Rhys Newell

So the bin information produced by aviary was all as expected?

Okay, I'm going to re-open this then. I'll have to figure out if this is an aviary issue or not

I haven't been able to reproduce this, all of the checkm results I've been testing seem to be correct. I've now added a kind of verification step where the completeness...

Oh, that's odd. The full output should definitely be there, if you have time it would be helpful if you could search your log files for any errors towards the...

Ah, good point I'll update the documentation at some point to include some usage for `rosella refine`

Hi Jianshu, This would be great to use within Rosella, however there is no UMAP rust implementation yet. The rosella algorithm heavily relies on UMAP and HDBSCAN working together back...

Could you try running this command manually? `mkdir -p pangenomes; cat data/pggb_metadata.tsv | parallel -j1 --colsep ' ' "samtools faidx {1}; pggb -i {1} -n {2} -o pangenomes/{3} -t 72...

Were the CheckM results empty?

Oh this looks like it is complaining about the `coverm_abundances.tsv` file, was that empty?

Does `coverm.cov` have the short read information? And can you find any error information for the get_abundances rule in the snakemake log?