Structure 2.3.4: Known issues and bugs

Pritchard Lab, Stanford University


Structure v.2.3.4, January 2012

  • Structure crashes 'silently'; this is associated with running multiple threads or on multi-user computers. See more details here.
  • Linkage model crashes due to a memory misallocation. Thanks to bug report and patch from Alexis Simon (University of Montpellier), February 2019. Recompile source code using this version of structure.c.

    • Previous Versions, up to 2.3.3
    • Population Information: If you used the USEPOPINFO flag in Structure 2.3.1 then you may encounter a problem which results in a premature completed run, an assertion error and a set of empty result files. This problem is no longer an issue in version 2.3.2.
    • Polyploids: If you are analyzing polyploid data then you might encounter problems with Structure stalling and not returning results. This is a limitation of the current implementation of our sampling function. This problem occurs mainly for loci with very large numbers of alleles, and especially in data with high ploidy. Version 2.3.2 partially fixes the problem. In the meantime you might consider removing the most variable loci, or merging rare alleles to get the program to run. This is no longer an issue in version 2.3.3
    • Frontend: The frontend had a multithreaded bug that would sometimes stop the console version from running and discarded output. This was fixed in version 2.3.4. All users are strongly encouraged to update.

    Windows Version
    • Windows with Frontend: Occasionally you may encounter a memory problem when trying to start the Java virtual machine and find the error message "Cannot create Java machine". This is because Structure is requesting more memory than what is available. As a result the user can run structure_start.bat which will fix the memory usage at 512Mb. If you choose to increase the memory usage you can edit this file and change the memory argument to an appropriate value based on your computer's resources.