Armin Töpfer

Someone needs to upload a file to reproduce. https://github.com/PacificBiosciences/pbbioconda?tab=readme-ov-file#file-sharing

We've fixed this error and will provide an updated lima version in future.

We can't help you with data processing. If you provide a small reproducible test case, we can have a look. Closing until reproducible case is available.

Adding @Magdoll to triage.

Assigning to @jmattick

Can you please provide an example to reproduce

Lack of input, closing

Does you data have polyA tails? Otherwise, please upload a tiny example BAM with reads that get removed in `refine`.

Please paste the footer of the log output if you run it with `--log-level INFO` and also check the reports

Closing due to lack of input