rps blast database 'formatrpsdb' problem

Question

[User 6777]

Hi..

After installing BLAST+ package from ncbi, when I try to build a database for rps blast analysis using:

formatrpsdb -t COG_first -i Cog.pn -o T -f 11 -n COG -S 100.0

it gives following error:

[NULL_Caption] FATAL ERROR: COG0001.smpInput
PssmWithParameters.pssm.intermediateData.freqRatios
Unable to match element in intermediateData. line 24227
[NULL_Caption] ERROR: no data found in file 'COG0001.smp'

Although I check all files needed to run the program are available.

Please suggest a solution.

Thank you

Answer 1

[allison.e.mann]

Instead of formatrpsdb use makeprofiledb:

makeprofiledb -in Cog.pn -title Cog -out Cog -dbtype 'rps'

Where Cog.pn is a list of the smp files you want to include and -title and -out is how you want your new database to be named.