Michael Shaffer

@SilasK this is really cool! And I think adding this data to `product.tsv` is a really good idea! I think I will start with adding this as a flag to...

I generated the `module_step_form.tsv` from the KEGG modules data as I had pulled down from our KEGG description. I have not updated it since DRAM release. I will add that...

I'm not ignoring this. I realized I had refactored the code used to generate the `module_step_form.tsv` so that it worked better for `etc_module_database.tsv` and now I'm having a hard time...

We decided to throw this error whenever a user tries to use a folder that already exists. There are a few risks to using a directory that already exists such...

Can you try running `annotation/working_dir/GF2_mjMb2B_input_S53_megahit.contigs/tmp/genes.faa` from the folder where you ran DRAM? It looks like maybe it can't find that file. Alternately how much RAM is available on this system?...

Hi @franztastic, What is in the folder `annotation/working_dir/GF2_mjMb2B_input_S53_megahit.contigs/tmp/`? Were any errors or warning raised before this? Also what version of DRAM are you running (you can run `DRAM-setup.py version` to...

When you set up DRAM did you give it the location of your KEGG proteins file or are you using KOfam?

This maybe because of a change in format of the KEGG pep file headers. We haven't renewed our KEGG subscription for a bit over a year so that could be...

Hello, When you ran `DRAM-setup.py prepare_databases` did it finish with an error or did it not have the MEROPs database in place even after finishing successfully? My hunch is that...

Hmm. Can you try running with more memory available if you have some. @mw55309 also created some scripts to deal with this issue that you could try out https://github.com/mw55309/DRAM_hacks.