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linnarsson-lab / loom-viewer

Tool for sharing, browsing and visualizing single-cell data stored in the Loom file format
BSD 2-Clause "Simplified" License
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Pipeline crashes with "Killed" #29

Closed slinnarsson closed 8 years ago

slinnarsson commented 8 years ago

loom_pipeline.py crashes mysteriously with the single word "Killed", when attempting to create a new Loom dataset.

Good news is that the pipeline works fine on my laptop and has now created the Oligodendrocyte dataset. I removed all the clustering etc functionality for now, not that it made a difference for this dataset (which was already clustered).

Bad news is that it still crashes mysteriously when run on a fresh Ubuntu VM instance. I created a VM and installed everything needed there, but still the same useless “Killed”, even when running from command line.

Maybe something about PyMySQL? Wrong package? Wrong version?

slinnarsson commented 8 years ago

Turns out it was a bad version of scipy, which segfaulted upon import. This seems to affect scipy 17.1 and later, but not 17.0. Downgrading fixed the problem.