.sterck]

not sure but perhaps you need to add that --taxonmap parameter when running the diamond search itself?

[Alessandro]

In this case I get another type of error:

diamond blastx -p SRR8217837_Trinity.fasta -p 16 -d /home/dbs/nr.dmnd -o SRR8217837_blastx_Trinity --outfmt 6 qseqid sseqid evalue bitscore pident staxids  stitle --max-target-seqs 5 --evalue 0.005 --taxonmap /home/dbs/prot.accession2taxid --taxonnodes /home/dbs/nodes.dmp 
diamond v0.9.14.115 | by Benjamin Buchfink <[e-mail]>
Licensed under the GNU AGPL <https://www.gnu.org/licenses/agpl.txt>
Check http://github.com/bbuchfink/diamond for updates.

#CPU threads: 16
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
#Target sequences to report alignments for: 5
Temporary directory: 
Opening the database...  [2.5e-05s]
Loading taxonomy...  [0.001613s]
Error: Inflate error.

[GenoMax]

Latest diamond is able to use pre-formatted databases that NCBI provides. Have you tried to download the pre-formatted database along with taxdb.tar file?

Or if you did build the db correctly you may not have downloaded the taxonomy file needed.

[fabineves7]

Alessandro, Were you able to solve the problem?