Blast "Argument "query". File is not accessible:" Error

Question

[logbio]

I am trying to run blastp locally using a multiple-fasta file as query, using this command:

 blastp -query homo.faa -db cow.faa -out human_blast.csv -outfmt 6 -evalue 0.00001 -max_target_seqs 1 -num_threads 4

Then I saw this error:

 "BLAST Database error: Argument "query". File is not accessible:" 

How can I solve this problem?

Answer 1

[lieven.sterck]

as it is mentioned, your query file is not available from the location you specified (in the directory where you run blast that is in your case).

can you do ls homo.faa in the folder where you start this blast?

how to solve this: likely you have to add the (correct) path pointing to where this input fasta file (query) is located.

Alternatively: it's also possible you don't have to correct permissions to access the file? you can check that by doing ls -l homo.faa and see if the permissions to that file are set OK for you to access it.

[logbio]

Thanks for your reply, but now I'm getting this error. `

BLAST Database error: No alias or index file found for protein database [human] in search path [/Usr/Desktop/irem/last::]

`

[lieven.sterck]

Can you post the cmdline you try to run again ?

this error points to the fact blast can't access the DB files, and looking at the initial cmdline it seems there was already an issue with that as well. There it looks like cow.faa is the DB so it's a bit weird blast complains about not able to access human as DB.

Also be sure that any (protein) fasta file you wish to blast again is correctly formatted to be used by blast as DB.

[logbio]

Thank you for answer