Can you rebuild a tree from where it stopped? The construction of my tree was stopped because of a problem in my machine.

[Alfredo Rodríguez Arteaga]

Can you rebuild a tree from where it stopped? The construction of my tree was stopped because of a problem in my machine.

I can not find in the manuals if there are commands for this

regards and hugs from México

[Alfredo Rodríguez Arteaga]

I found this  

I put it here in case someone else serves

6.2 Checkpointing to resume stopped run 

Starting with version 1.4.0 IQ-TREE supports checkpointing: If an IQ-TREE run was interrupted for some reason, rerunning it with the same command line and input data will automatically resume the analysis from the last stopped point. The previous log file will then be appended. If a run successfully finished, IQ-TREE will deny to rerun and issue an error message. A few options that control checkpointing behavior:

 Option        Usage and meaning 

-redo           Redo the entire analysis no matter if it was stopped or successful.                           WARNING: This option will overwrite all existing output files.

 -cptime       Specify the minimum checkpoint time interval in seconds (default: 20s)

NOTE: IQ-TREE writes a checkpoint file with name suffix .ckp.gz in gzip format. Do not modify this file. If you delete this file, all checkpointing information will be lost! 

[Bui Quang Minh]

Hi Alfredo,

That’s right, good that you found the solution yourself ;-) Moreover, another tip: you can actually copy all the intermediate files (incl. this checkpoint file) to another machine and restart the run there. This is helpful in case your current machine is broken or you want to use a more powerful machine.

Minh

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Bui Quang Minh

Center for Integrative Bioinformatics Vienna (CIBIV)

Campus Vienna Biocenter 5, VBC5, Ebene 1

A-1030 Vienna, Austria

Phone: ++43 1 4277 74326

Email: minh.bui (AT) univie.ac.at