Errors using LEfSe tool through the Galaxy/Huttenhower lab website

[tosha]

Hello! I am a dentist pursuing Ph.D. wherein my project requires some microbiome analysis. I am trying to use the LEfSe function through the Galaxy/Huttenhower lab website. However, I am unable to conduct the analysis and am getting a similar error (as below):

Traceback (most recent call last):
File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py”, line 435, in
feats = numerical_values(feats,params[‘norm_v’])
File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/format_input.py”, line 174, in numerical_values
feats[k] = [float(val) for val in v]
ValueError: could not convert string to float:

As per your suggestion, could I request if you could guide me in detail, as to how do I check where is the problem with the input data file?
Owing to my lack of experience in coding/microbiome analysis/R, hence, the humble request.
Thank you for your kind help.

[jennaj]

Hi @tosha

Moved your post into it’s own topic.

For the prior Topic, it was clear where that individual was using the tool, so it was recommended to use the updated tool version. Why is here for reference:

@jennaj

You are also using a version of the tool that was sourced from the Test ToolShed , which means that it might not be “production-ready” or have unresolved development bugs.

For your question:

@tosha

I am trying to use the LEfSe function through the Galaxy/Huttenhower lab website.
…

As per your suggestion, could I request if you could guide me in detail, as to how do I check where is the problem with the input data file?

The problem may not actually be with your inputs. Why? See:

Tool request failed Maaslin -- Uncaught exception in exposed API method

This tool is only installed on the huttenhower Galaxy server that runs a very old version of Galaxy. We cannot help you there.

Contact information for that server, and the administrators that run, it is here:

@jennaj

Please find links to contact information for the public Huttenhower Galaxy server hosted at http://huttenhower.sph.harvard.edu/galaxy/ in the Galaxy directory here: https://galaxyproject.org/use/huttenhower-lab/

In summary – three problems:

1. Using a tool that is not in a “production” version
2. Running the tool on an outdated version of Galaxy
3. The administrators of that server do not follow this forum

What you can do:

1. Contact the public Huttenhower Galaxy server admins for help.
2. Try using the tool at a different public Galaxy server and see what happens.

• UseGalaxy.eu and UseGalaxy.org.au are two choices
• UseGalaxy.org is another. Note the server this server undergoing maintenance right now, so you won’t be able to use it until that is completed. Notice and updates here: UseGalaxy.org scheduled maintenance downtime October 13, 2020 -- Completed - #11 by jennaj

For general troubleshooting of inputs/tool errors – there is much Q&A at this forum – including a summary here that includes tutorials: Troubleshooting resources for errors or unexpected results.

That said, given the Huttenhower server’s unique configuration, your inputs could be completely fine – and the tool will still fail there. Other problematic tools have been reported. How to proceed is your decision but since you are new, using an updated server/tool will make getting started with much Galaxy easier.

If you do run into problems at a usegalaxy.* server, with the most current version of any tool, we can certainly help more at this forum.

Best, Jen