The Circleator component of the CloVR-Comparative pipeline is having memory usage issues when it's fed a large SNP file for the SNP_Table module to parse. In part I suspect this needs to be addressed with upstream filtering on the SNP file itself, but regardless Circleator is running out of memory when given a SNP file that contains ~600,000 SNP lines. It may be the case that fixing this properly is going to entail revisiting the use of BioPerl data structures for internal feature storage, since they are known to use quite a bit of memory.
The Circleator component of the CloVR-Comparative pipeline is having memory usage issues when it's fed a large SNP file for the SNP_Table module to parse. In part I suspect this needs to be addressed with upstream filtering on the SNP file itself, but regardless Circleator is running out of memory when given a SNP file that contains ~600,000 SNP lines. It may be the case that fixing this properly is going to entail revisiting the use of BioPerl data structures for internal feature storage, since they are known to use quite a bit of memory.