I have a couple of issues using Topaz picking which I hope to get some help with here.
I was able to create a subset of 20 micrographs out of ~2000, template pick, create 2D classes to train a topaz picking model. I can also extract the particle locations using Topaz extract on these exact 20 mics and inspect picks, all looks good.
However, I cannot extract from all micrographs using the trained picking model. It seems that the job spends two days trying to preprocess the micrographs which for 20 mics takes 22sec but just won’t finish on the 2000 mics even after two days. What am I doing wrong? Anyone else who has this issue? Do I need to use smaller subsets, of say 250 mics for extraction?
I should say that I’m running these jobs on an HPC, so I’ll taking the issue up with them next week in case there are some underlying issues that I can’t see or solve. Perks of working between the years, if anyone has any suggestions in the meantime, I’d be very grateful since I work with a challenging, small protein! Let me know if you need more details to narrow the issue down.