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nanoporetech / Pore-C-Snakemake

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rule assign_fragments crashes due to pyarrow problem #30

Open Mittmich opened 2 years ago

Mittmich commented 2 years ago

When running the pipeline, I encountered sporadic crashes in the assign-fragments step that seem to be related to an open issue of aws-sdk-cpp, a dependency of pyarrow. Details of the issue can be found here.

I could fix the problem by freezing the aws-sdk-cpp version in the pore_c.yml environment to version 1.8.186, which could be an option as a short-term workaround.

aallahyar commented 2 years ago

Thanks @Mittmich! Indeed I encountered a similar problem and through google I made the same conclusion.

To be clear (and as @Mittmich mentions), simply modify your pore_c.yml files to (i.e. add the last line):

channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - pore-c==0.4.0
  - python==3.8
  - aws-sdk-cpp=1.8.186=h9ad65fb_2