-
Notifications
You must be signed in to change notification settings - Fork 62
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
One file from Gubbins output is missing #510
Comments
Hi @andreaniml I will take a look at this and get that file exported. Another note, I should have the update to bactopia-py completed today Cheers, |
This one might have been an easy fix: 9a532ac I do have a question for you. If you are using |
I think that the current behavior is ok, but I do not have much experience on this, so someone may have a different opinion I am still deciding on what to do with the tree (If I use the that comes directly from Gubbins for downstream analysis or to use the recombination free alignment while informing constant sites in order to create another tree). |
Sounds good, I'll leave it as is. |
Description
Hi Robert! It's me again, I think I've found another bug
I am running the snippy workflow, I passed the bootstrap options to gubbins and it ran flawlessly, except that when I checked the results, the bootstraped final tree from Gubbins was missing.
Steps to Reproduce
Steps to reproduce the behavior:
The resume flag is there because I made a typo onthe gubbins options the first time
Expected Behavior
All the gubbins outputs into the gubbins folder.
Execution Environment
Additional Information
I was able to find the tree into the work directory, I think that maybe bactopia did not copy that tree into the final folder because it's named "core-snp.final_bootstrapped_tree.tre" and the other trees are named "core-snp.final_tree.tre" or "core-snp.node_labelled.final_tree.tre"
I can provide the logs, just not sure which one as there is no error message.
Cheers!
The text was updated successfully, but these errors were encountered: