Daniel Portik

Was just about to post this myself, I'm also getting the same error. **I am wondering if something changed about the Zenodo API very recently, as it seems like the...

Hi @jsgounot - as @ctb mentioned the error profile of ONT appears to negatively affect sourmash's performance (at least for now). There are two good options for ONT. We found...

Hello @Ufungi , The `Reference_Blast_Extract.py` module is intended to be run with a small number of reference sequences. The use-case is to identify particular loci. I am not sure what...

Thanks for highlighting the issue, it was resolved in #70

Hi @Rafa-Seong , @nallsing-salk , and @MicroSeq , Thanks for your patience. This might be related to an issue with CheckM2 and specifically the Zenodo API. See thread here: https://github.com/chklovski/CheckM2/issues/83...

I am unable to reproduce errors related to the checkm2 conda env, but keep me posted on any progress or continued challenges here. Downloading the checkm2 database manually before beginning...

Hi @oushujun, Can you describe in more detail what this information will be used for? It is possible to write code to dump the values per read into bed format,...

Hi @luispedro, Thanks for all of your work on semibin2! I still think this would be a great feature to add, particularly for long-read assemblies. Specifying some set of contigs...

Yep! Those should be plenty.

Pretty sure I am encountering the same issue with snakemake 8.25 and the cluster-generic plugin. I made a detailed comment here: https://github.com/snakemake/snakemake/issues/2947#issuecomment-2537463415 Increasing `--cores` did not solve my issue, I'm...