--taxonlist error

longzhang

New member
i would like to align my data to nr nrdatabase with diamond,bacause i hear i runs fast. But when i tried my aligning my data to the bacteria protein in nr after finishing makedb,it goes "Error: Option --taxonlist used with invalid argument (0 or 1).".i don't know what's wrong ,and my code is as fillows:
diamond blastx --db nrdia_inde.dmnd --query sequence.fasta --taxonlist BBBBB.taxid --taxonmap prot.accession2taxid.gz --taxonnodes nodes.dmp --evalue 1e-5 --out bac17align_diam --outfmt 6 qseqid sseqid pident nident mismatch gapopen qstart qend qlen sstart send length evalue bitscore staxids --max-target-seqs 1 --threads 8

when i was doing makedb,"--taxonmap" and "taxonnodes" are added ,too. So I can't figure out where i did wrong. So can you give me some advice? Thankyou!
 

Benjamin Buchfink

Administrator
Staff member
--taxonlist takes a list of numerical values (taxon ids). So for searching all bacterial proteins, use --taxonlist 2.

Btw, --taxonnodes and --taxonmap need only be added to makedb.
 
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