Sorting BAM files never fully finished

Question

[dolphin6906]

I have some large BAM files that were created based on large indexes. I trying to sort and index them and threading the sort with 36 threads and 180GB of memory. For some of my files the sort keeps getting stuck (see image). Is there away without increasing the memory to sort, to move past this to sort?

Answer 1

[ATpoint]

That is all the same file. Once memory is full samtools starts spilling chunks to disk which eventually will be merged into the output file and then will be deleted. You'll simply need to wait until finished.