When using CPU/juicer.sh and CPU/mega_from_bams_diploid.sh, users can define memory per thread in samtools sort using --mem, for example, --mem 8G
For PBS and Slurm schedulers, the memory per thread setting in samtools sort is calculated based on the preexisting resource requests
With the ability to increase the memory per thread setting, it will reduce the number of temporary files produced during sorting. With large dataset, users can set a larger value to prevent the "Too many open files" error from happening (e.g. #343), as the default used by samtools sort is only 768M per thread.
This PR makes the following changes:
CPU/juicer.shandCPU/mega_from_bams_diploid.sh, users can define memory per thread insamtools sortusing--mem, for example,--mem 8Gsamtools sortis calculated based on the preexisting resource requestsWith the ability to increase the memory per thread setting, it will reduce the number of temporary files produced during sorting. With large dataset, users can set a larger value to prevent the "Too many open files" error from happening (e.g. #343), as the default used by
samtools sortis only 768M per thread.