chroder MemoryError about syri HOT 5 CLOSED

Hi. The script ran out of memory, adding more memory should fix this. Alternatively, remove small contigs and contigs consisting of repetitive sequence.

from syri.

Thank you for your reply！Could you tell me how to add more memory? I don't know where to add parameters。

from syri.

To add more memory, you would just need to run it on a machine with more memory. This is a problem of the current heuristics where in some cases the amount of required memory increases significantly, which makes the script rather useless.

So, I would guess that the more pragmatic solution would be to try using it with a smaller number of only large contigs.

from syri.

OK！I get it，Thanks again！

from syri.

The chroder script now uses the string clustering algorithm developed in Gunnar Klau's lab and is now much more memory efficient.

This should resolve this issue with most of the practical cases.

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