Roger Volden

Try deleting the binary and building manually using `go build src/gonk` from the base directory

This makes me think that it isn't adding on the filename for the output file correctly. gonk should have been given the path from your C3POa command line arguments (`--path`...

In any case, I've updated the gonk source code so that if it's given a directory with no filename (what seems to be happening here), it will automatically add the...

I've pushed an update to gonk that fixes the error you've been getting. You should be able to give it a directory or a filename. As for how you're running...

This is a debugging statement that gets run at the very end of the script. Your consensus sequences should be intact. To squelch the message, update C3POa by pulling from...

Can you post your config file? Also did you build gonk? This is almost certainly a path issue since everything else is working but gonk isn't running.

There's a good chance you didn't build the package, or it has the wrong path

The splint sequence is fine, but I'm adding `splint.fasta` with the exact sequence that was used in the paper. I'm also adding `adapter.fasta` that contains the 3' and 5' adapters...

Sorry this took a while to get to you, but I've added the indexes and the demultiplexing script to the paper directory on the repo. Let me know if you...

What version of C3POa are you using? If you're running something older, I suggest updating to the latest version (v2.2.2). I haven't seen this come up in my test dataset....