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cole-trapnell-lab / garnett

Automated cell type classification
MIT License
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train_cell_classifier getting stuck with no error #47

Closed dmiyagi closed 4 years ago

dmiyagi commented 4 years ago

Hi there,

I am trying to use the train_cell_classifier, but it has gotten 'stuck' multiple times using R Markdown on iMac Pro (Processor: 3.2 GHz 8-Core Intel Xeon W, Memory: 32 GB 2666 MHz DDR4) using macOS Catalina v.10.15.4). I was able to use 'check_markers' without any issue. Now, when I try to use the train_cell_classifier on a dataset of ~3,000 cells, it keeps getting 'stuck' (as shown in the first screenshot).

Screen Shot 2020-07-04 at 3 23 31 PM

There is no error. I have let it run > 18 hours and it remains the same after printing out that 'There are 4 cell type definitions' and 'traning_sample' with each cell type (as shown in the second screenshot). I have tried using max_training_samples down to 150 and nothing seems to solve the issue.

Screen Shot 2020-07-04 at 3 23 19 PM
dmiyagi commented 4 years ago

Hi again, I updated my R studio, reinstalled monocle3 and garnett, uninstalled monocle2, and tried this again and it finished in ~1 hour (using max_training_samples = 300).