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Koina error ericw04  2024-09-27 12:01
 

Hi,

I'm trying to run an EncyclopeDIA search through Skyline with an experiment-specific FASTA file. This has worked for me in the past, however, when I run the search now I get a "GO AWAY" error from Koina before it's finished processing the FASTA and the search fails. The text of error is attached. When I check the Koina configuration in Skyline (Skyline (64-bit) 24.1.0.199 (6a0775ef83)) it says the connection is active.

Any help is much appreciated.
Thanks,
-Eric
 
 
Nick Shulman responded:  2024-11-04 15:48
Eric,

Thank you for reporting this. This only seems to happen for sufficiently large FASTA files.

Koina seems to fail on the millionth prediction that Skyline requests of it. Skyline typically requests one retention time per peptide, plus one spectrum per charge state, so you can get through a few hundred thousand peptides before the first error happens.

The next update of Skyline-daily will retry when errors like this happen, so you should be able to successfully analyze your dataset.
If you do not want to wait for the next official update of Skyline-daily, there is a special build with this fix here:
https://proteome.gs.washington.edu/~nicksh/SpecialSkylines/KoinaRetry/
-- Nick