The paths I provided to Galaxy are full paths. I checked the location of the temporary files ; Galaxy looks for an index file in the directory /home/john/galaxy-dist/database/job_working_directory/000::
This directory is empty after the execution of the workflow (but I guess this is normal since it store temporary files)
I guess the problem is there, but I don't know how to fix it.
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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 :
.nhr,.nin,.nsd,.nsi,.nsqIn
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.
In
blastdb.locyou used an absolute path (which is sensible),/home/john/databases/SSUref_111_tax_silva/SSURef_111_tax_silva.fastaHere 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 fromblastdb.locinstead?