Jordan Eizenga

If the `.gcsa` and `.gcsa.lcp` files aren't empty, then I believe it exited correctly. Did you give it a higher memory limit this time?

It's surprising to me that it would take so much memory in that step. I'll need to ask the author of that component why that might happen.

How large did the GCSA and LCP files end up being? Their on-disk size is roughly the same as their in-memory size, so the answer has some bearing on what...

Okay, that's definitely larger than usual but not deadly. Usually, the GCSA and LCP would be maybe 10-15 GB combined, but you can still use those in a server environment....

Sorry, it looks like I missed your message from a few days ago. > What do the '_1' and '_2' represent in the joint file, two different calculations? I believe...

> I notice some TPM values to be quite low, and the corresponding read count to be very low. How are the read counts determined, and ideally should I apply...

Can you share an example or two?

Which of these commands is the one that led to the crash? The warning suggests you may have started the pipeline with one version of VG and then switched at...

> vg v1.36.0 works. vg v1.40.0 and v1.48.0 has this problem. I think it's actually that we added these warnings since v1.36.0, not that the mapping got slower. If you...

You seem to have added some steps to the indexing pipeline that I can't see a purpose for. You don't need to create an XG, a snarls file, or a...