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nickmachnik committed Nov 18, 2020
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Expand Up @@ -3,10 +3,10 @@ Frequently Asked Questions
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Why is `chess sim` so slow?
Why is ``chess sim`` so slow?
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A common cause for long runtimes of `chess sim` is when the input files are
in `Cooler <https://github.com/mirnylab/cooler>`_ format. `chess sim` compares
in `Cooler <https://github.com/mirnylab/cooler>`_ format. ``chess sim`` compares
observed/expected transformed matrices, and these are often not precomputed
and stored in this format. If your runs spend a long time in the
"INFO Loading query contact data" step, consider converting your data to
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