Odd Error with OMSSAadapter

Dear community,

I am stuck with running even simple tasks that involve OMSSAadapter. Just for the sake of testing, I reran some of the tutorial examples and keep getting OMSSAadapter error saying that files are not found.

Specifically, missing files: pin,psq and phr - although they are contained within the fasta file directory (Protein Database). I am not sure what I am doing wrong as I followed the tutorial step by step…

I am running KNIME on windows10

Maybe someone has insigihts/advice?

Thanks in advance,

Hi Aya,

if you look into the online documentation that is linked in the help text of the node, it will tell you that you need to create an NCBI index for your fasta database first.

For our tutorial files, this should not happen, since we provide them for you. I would advise just to use another search engine node for simplicity (e.g. CometAdapter, which does not need an index). Their settings are very similar.



Thank you, Julianus, for your reply and explanation - I will try this out then as I was also not sure what’s the issue as index files should be there…the error message essentially says that files are not found in the location (although they exist).

Will have a go with CometAdapter! Thank you for your kind help :smiley:

ERROR OMSSAAdapter 0:76 Failing process stdout: [OMSSAAdapter took 0.06 s (wall), 0.02 s (CPU), 0.02 s (system), 0.00 s (user); Peak Memory Usage: 23 MB.]
ERROR OMSSAAdapter 0:76 Failing process stderr: [Input database ‘D:\Research work\Mass spectrometry\References\s_pyo_sfHS.fasta.psq’ not found (the file ‘D:\Research work\Mass spectrometry\References\s_pyo_sfHS.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 ‘D:\Research work\Mass spectrometry\References\s_pyo_sfHS.fasta.psq’ (searched all folders). Did generate the PSQ file (see OMSSAAdapter documentation).]
ERROR OMSSAAdapter 0:76 Return code: 6
ERROR OMSSAAdapter 0:76 Execute failed: Failed to execute node OMSSAAdapter

Ah! I didn’t know that you already generated it. I actually overlooked your statement, sorry. Some nodes have problems with network paths or paths with whitespaces. It might be a good idea to avoid them to rule this out. E.g. use “…\Research_work\MassSpec” or something like that.


This actually solved it :slight_smile: thank you very much for your time and advice - will make sure to correctly name my folders!

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