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zamboni-lab / SLAW

Scalable and self-optimizing processing workflow for untargeted LC-MS
GNU General Public License v2.0
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Alignment step very slow for large datasets #31

Closed YasinEl closed 12 months ago

YasinEl commented 1 year ago

Hello and thank you for this tool. It seems that for large datasets (2.5k mzML files) using default settings the alignment steps seems to be very slow i.e. never finishes. I was wondering if there have been further developments on this?

This was on a Windows11 PC.

Thank you, Yasin

htmonkey commented 1 year ago

I would need examples/data to check. The performance should be similar to or better than what we reported in the Anal Chem paper with 2'500 QExactive data. If your run the docker with -e logging=DEBUG I can get a sense of what steps are taking longer in your case. You might also try the dev branch, which includes a couple of fixes.