error in reading pyslim burnin trees file in SLiM 5.0

[John Michael Basaca]

Hello! I was wondering how to remedy the error when loading the pyslim generated burnin trees file under SLiM 5.0? Specifically, the error "ERROR (Species::ReadTreeSequenceMetadata): the version of this file appears to be too old to be read, or the file is corrupted; you can try using pyslim to bring an old file version forward to the current version, or generate a new file with the current version of SLiM or pyslim" appears when reaching the in sim.readFromPopulationFile() of the slim script. I figured out this must be something to do with the SLiM version because I was able to successfully run the same script in my laptop which has the SLiM v4.3 installed, but was not able to successfully run it in an HPC which has the v5.0 installed. Looking forward to your guidance on this matter.

Sincerely,

JM

[Peter Ralph]

IIUC, you've generated a tree sequence entirely in python (e.g., by doing msprime + pyslim.annotate()), and then want to load it into SLiMv5. To do this, use the next version of pyslim (currently in beta): https://pypi.org/project/pyslim/1.1b1/; AFAIK there are no issues and I'm going to do a real release in the next few days. And please report any issues you encounter!

Happy slimulating,

--peter

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From: slim-d...@googlegroups.com <slim-d...@googlegroups.com> on behalf of John Michael Basaca <john....@gmail.com>
Sent: Tuesday, August 12, 2025 12:26 AM
To: slim-discuss <slim-d...@googlegroups.com>
Subject: error in reading pyslim burnin trees file in SLiM 5.0

 

Hello! I was wondering how to remedy the error when loading the pyslim generated burnin trees file under SLiM 5.0? Specifically, the error "ERROR (Species::ReadTreeSequenceMetadata): the version of this file appears to be too old to be read, or the file is corrupted; you can try using pyslim to bring an old file version forward to the current version, or generate a new file with the current version of SLiM or pyslim" appears when reaching the in sim.readFromPopulationFile() of the slim script. I figured out this must be something to do with the SLiM version because I was able to successfully run the same script in my laptop which has the SLiM v4.3 installed, but was not able to successfully run it in an HPC which has the v5.0 installed. Looking forward to your guidance on this matter.

Sincerely,

JM

--
SLiM forward genetic simulation: http://messerlab.org/slim/
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