One file from Gubbins output is missing

[andreaniml]

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:

bactopia --wf snippy --bactopia Results_Processed --reference genomic_LT2.gbff --iterations 8 --gubbin_opts="--bootstrap 1000 --tree-builder iqtree --custom-model GTR+I+G" --skip_phylogeny --outdir Results_Processed --max_cpus 15 -qs 1 -bg -resume

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

• Bactopia Version:bactopia-dev
• OS: Ubuntu
• Environment: conda

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!

[rpetit3]

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,
Robert

[rpetit3]

This one might have been an easy fix: 9a532ac

I do have a question for you. If you are using --boostrap would you like the final IQTree to be based off the final_tree (current behavior) or the bootstrap_final_tree?

[andreaniml]

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).

[rpetit3]

Sounds good, I'll leave it as is.