Diamond makedb error: Error: Invalid nodes.dmp file format.


New member
I am trying to make diamond NR database with its --taxonmap and --taxonnodes parameters. After making the db file around 102 gb, it gives the 'Error: Invalid nodes.dmp file format.' error. I downloaded the file 'taxdmp.zip' twice from NCBI ftp site but it is still giving same error.
I am using this command: diamond makedb --in nr_fastaSeqs --taxonmap prot.accession2taxid.gz --taxonnodes taxdmp.zip -d nrDB_taxonmap
I will be very grateful if someone guide me to resolve this error.

Benjamin Buchfink

Staff member
You need to unpack the taxdmp.zip first. The parameter to the --taxonnodes needs to be the nodes.dmp file contained within the taxdmp.zip.