Restart from iteration 4 stopping when entering main loop for Iteration 5 about gubbins HOT 6 OPEN

This is a lack of detailed documentation/bug, sorry - it should work if you run:

cp SX519_Chromosomal_Ref_clean.core.full.iteration_4.tre.rooted SX519_Chromosomal_Ref_clean.core.full.iteration_4.tre
run_gubbins.py --first-tree-builder rapidnj --first-model JC -p gubbins -c 32 -v SX519_Chromosomal_Ref_clean.core.full.aln --resume SX519_Chromosomal_Ref_clean.core.full.iteration_4.tre

The problem is that Gubbins expects [tree file].phylip to exist, which is not the case if (a) .rooted is at the end, or (b) the file is in the temporary directory still. Apologies, I will try to fix this, or at least put in a more informative error message.

from gubbins.

Thank you for the quick response!

I reran as you suggested, but it unfortunately did the same thing and stopped in the same spot. Below are the details. Please let me know you need any other information.

If it helps, the [tree file].phylip from iteration 4 was not even in the temporary directory near as I can tell, although as you said it would not exist if it was rooted. When the slurm run requeue and reran in the middle of the night before I could stop it, it replaced anything that was not in the temporary directory near as I can tell, so if any of those files were necessary to restart, I would not have them.

Thanks for your time and help.

Code ran via slurm/sbatch per your advice after cping [tree file].tre.rooted to just {tree file}.tre file:
run_gubbins.py --first-tree-builder rapidnj --first-model JC -p gubbins -c 32 -v SX519_Chromosomal_Ref_clean.core.full.aln --resume SX519_Chromosomal_Ref_clean.core.full.iteration_4.tre

Attached is the stdout file
post_github_advice_stdout.txt

ls -lah - Anything made on May 2nd was from the latest runs post your advice:

from gubbins.

My other run completed, and I was able to get all the expected outputs. So, I no longer need to restart from a killed and restarted slurm run with deleted non-temporary folder intermediates. If you no longer need this thread to be reminded of the documentation/bug you referenced, please feel free to close it. Thank you very much for your time, expertise, and wonderful tool!

from gubbins.

Thanks, I'm glad that run worked! Sorry for the lack of response - I will keep this open to remind me this needs fixing.

from gubbins.

No worries, can imagine you being very busy. Aye aye to keeping it open.

from gubbins.

I'm having the same problem resuming my run even if I have the .tre and .phylip files in my main folder.

from gubbins.