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thh32 / Protologger

Protologgger is a tool for the description of novel taxa by providing taxonomic, functional and ecological insights
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Suggestion for a new KEGG grouping #5

Closed Anto007 closed 3 years ago

Anto007 commented 3 years ago

Hi,

Nice tool but I'll wait for the full conda version to start using it more extensively [not enough patience to use it over Galaxy;-)]. May I suggest the addition of a new KEGG grouping "Methane/C1 metabolism" for methylotrophic bacteria? Methylotrophic bacteria that are capable of growing on C1 compounds (e.g., methane, methanol) as their sole carbon and energy sources can have the prefix 'Methyl' added to their taxon names.

thh32 commented 3 years ago

Hey,

Yeah I totally understand not wanting to queue for access, hopefully you wont have to wait too long for the conda version!

Regarding the inclusion of methane utilisation, is there a specific KEGG module you would wish to be included? From looking at the modules methane is assigned to, I would assume "Methane oxidation, methanotroph, methane => formaldehyde " would be best suited? Thanks for the suggestion as well for names, this is exactly what we are after from the community so are very grateful for your input!

Anto007 commented 3 years ago

Thank you for your response. Yes, the KEGG module "Methane oxidation, methanotroph, methane => formaldehyde" would be suitable for the specific case I mentioned. Btw, I had submitted this Job 811210de8067609a (UUID: | 6c8b8b4d-9cc6-4c60-a6d7-9455728cd758) on Galaxy last Sunday and I'm yet to see any results. I suppose my job will start running when resources become available?

thh32 commented 3 years ago

Perfect, then I will start including that module into the pathway analysis.

Unfortunately our server is seeing extremely high use at the moment as some users submitted ~50 jobs each but yes your job will start running once resources are available. Hopefully that is soon and we are looking into options to expand our resources but currently we are limited to running 3 jobs at a time.

thh32 commented 3 years ago

The additional module has now been included within Protologger if you wish to rerun your analysis.

I have noticed that our queue on the web-server is now reduced so I hope you job finally finished! My apologies for the long wait and if you have any further suggestions for additional pathways, let me know!

Anto007 commented 3 years ago

Thank you. The main analysis result files have become available but when I tried to run GAN on Galaxy, I got the below error message:

WARNING: You are using pip version 20.1; however, version 21.1.2 is available. You should consider upgrading via the '/DATA/galaxy-run/galaxy/.venv/bin/python3 -m pip install --upgrade pip' command. WARNING: You are using pip version 20.1; however, version 21.1.2 is available. You should consider upgrading via the '/DATA/galaxy-run/galaxy/.venv/bin/python3 -m pip install --upgrade pip' command. WARNING: You are using pip version 20.1; however, version 21.1.2 is available. You should consider upgrading via the '/DATA/galaxy-run/galaxy/.venv/bin/python3 -m pip install --upgrade pip' command. ----- G A N -----
the great automatic nomenclator

Input files loaded

Anto007 commented 3 years ago

Also, nice Spider plot but I noticed a minor typo on it- "Prevalence"

thh32 commented 3 years ago

Hmm that is very strange about the GAN, I saw a job failed and ran a test dataset through and it worked fine, would you mind emailing me your Protologger overview file for me to identify the issue with?

Also thanks for spotting the spelling mistake for the spider plot and Im glad you like it (corrected the spelling now).

Anto007 commented 3 years ago

Emailed you now the file; thanks!

thh32 commented 3 years ago

So I have found the issue, firstly 'oral' was searched for before 'coral' so your microbe was assigned to the wrong environment (resolved) and secondly the oral file had a duplicate entry from the combination of multiple lists, which has also been resolved.

Hopefully the GAN-extension should now work for you! Please let me know if it does.

Thanks, Tom

Anto007 commented 3 years ago

Many thanks Tom; I can confirm that the rerun has worked.

thh32 commented 3 years ago

Thanks for the confirmation!