Question: No alias or index file found for nucleotide database BLASTn HELP
gravatar for andrew.allee590
5 months ago by
andrew.allee5900 wrote:


I'm trying to BLAST against a database and I keep getting this error code:

No alias or index file found for nucleotide database [SILVA_132_LSURef_tax_silva.fasta] in search path [/array4/users/x/Project_MDC2017_Backup_AA/mdc_new_names_trial2/MDC2017_04_16_18::]

Here is my command line: blastn -db SILVA_132_LSURef_tax_silva.fasta -query 200150_abundantotu.cons -out 200150_blastn.txt -outfmt 6 -max_target_seqs 1 -num_threads 6

It seems as if the program isn't recognizing that my SILVA_132_LSURef_tax_silva.fasta as a database.

I've also tried making my .fasta file into a database using the command: makeblastdb -in SILVA_132_LSURef_tax_silva.fasta -dbtype 'nucl' -out SILVA_db which gave me three different files each .nhr, .nin, .nsq

Can anyone offer insight into how to fix this? Am I missing a portion in the command? Or do I need to manipulate my database?

I am following a pipeline, and am relatively new, so it could be an easy fix, but i'm just lost. Thanks for any help in advance!

error blast index alias • 279 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 5 months ago by andrew.allee5900
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:


This forum is best for questions about Galaxy. For general bioinformatics, try instead. I suspect this is answered there already in prior Q&A.

That said, this problem is clear -- the database needs to be indexed before using it as a -db input. The utility that indexes is called makeblastdb and comes in the BLAST package. Also, double check both that the query and target are both nucleotide, not protein, when using Blastn.

See the BLAST help for details, or do a google search for the utility or general usage questions that might come up later, there is a lot of help online.

Since you're here, I'd like to suggest using BLAST in Galaxy. The tool forms make all of this much easier to do plus your analysis is tracked/reproducible/sharable. If interested, start here: >>> Use: Main Galaxy && Education: Learn Galaxy

Thanks! Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 172 users visited in the last hour