After I run the nextstrain pipeline, I would like to look at some of the log files (most notably results/aligned-delim.iqtree.log) but I think these are removed through the pipeline.
Is there any way to keep these around? I didn’t see anything in the documentation.
Hi Erin,
There isn’t currently a way to keep these log files, but I also don’t see a reason why we delete these files when we keep the log files for the multiple sequence alignment. I’ve created a pull request to prevent augur from deleting tree logs. We are about to release augur v9.0.0, so this change should appear soon in that version.
I will post an update here when that new version with this change is available.
Hi again @ErinYoung, we’ve just release augur 9.0.0 which includes a change to augur tree's clean up behavior such that tree logs are not deleted.
If you are interested, you can upgrade your current installation with:
python3 -m pip install --upgrade nextstrain-augur
Please let us know here if you notice any further issues with augur tree related to this issue, though.