Entering edit mode
9.5 years ago
Henry Helgen
•
0
I am trying to run blastdbcmd on the nr protein database, but it is looking for the nucleotide database index file.
I downloaded the pre-formatted databases into a new folder
[nr201410]$ blastdbcmd -db /vol1/blast/blast-nr-db/nr201410/nr -info
BLAST Database error: No alias or index file found for nucleotide database [/vol1/blast/blast-nr-db/nr201410/nr] in search path [/vol1/blast/blast-nr-db/nr201410:::]
[nr201410]$ ls -l /vol1/blast/blast-nr-db/nr201410/nr.pal
-rw-r--r-- 1 hhelgen hhelgen 423 Oct 13 18:47 /vol1/blast/blast-nr-db/nr201410/nr.pal
The blastdbcmd is working on the existing nr datafiles.
[blast-nr-db]$ blastdbcmd -db nr -info
Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects
18,280,215 sequences; 6,265,275,233 total residues
Date: May 28, 2012 4:41 AM Longest sequence: 41,943 residues
Volumes:
/vol1/blast/blast-nr-db/nr.00
/vol1/blast/blast-nr-db/nr.01
/vol1/blast/blast-nr-db/nr.02
/vol1/blast/blast-nr-db/nr.03
/vol1/blast/blast-nr-db/nr.04
/vol1/blast/blast-nr-db/nr.05
/vol1/blast/blast-nr-db/nr.06
[blast-nr-db]$
Any ideas?
You looked at the .pal which makes sense as it is the alias file. Have you checked for the index files as well, i.e. .pin files for each of the nr volumes listed in your .pal? You are supposed to have 26 volumes if you're interested in the current version.
Yes, I see the .pin files
I unzipped the nr files to the new blast executable db directory keeping the existing privileges. but got the same error.
The search path is the local directory not the
ncbi-blast-2.2.29+/db
directory.Then I changed to the db directory and it found it. But why doesn't it find it when using the full path?