makedb process issue - Error: staxids output field requires setting the --taxonmap parameter #601

Question

[fabineves7]

I need your help with this issue. I tried to build the database diamond makedb --in viral_proteins_merged.faa.gz --db file --taxonmap prot.accession2taxid.FULL.gz --taxonnodes nodes.dmp --taxonnames names.dmp and it looks that it is concluded successfully.

However when I run the script diamond diamond blastx -q contigs.fa -d file.dmnd -o file.txt -k 1 --very-sensitive -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sscinames sphylums it instantaneously stops with the error:

#CPU threads: 160
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Error: staxids output field requires setting the --taxonmap parameter.

I already tried to perform the run with files zipped and unzipped and also erase all the files and made new downloads from the reference databases, but I always get the same error..

Can anyone help me with this?

Regards Fabiana

[lieven.sterck]

Welcome fabineves7,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[GenoMax]

The error is clear. You need to provide that additional parameter which needs a file.

--taxonmap               protein accession to taxid mapping file

[fabineves7]

But I provide the file, and also tried the zipped and unzipped file

diamond makedb --in viral_proteins_merged.faa.gz --db file --taxonmap **prot.accession2taxid.FULL.gz** --taxonnodes nodes.dmp --taxonnames names.dmp

[GenoMax]

Since you made your custom database you may need to provide a accesion2taxid file only for those entries.