Sean’s Notebook: My FALCON won’t fly.

I’ve been trying to install FALCON, a PacBio based assembler, and it’s been a huge pain. Mostly typical Hyak permission issues, but also lots of errors with no way to figure out what they mean. LFS error code 32512?

That’s super useful, especially when it doesn’t specify if that’s Git’s LFS, or Lustre File System, or who knows what else (It’s likely the Git LFS option, but they don’t seem to have documented error codes easily accessible).

Going to look through the FALCON repo’s issues and see if there’s anything of use there, then post an issue of my own if not.

In other, more successful notes.

Uploaded more TA data to GitHub. The titratior seems to be behaving better, but still showing a ~40 point swing between beginning and end of day samples.

Finally finished the methylation count files for the C. virginica stuff and will start MACAU chewing on them tonight most likely. Played around with SQLShare way too long, but Tuesday I got a response from their helpdesk and learned that SQLShare converts all input to lower case letters, so if you’re trying to load the Loc column from your dataset, it sees dataset.Loc as dataset.loc, and then gets angry. Gotta use dataset.”Loc”. Even after figuring that out, it was still a giant pain, so I just subsetted my sample count files, and welded them back together at the end.

I started with 10x coverage, and will pare that back to probably 5x for a second run.


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