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nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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How to restart a gubbins run using the --resume flag #413

Open mattbird567 opened 3 months ago

mattbird567 commented 3 months ago

Hello,

As the tite suggests i am trying to restart a run using the --resume flag as i had to stop my inital run on a HPC. I am confused as to what the resume flag needs to restart the run? I am currently running the following command:

run_gubbins.py --resume path/to/last/generated/t25_tree.iteration_1.treefile --threads 16 --tree-builder iqtree /path/to/corresponding/alignment.iteration_1

However, when i run this i am getting an error telling me that the t25_tree.iteration_1.treefile.phylip isn't detected. Now a .phylip file is being created although its called alignment.iteration_1.phylip. Can't seem to think what i'm doing wrong to restart this run i would assume i'm just missing something obvious. Any help would be great.

nickjcroucher commented 3 months ago

There should be a .tre/.phylip pair to resume from? See #406 for the current state of this functionality.