Import of EER super slow

I am trying to import eer files in cryosparc. While it works in principle but it takes for ever. For importing 7000 files it needed almost 24 hours. Is there anything that can be done? It also seems like adding more cpus does not really increase the speed. When I import mrc files it is much faster.



Hi David,

Out of curiosity, did you skip header check?


yes I tried it and then its much faster however but then there seems to be issues with later steps

@david.haselbach Please could you provide details on the issues you encountered in later steps?

motion correction repeatedly crashed and I thought it may had to do with not probably reading the headers and that seemed to be the case

@david.haselbach Ideally, one shouldn’t have to choose between rapid eer data import and error-free processing. To that end, please can you

  1. confirm that downstream processing proceeds as expected after (slow) import?
  2. provide details that could help us understand how skipping the header check causes errors in downstream processing. For example, do downstream jobs fail immediately or do errors appear to be linked to specific eer files?
  3. post error messages (after obfuscating confidential information).
  1. I do confirm
  2. it is later so I do think it is specific EER files.
  3. I have to reproduce.