Files required for steps 4-7

[carlahurt]

Hello! I am running a very large data set (~200 individuals) using the denovo pipeline and steps 3 and 6 are slow (like 40 days slow). We have been syncing data to a temp folder to speed things up. However, we are running out of space on the temp folder after step 3. Can you tell me which folders are needed to run steps 4-6? are some of the folders unnecessary at that point? Any suggestions would be greatly appreciated.

Thank you,
Carla