Robert Vaser comments

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                                            Robert Vaser

Racon for low heterozygote diploid genome

Looks alright. Not sure what to tell you here :/ You can try with `minimap2 -ax sr` and check whether it is better or not.

Racon for low heterozygote diploid genome

Not sure what to tell you here.

Racon for low heterozygote diploid genome

Did you by any chance try Pilon in the same setting?

layer begin and end positions are invalid

Hi Urmi, please verify that each contig name is unique up to the first white space. Best regards, Robert

layer begin and end positions are invalid

Nope, that looks alright. No idea where the problem is at this point. Could you share your data perhaps?

layer begin and end positions are invalid

It would be marvelous if you could find a subset which exits with the same error :)

layer begin and end positions are invalid

That amount of reads should not be a problem. Can you extract all contig headers and send this file to me via email?

layer begin and end positions are invalid

Thanks Urmi, I am currently looking at them, sorry for the delay.

layer begin and end positions are invalid

The contig headers are unique and completely different from those of reads, which should rule out the error that occurred in #118. I saw that you have some really short...

layer begin and end positions are invalid

Can you try generating a PAF file with minimap2 and rerun the polishing?