.psq database format needed?

Hi,

 

I wanted to use KNIME with OMSSA adapter and I get this error message after a few seconds:

 

ERROR OMSSAAdapter         0:74       Failing process stdout: [OpenMS data path ('C:/Program Files/KNIME_OpenMSsession/plugins/de.openms.win32.x86_64_2.1.0.201609092116/payload/share/OpenMS') retrieved from OPENMS_DATA_PATH (environment)., OMSSAAdapter took 0.12 s (wall), 0.03 s (CPU), 0.03 s (system), 0.00 s (user).]
ERROR OMSSAAdapter         0:74       Failing process stderr: [Input database 'C:\Users\Dennis\Desktop\Test_KNIME\uniprot_Human_reviewed_concatenated_target_decoy_noX.fasta.psq' not found (the file 'C:\Users\Dennis\Desktop\Test_KNIME\uniprot_Human_reviewed_concatenated_target_decoy_noX.fasta.psq' could not be found). Make sure it exists (and check 'OpenMS.ini:id_db_dir' if you used relative paths. Aborting!, Unable to find database 'C:\Users\Dennis\Desktop\Test_KNIME\uniprot_Human_reviewed_concatenated_target_decoy_noX.fasta.psq' (searched all folders). Did you mistype its name? Is the .psq-formatted version available?]
ERROR OMSSAAdapter         0:74       Execute failed: Failed to execute node OMSSAAdapter

 

My question is if I really need a .psq db format, and if yes what that looks like/ how I can create that from a database I have on my computer. I found something about ncbi-blast but I think I am handling it wrong.

 

Thanks for your help!

 

Hi,

Yes, the PSQ file is needed as an index of your database so that OMSSA can quickly search it.

You need to install the ncbi-blast toolbox (at least the makeblastdb tool) and run it like described here:

http://seqanswers.com/forums/showthread.php?t=9452

Do not forget to include

-dbtype 'prot'

in your options.

Cheers

Julianus