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kharchenkolab / Baysor

Bayesian Segmentation of Spatial Transcriptomics Data
MIT License
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Baysor is killed unexpectedly #106

Closed sebherbert closed 7 months ago

sebherbert commented 7 months ago

Hi,

Thanks for this very interesting method! I've been testing it on a small dataset (a single FOV from a whole mosaic) and it worked smoothly. So I've tried on the whole mosaic and ended up with this error message:

[10:10:35] Info: Run Rd15c308ba
[10:10:36] Info: (2023-12-11) Run Baysor v0.6.2
[10:10:36] Info: Loading data...
[10:11:37] Info: Loaded 102793946 transcripts
[10:11:51] Info: Estimating noise level
Killed

output_run_s60_log.log

I have the feeling that RAM hasn't been fully used (but I'm triple checking) and I also had the same error with another machine, so I'm wondering what could be the source of the problem?

(I'm attaching the detected genes csvs, but the full mosaic is 102793946 transcripts long so it's also 3GB big https://drive.switch.ch/index.php/s/tG20DQWufPGoql4)

Best, Sebastien

sebherbert commented 7 months ago

Sorry it was simply the RAM indeed :) Maybe a clearer error message could help