Zoey Werbin

A late follow-up on this: I also have co-assemblies that I would like to use as input for cross-mapping. I noticed in earlier metaGEM development you tested this approach, do...

Thank you so much for the thorough response! Your comments do makes sense. Our assembly had already been running before I saw this advice, but if we have to re-run...

Thank you for the feedback! I've started a repository here: [zoey-rw/metabolic_model_curation](https://github.com/zoey-rw/metabolic_model_curation/tree/main) Right now, it just has placeholders for tasks, and links to relevant scripts by @ChristianLieven and @SysBioChalmers. I'll be...

Thank you for your response! Could you provide any additional information on your docker setup with CPLEX? Or how results differ with Gurobi?

The workaround (loading the JSON model with cobrapy v.0.17, but saving as SBML) isn't quite working for me. It results in the error: ``` --------------------------------------------------------------------------- AttributeError Traceback (most recent call...

No, after loading the model & before saving as SBML, I removed the annotation attributes as follows (lines 9-10 in the error message above): ``` for reaction in univ_bigg.reactions: reaction.annotation...

I believe I'm facing a similar error from loading a .mat file with a space in a variable name, rather than a compartment name. If there are any short-term workarounds...

Thanks for these solutions - the first 2 seemed to help for the 16 taxa/100 samples situation, but the build process is still crashing when I scale up to ~50...

Okay, I think this works for reducing the logging while preserving the multiprocessing: ``` import logging logging.getLogger("micom").setLevel(logging.ERROR) logging.getLogger("micom.logger").setLevel(logging.ERROR) if __name__ == '__main__': multiprocessing.set_start_method("spawn", force=True) logger = multiprocessing.log_to_stderr() logger.setLevel(logging.ERROR) manifest =...

Hi! Just wondering if support for Megahit is still a planned feature (in my case, I've already carried out contig assembly with Megahit and binning with MaxBin2 and would like...