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Update troubleshooting.md
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pdimens authored Nov 13, 2024
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## Common Issues
### installation issue
Conda is an awesome package manager, but it's _slow_ and uses a ton of memory
as dependencies increase. Harpy has a lot of dependencies and you might stall
out conda trying to install it. Use mamba instead-- it'll work where conda fails.

Conda is an awesome package manager, but _was_ slow and used a ton of memory
as dependencies increased. Recent (`23.10+`) versions of Conda [now use the `libmamba` solver](https://www.anaconda.com/blog/a-faster-conda-for-a-growing-community),
the super-fast and super-lightweight solver from Mamba. If you're experiencing
a suspiciously slow Harpy installation, either update Conda to at least version `23.10` or use Mamba.

### imputation or phasing failure
If you use `bamutils clipOverlap` on alignments that are used for the [!badge corners="pill" text="impute"](Workflows/impute.md) or
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Call the script with no arguments to see the full usage instructions.


**More cases will be added here as they become apparent to us**
**More cases will be added here as they become apparent to us**

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