Themisto-v3.2.1 (19 December 2023)

This release contains two minor bugfixes:

• Fixed a bug that resulted in incorrect FASTA parsing if the file contained an empty line. Now, the program terminates instead with an error message.
• There have been problems with running Themisto on cluster architectures. We think that this might be due to how the KMC sorting subroutine always uses the maximum number of threads supported by the hardware, even if the user specifies a smaller amount on the command line. In cluster environments, the job scheduler may limit the number of parallel threads to a much lower amount than the maximum amount allowed by the hardware, which seemed to sometimes hang construction on our cluster. We fixed this by limiting the number of threads available to KMC sorting to the number specified on the command line. This solved the issue on our cluster, but it could be the case that this did not fix the underlying issue, and there might be some kind of a deadlock in lurking KMC that was only exposed by having such a high amount of thread contention. We leave closer investigation as future work.