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Error: Database file is not a BLAST database

Open lida56 opened this issue 2 years ago • 5 comments

Hi, I have used the following command to download the nr database on HPC, by simply replacing the swissport command on your wiki by nr: update_blastdb.pl --decompress blastdb 5 nr

1-The directory now have a mix of file formats as bellow as example: nr.82.tar.gz.md5 nr.82.pin 0 nr.81.phd nr.81.phi nr.81.pog nr.81.ppd nr.81.ppi nr.81.phr nr.81.psq

I tried to make the database using the below command and it gave me the error. diamond prepdb -d nr

I would appreciate your help

lida56 avatar Nov 27 '23 02:11 lida56

Can you check for a nr.pal file in that directory? If it doesn't exist, the database was probably not downloaded correctly.

bbuchfink avatar Nov 27 '23 13:11 bbuchfink

Hi, Thanks and yes it does have the nr.pal file but still giving the error. May I ask what is the difference between using "update_blastdb.pl --decompress blastdb 5 nr" and " wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz" for obtaining the latest nr database?

lida56 avatar Dec 13 '23 01:12 lida56

The second command downloads the database in FASTA format, not as a BLAST database.

bbuchfink avatar Dec 13 '23 14:12 bbuchfink

Thanks a lot, which one would you recommend for building the nr database to be used for Diamond? Sorry I am more of a user and not a bioinformatician.

lida56 avatar Dec 14 '23 01:12 lida56

Both is fine, if you need taxonomic information you need to build the database from fasta.

bbuchfink avatar Dec 19 '23 14:12 bbuchfink