The calculation time of i05 step is huge

[IamksGEEK]

Hi,
Sorry to bother, but the computation time of step i05 is huge, it may take several month to count variant for larger sample size like 400. In fact , it took me more than 5 hours to count variant for one sample in a HPC node which have 64 core and 1 T memory, and the job used all thread of the node and half of the memory. So, if there are any possible way to further reduce the computation time . maybe , if I could divided the gnomAD database into 2.5 Mb windows? please give me some suggestion to make the algorithm faster, or tell me if i doing somthing wrong.
By the way , we found the concept of regional difference is pretty useful, the accuray of cervical carcinoma prediction model which was build based on regional difference was 95%.
kongshuang

[yeyup]

Yes, I totally concur with your viewpoint.
I attempted to avoid using the 'foreach' function and packages associated with parallel processing. Instead, I aimed to divide the Rcode into several sections and manually execute them in parallel. This way, there would not be a high demand for threads and the execution speed would increase. This method proved to be beneficial as I previously failed with a HPC node that had fewer cores and memory than yours when running the original code.