These are chat archives for dereneaton/ipyrad
-t 8or similar, since the slowdown may be due to memory limitations, and fewer threads will minimize that. But it sounds like you are requesting a lot of RAM. What are you using for your mindepth settings in step5? If you exclude lowdepth clusters (e.g., <5 or 10) that can greatly reduce the amount of singletons reads and make everything run quite a lot faster. For step 6 the number of reads is not so relevant as the number of consensus sequences per sample: is it ~30K or more like ~1M per sample?