No alias or index file found for nucleotide database BLASTn HELP

Question: No alias or index file found for nucleotide database BLASTn HELP

5 months ago by

Hello,

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

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modified 5 months ago by Jennifer Hillman Jackson ♦ 25k • written 5 months ago by andrew.allee590 • 0

5 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This forum is best for questions about Galaxy. For general bioinformatics, try https://biostars.org 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. https://www.ncbi.nlm.nih.gov/books/NBK279688/

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: https://galaxyproject.org/ >>> Use: Main Galaxy && Education: Learn Galaxy

Thanks! Jen, Galaxy team

ADD COMMENT • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

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