Why iq-tree build bionj tree and parsimony tree again when rerun from checkpoint?

[Chang Ye]

the command that I used.

iqtree -s input.fa -nt AUTO -bb 2000

Although the log file show that it is resume from check point, I notice that the xxx.parstree and xxx.bionj file is generated again, which waste lots of time.

[Minh Bui]

Can you please paste the last 20 lines of the log file?

(It looks like you are still at the very beginning of the run, where IQ-TREE hasn’t finished starting trees yet).

Cheers, Minh

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[Chang Ye]

I can't not reproduce it in other dataset. Seem that there is some error in my previous run.

It works as expected now. Thank you, Minh!