Longcombiner
Katherin Hinojosa
Maybe some recommendation ???
Omar Idris
Subject: Re: Help with LogCombiner
Hi Katherin,
Sure, happy to help!
The error you’re seeing — “If your runs have different logging steps they may not match” — usually means that the .trees (or .log) files you’re trying to merge were generated using different logging intervals during your MCMC runs.
Here are a couple of things to check and try:
-
Check logging frequency:
Make sure that all your runs used the same logEvery value in the XML setup. If the logging intervals differ, LogCombiner can’t align them directly.
-
Use the -resample option:
You can still merge them if you resample the logs to a common frequency. Try something like:
logcombiner -resample 1000 -burnin 10 -log file1.trees -log file2.trees -o combined.trees-
Adjust the resample value (1000 here) to match a reasonable common interval based on your runs.
-
Burn-in syntax:
Just a note—when you wrote “burning 10 000000”, that may be a formatting issue. In LogCombiner, the burn-in is usually specified as a percentage (e.g., -burnin 10 for 10%) or as a raw number, but it shouldn’t have a space.
Let me know if you’re still stuck or want to send me your command line — I can take a closer look!
Best,
[Your Name]
Let me know if you’d like to make it more casual or technical depending on your relationship with Katherin.
Hello friend, could you help me... I'm trying to merge my .t files in logcombiner burning 10 000000, I've tried everything but it doesn't work.
Maybe some recommendation ???
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