Question: rps blast database 'formatrpsdb' problem
1
gravatar for User 6777
5.0 years ago by
User 677710
United States
User 677710 wrote:

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,

blast formatdb • 2.3k views
ADD COMMENTlink modified 3.6 years ago by allison.e.mann10 • written 5.0 years ago by User 677710
1
gravatar for allison.e.mann
3.6 years ago by
allison.e.mann10 wrote:

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.

ADD COMMENTlink written 3.6 years ago by allison.e.mann10
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