Michael Alonge

Yes the first field in the fasta header must uniquely identify each sequence. This is why the output AGP file was considered invalid, since the object ID depends on the...

Did you delete the old alignment file? Or else run with `-w`? If you are using the same alignment files (which is default), then RagTag would still be working with...

If the alignment step was really expensive for you, I suppose you could try to manually change the alignment headers to match the new headers. But if the alignment was...

And you still see the error? Assuming yes, I will download your files and take a look.

Hmm yeah I'll take a look at these fasta files and see if I can diagnose it. Sorry for the delay

So it seems like a rather foolish bug on my part. The files you sent had fasta headers that were just incremented integers. So for example, both the reference and...

Hi there, Yes it looks like 2 is the minimum: https://github.com/malonge/RagTag/blob/11f670b373fbbd4139df470ac676943665ac0f18/ragtag_scaffold.py#L528 I don't know why I did it this way ... I will leave this as a feature request for...

I think it should work if you change: `if i_gap_size

Hi there, Can you please share the output logged to stderr? Thanks, Mike

Hi there, Would you be able to update to [v2.0.1](https://github.com/malonge/RagTag/releases/tag/v2.0.1)? If so, rerun using the latest code and let me know how it goes, again sharing the stderr if there...