[EMBOSS] fuzzpro memory consumption

[Rozenbaum, Daniel (Biocceleration Inc)]

Dear all,

We attempted to run a fuzzpro search of the UniProt database with the following pattern:

[LIVMSTAC]-[LIVMFYWSTAGC]-[LIMSTAG]-[LIVMSTAGC]-x(2)-[DN]-x-{P}- [LIVMWSTAC]-{DP}-[LIVMFSTAG]-W-[DEN]-[LIVMFSTAGCN]

The job appears to have brought the server into a hung state, and my best guess is that the process consumed so much memory that it caused heavy swapping.

I'm still not 100% sure that my assumption is correct, but in any event, is there a way to gauge how much memory will a fuzznuc/pro or dreg/preg job consume, based on the complexity of the pattern, size of the database, expected number of matches, etc?

Many thanks,
Daniel

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Daniel Rozenbaum
Biocceleration, Inc.
OCIO/Office of Application Engineering & Development/Patent System Division
600 Dulany St.
Alexandria, VA 22314