search

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
175 stars 51 forks source link

Run has already reached the number of specified iterations #344

Closed nicolettacommins closed 12 months ago

nicolettacommins commented 2 years ago

My runs were interrupted on the final iteration, but when I try to resume the run I get "Run has already reached the number of specified iterations." The intermediate files from the final (5th) iteration are still in a temp directory and final output files of Gubbins have not been created. This only seems to be happening with my runs that were in the middle of the 5th iteration and not ones that were in earlier iterations. Is there a way to force Gubbins to finish the final iteration and produce the output files? I'm using v3.2.1.

nickjcroucher commented 2 years ago

What's the command you're using?

nicolettacommins commented 2 years ago

Here is the command that I'm using:

run_gubbins.py mab_all_samples_bolOutgroup.fasta -t raxmlng --threads 8 -o SAMEA2070538_mapped_to_MAB -u -v -p default_params -f 25 --resume mab_all_samples_bolOutgroup.1658263885.iteration_4.tre

nickjcroucher commented 2 years ago

Sorry, daft mistake now fixed in 4581de1ee1436d68dd4357e53f60d2f485582983 - if you can clone the repo and run a local install, that should fix the problem