Restart from checkpoint function available

biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

https://huttenhower.sph.harvard.edu/phylophlan

MIT License

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Restart from checkpoint function available #107

Closed ganiatgithub closed 1 year ago

ganiatgithub commented 1 year ago

Hi,

I was wondering it is possible to restart a previous run from checkpoint? I'm using 20 core with 7-day wall time to constructed a maximum likelihood tree with IQ-TREE2, which was cancelled due to wall time limit on a slurm-managed cluster. The cluster can schedule maximum 7 days, and dataset contains over 1000 MAGs.

Sorry if there's an obvious answer I have missed.

Many thanks, Gaofeng

ganiatgithub commented 1 year ago

Hi, I came to realize the long wall time is related to the mapping stage, which appeared to be an issue related to Diamond. I've also posted an request on Biobakery helpforum link.

Is there a work around for this issue?

Many thanks.