Thank you, that was it!
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BlastX Database error: No alias or index file found for protein database
Hello,
I downloaded the indices for the nr database with wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz in order to run blastX locally. I put the files in a directory refDir, the nucleic acid sequence of interest in qFile and launched blastx with
blastx -db $refDir -num_threads 14 -max_target_seqs 10 -outfmt '6 qseqid sseqid evalue bitscore sgi sacc staxids sscinames' -query $qFile
but I got:
BLAST Database error: No alias or index file found for protein database [<path to refDir>] in search path [<path to refDir>::]
What am I missing? Thanks
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marongiu.luigi
1 answer
you need to also specify the DB name, not only the path to it.
should be something like: -db $refDir/DB_name
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lieven.sterck
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You are right, actually I did not use the FASTA nr.gz (that was another thread I opened and pasted here) but the indices from ftp://ftp.ncbi.nih.gov/blast/db/