Hi.
I created a database from a reference genome and I got this error message when I run the blastx command. Earlier today I did the same process for blastn and it was fine.
The entire error message:
BLAST Database error: No alias or index file found for nucleotide database [/index/path] in search path [/current/path:/ncbi-blast/ncbi-blast-2.10.0+/blastdb:/index/path:]
The commands:
Creating the index:
makeblastdb -in "/ncbi_genome.fna" -dbtype prot -parse_seqids -out "/index"
Calling blastsx:
blastn -query "input.fa" -db "reference" -max_hsps 1 -max_target_seqs 50 -num_threads 10 -evalue 1e-5 -out "output.txt"
I'd love to hear your opinions. Thanks.
1 answer
blastn -query "input.fa" -db "reference" -max_hsps 1 -max_target_seqs 50 -num_threads 10 -evalue 1e-5 -out "output.txt"
Wait .. that looks like protein database and you are using blastn in your command line. Since you are saying
Calling blastsx:
that must be a typo in command line.
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Do you actually have these files right under your
/(root) directory? Are you able to write to that location using a standard user account? What doesls -lRh /index*show?It's not the actual path. I shortened the paths for simplification.
The command you asked about printed the following files: