.psq database format needed?

[StullenBrot]

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!

 

[jpfeuffer]

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