Scaffold profiling error

[elizabethmcd]

I have a genome from IMG that has 'N' characters at some positions. The error when trying to profile scaffolds is:

ValueError: 'N' is not in list
whole scaffold exception- Ga0131788_11
We had a failure profiling a scaffold! Not sure which!

Should I remove the N's from the reference genome, or replace with some other character?

[MrOlm]

Hi Elizabeth,

Thanks for pointing this out- I will fix this bug and push an update ASAP.

Best,
Matt

[yanhui09]

Same problems if using mags binned from scaffolds.

[MrOlm]

This bug has been fixed in version 1.2.4, and it will no longer crash if N is the reference sequence