Bugs and Feature Requests
If you plan to process a large number of genomes, you may wish to break these into smaller batches. On a 64GB machine running a 1,000 genomes at a time with 40 threads works well. Exceeding the available memory of your machine will cause CheckM to use swap space (as per any program) which will substantially increase the time to process genomes.
It has also been reported that processing large numbers of genomes at once can cause a Python recursion error. As such, splitting large runs into batches of 1,000 genomes is recommended.
When submitting a bug please provide as much information as possible and, if feasible, a simplified version of the data set which is causing the issue. The more information you provide the quicker we will be able to resolve the issue. The preferred method for reporting bugs is through GitHub. However, bug reports can also be submitted to Donovan Parks (donovan.parks [at] gmail.com).
CheckM is in active development and we are interested in discussing all potential applications of this software. We encourage you to send suggestions for new features to Donovan Parks (donovan.parks [at] gmail.com).
There are currently no known issues! :)