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mgleeming / synthedia

Create synthetic DIA LC-MS/MS for proteomics experiments
https://synthedia.org
BSD 3-Clause "New" or "Revised" License
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Microbial communities #43

Open rvaldes opened 7 months ago

rvaldes commented 7 months ago

Hi,

I'm attempting to generate synthetic LC-MS/MS data from complex communities of bacteria. I tried a community of 40 different bacterial species using Prosit (Oktoberfest) and Synthedia, but the RAM required was higher than 1000Gb and crushed every time I tried. I reduced it to 10 different species and still had the same problem. Only with one bacterial species, I manage to make it work. Is there any way to overcome this problem without using this RAM limitation? Can I divide the process by individual species and combine it later? Thanks! Rafa

mgleeming commented 7 months ago

Hi Rafa,

Could you please let me know the command line you're using to execute Synthedia? Are you trying to generate profile data, or centroid? Profile has a substantially higher memory requirement...

Thanks! Michael