Jack Wadden

@ktan8 I'm facing a similar issue. One possible workaround (hack) might be to just concatenate your ground truth sequences to the input reference. I can't imagine a relatively long read...

Thanks @iiSeymour. I've found that this works better than using the taiyaki prepare_mapped_reads.py script as a training frontend. This is the pipeline I'm using to fine-tune the dna_r9.4.1 model given...

I'm also having this issue with v5.3.0 and have the same top level keys: `['Batches', 'read_ids']`

@addyblanch I was able to downgrade to Taiyaki 5.0.0 and it worked. The issue seems to stem from this Taiyaki change in 5.2 linked to by @iiSeymour > The batched...

This turned out to be a small bug in Taiyaki, and was an easy fix. I've submitted a pull request with the fix [here](https://github.com/nanoporetech/taiyaki/pull/109/commits/5054b4993c6baa50829fcd2d64e32665147baccb).

I'm having issues with bonito now that were resolved by downgrading back to Taiyaki 5.0.0. The specific error was thrown by parasail. Let me know if you get a similar...

@addyblanch the fact that the 'Reads' directory doesn't exist means that Taiyaki (probably) still isn't emitting the non-batched version. Are you seeing the same output from `list(f.keys())`? You might have...