Running problem with staxid option

[Hoberti]

Hey I am having some problems running diamond.

I run this command for db creation:

diamond makedb -p 40 --in /home/blast_db/nr.fasta --taxonmap /home/blast_db/nr.acc2taxid.txt --taxonnodes ../taxdump/nodes.dmp -d nr.dmnd

(...) Writing trailer... [3.67785s] Closing the input file... [1.2e-05s] Closing the database file... [3.5e-05s] Processed 287467303 sequences, 103466633494 letters. Total time = 2607.65s No errors after running this command.

diamond dbinfo --db nr.dmnd diamond v0.9.14.115 Database format version = 1 Diamond build = 115 Sequences = 287467303 Letters = 103466633494

Then I run:

diamond blastx --query contig.fasta --db /home/blast_db/nr.dmnd --outfmt 6 qseqid staxids bitscore qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore --sensitive --max-target-seqs 1 --evalue 1e-25 --threads 40

This error shows up: Error: staxids output field requires setting the --taxonmap parameter.

So I run:

diamond blastx --query contig.fasta --db /home/blast_db/nr.dmnd --outfmt 6 qseqid staxids bitscore qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore --sensitive --max-target-seqs 1 --evalue 1e-25 --threads 40 --taxonmap /home/blast_db/nr.acc2taxid.txt

Error: Inflate error.

Do you know what could happened here? If I delate staxid from outfmt the command run perfectly.

Thanks!

Héctor

[bbuchfink]

You seem to be using v0.9.14 for which you might need to input that file gzip compressed. I would recommend though updating to the latest version which does not need the --taxonmap parameter for the blastx workflow, but only for makedb.