I am currently trying to use megablast on a Galaxy server. I use a custom db that I prepared with
makeblastdb -in some_sequences.fasta -dbtype nucl -out some_sequences. I put the path to my database in galaxy-dist/tool-data/blastdb.loc, I restarted my Galaxy server, but when I want to perform a megablast, the following error is raised ;
Cannot execute megaablast. BLAST Database error: No alias or index file found for nucleotide database [/home/john/databases/database_name/some_sequences] in search path [/home/john/galaxy-dist/database/job_working_directory/000/119::]
what have I done wrong?
This is odd. For some reason BLAST is not recognizing "/home/john/databases/database_name/some_sequences" as a full path to a database, but instead as a database string name. Could you dump here the line in your blastdb.loc? Could you check if you are correctly using TABs in that file?
here is the content of my blastdb.loc ;
SSUref_111_tax_silva SSUred_11_tax_silva /home/john/databases/SSUref_111_tax_silva/SSURef_111_tax_silva.fasta
I checked that the fields are tab-delimited in my blastdb.loc
the same error is raised even if I try blast from command-line
OK, If this is a nucleotide database do you have these files in the same directory?: SSURef_111_tax_silva.fasta.nhr SSURef_111_tax_silva.fasta.nin SSURef_111_tax_silva.fasta.nsq
And, what error do you get when you run blast manually? Could share here the error and the command line invocation you are using.
In the directory of my database, I have files with the following extensions :
blastdb.loc, the file name I provided is the root of all these files.
When I run
blastn -db databases/SSUref_111_tax_silva/SSURef_111_tax_silva.fasta -query some_random_sequences.fastathe output is ok (I mean, the blastn command obviously works)
I though you said above the same error is raised in your environment if you tried to run blast from the command-line.
Sorry I can't be of much help.
blastdb.locyou used an absolute path (which is sensible),
Here you used a relative path,
-db databases/SSUref_111_tax_silva/SSURef_111_tax_silva.fastaso presumably you were in the directory
/home/john/when you did this? Try using the exact full absolute path copied from