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gtonkinhill / panaroo

An updated pipeline for pangenome investigation
MIT License
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UnboundLocalError: local variable 'prot_outname' referenced before assignment #278

Closed fengyuchengdu closed 7 months ago

fengyuchengdu commented 8 months ago

This was raised when I ran 'panaroo -i *.gff -o panaroo_default' followed by 'panaroo-msa -o panaroo_default -a core --codons', whereas it ran smoothly after removing '--codons' flag.

Many thanks

nzmacalasdair commented 8 months ago

Hello!

Thanks for letting us know about this -- could I just check which version of panaroo you are running?

fengyuchengdu commented 8 months ago

Hello! I'm running Panaroo 1.4.2 (conda installed).

nzmacalasdair commented 8 months ago

Thanks! I'm almost positive that this is a bug introduced in 1.4.2 by mistake along with a fix for another issue. If you have the original error message saved, the line number should confirm this.

This bug should therefore be fixed in commit ace63a5, and will be installable with conda in the next release.

In the meantime, if you would like to generate codon-based multiple sequence alignments from your panaroo output, you can clone this git repo and manually run the code (with the panaroo conda environment active) by running python panaroo-msa-runner.py. Let me know if you have any problems with this!

fengyuchengdu commented 8 months ago

thanks!

gtonkinhill commented 7 months ago

This should hopefully be resolved in v1.5.0