Output files are empty

[d-cameron]

I've finally manage to run Weaver on COLO829 and the output SV_CN_PHASE, SV_REMOVED, and SV_SELECTED are all empty, and SNPO_CN_PHASE and EACH_REGION contains all zeros. Looking a bit further I can see that tempread contains all zeros which was not the case when I ran the ploidy step.

How do I resolve this issue?

[d-cameron]

I managed to work around this issue by rerunning Weaver PLOIDY with -r 1 then running Weaver LITE with -r 0 so it wouldn't overwrite tempread with a file contains all zeros.