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amkozlov / raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible
GNU Affero General Public License v3.0
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Tree reporting with --all #107

Closed NatJWalker-Hale closed 3 years ago

NatJWalker-Hale commented 3 years ago

Based on the log reporting, under --all raxml-ng first completes all 20 ML tree searches, and then begins bootstrapping. I wonder if it would be possible to write the trees from each search (and the best ML tree) to the output file at this stage, and not only at the completion of the entire bootstrapping analysis? This would be helpful for checkpointing if the run is accidentally killed during bootstrapping.

If there is already a way to extract the trees at this stage and I have missed it, many apologies.

Thanks in advance,

Nat

amkozlov commented 3 years ago

Dear Nat,

with the newest version (1.0+), intermediate results are printed into respective *.TMP files, please see:

https://github.com/amkozlov/raxml-ng/wiki/Output:-files-and-settings#output-files

In addition, search state is periodically saved to a checkpoint file, so you can resume a killed/interrupted run by simply issuing the same raxml-ng command again.

NatJWalker-Hale commented 3 years ago

Dear @amkozlov

Thanks, that's perfect! I hadn't realised but I was still on 0.9, so I will update accordingly.

Best,

Nat