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!