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Question 1:

I'm running the following:

blast-2.2.26/bin/blastpgp -i protein.fasta -j 5 -o file -d nr

where protein.fasta is a fasta file containing a single protein sequence. This produces no output and the -o file is empty.

Question 2:

I was able to successfully use:

blast-2.2.26/bin/formatdb -i family_of_proteins.fas -o T -s T

to create database files. However, this produced multiple files, .phr, .pin, .psd, .psi, .psq. Which one of these should I pass with the -d flag to use my own database?

Thank you!

user1539097
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  • Are you running blast from the folder that you downloaded the nr database to? If not, you'll need to specify the path to the database. Or use the -remote flag – heathobrien May 19 '15 at 08:26

1 Answers1

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For question 2:

You should pass the base name with the -d flag, so in you example, it would be "-d family_of_proteins.fas"

heathobrien
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  • Thank you, this worked to pass the database as long as the *.fas file is in the same directory as the *.pin etc files. Now I get an output file, which answers question 1 as well. – user1539097 May 19 '15 at 17:37