John Lees
John Lees
This is a useful piece of software that is a substantial contribution to the field. I have the following comments on the checklist: > Example usage: Do the authors include...
Issues https://github.com/kidusasfaw/spatPomp/issues/26 and https://github.com/kidusasfaw/spatPomp/issues/27 addressed and I have marked those boxes as complete accordingly
@ionides Thanks for these changes, I think both sections read very well. Thanks also for the small tweaks to the package you already addressed in the issues. Congratulations and thank...
Try without `--lineage` perhaps, and I would also recommend using the LMM (https://pyseer.readthedocs.io/en/latest/best_practices.html)
That looks ok to me, the likelihoods in your file should be ignored. To debug further we would need you to make a minimal reproducible example, including input files and...
Not in the output file, but they will appear in the bwa output (which you can direct with `--tmp-prefix`, but it will still be removed at the end of the...
I think these are omitted in the output file sorry. @mgalardini does your new pipeline help with this at all?
See https://poppunk-docs.bacpop.org/troubleshooting.html#samples-are-missing-from-the-final-network
Sorry for the slow reply. Can you first please try upgrading poppunk to the most recent version (v2.7.6), v2.4.0 is over four years old
Thanks for confirming. I can replicate this -- it's because our pseudomonas database is misformatted, sorry about that! We will fix this on the website, but in the mean time...