Open lida56 opened 7 months ago
Can you check for a nr.pal
file in that directory? If it doesn't exist, the database was probably not downloaded correctly.
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?
The second command downloads the database in FASTA format, not as a BLAST database.
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.
Both is fine, if you need taxonomic information you need to build the database from fasta.
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