Marcus Stoiber

The `--modified-bases` argument triggers bonito to lookup the corresponding remora model. But it appears that you have also specified the path to a remora model with the `--modified-base-model` argument which...

This appears to be an error with your conda environment. The error notes missing libraries expected with a python installation that I've observed can be missing for some conda installations....

The current MM tag specification was updated less than 2 months ago (to resolve this ambiguity) and we have not yet applied an update to the Bonito/Remora code bases to...

Could you confirm the contents of the calibration file? The following short python command should expose these values: ``` import numpy as np with np.load("$WDR/megalodon_calibrated/mod_calibration_statistics.npz") as calib_fp: print(calib_fp.files) ```

What was the output of the calibrate command? In the code the command to save the calibration information should contain the stratification type (see [here](https://github.com/nanoporetech/megalodon/blob/master/megalodon_extras/calibrate_modified_bases.py#L131)). I'm not sure how this...

This certainly looks like a corrupt FAST5 file. I'm not aware of a simple way to identify the corrupt FAST5 file. There are catches for corrupted files at the signal...

Could you post the entire megalodon command submitted? This may be related to the post-out option required for older style modified baes calling (judging from the model noted in these...

I think this issue is related to Rerio/Remora models, but the main issue here is that the old-style flip-flop modified base models required the basecalling posterior matrix to be returned...

Apologies for my miscommunication, but the e8 models are applicable to LSK109/LSK110/LSK111 kits. So the available Remora models should support your needs.

We do not have any direct accuracy comparisons between these two models at the moment, but are working on this. The main issue we have at the moment is an...