Need Help with Galaxy LEfSe LDA Step Error

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Hi, I haven’t used Galaxy LEfSe analysis for a while, and I recently tried to use it again. However, I’m unable to proceed beyond the LDA Effect Size step. I even tested an old text file that worked perfectly a couple of years ago, but now, the same file is not working, and I keep encountering an error message. I’m not sure what I might be missing.

I’ve included a link to my text file, and I would greatly appreciate it if anyone could help me resolve this issue. Thank you!

admin redacted link

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Hi @jeylee
Can you please share the history and post the link?
Thank you!
Igor

1 Like
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Continuing from Need Help with Galaxy LEfSe LDA Step Error

We discussed posting over to the Biobakery forum. Were you able to find out what is going on over there? You can link back more Q&A threads since it seems many people are having similar trouble when I checked yesterday. I think these are technical problems, not data problems, so the server administrators will need to help to solve them. But a shared history link can help to confirm that.

All followup is welcome! :slight_smile:

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I was using the same file as before, but now I can’t even get past the format data step. Here is the error code I received.
raceback (most recent call last):
File “/galaxy_venv/bin/lefse_format_input.py”, line 33, in
sys.exit(load_entry_point(‘lefse==1.1.2’, ‘console_scripts’, ‘lefse_format_input.py’)())
File “/galaxy_venv/bin/lefse_format_input.py”, line 25

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and this is the txt. file that I’ve used.

admin-redacted-link

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Hi @jeylee

We would like to help you but if you do not clarify the server URL where you are working, the exact tool version, the full parameters used, and the inputs – all in context within a history – it will not be possible to troubleshoot this specific error. Please do not link in text or other types files from other locations. You can post screenshots but only if you clarify all the other “metadata” about how the job is working. This is why a link to a shared history is so much better and informative.

Also, if you are working at this server, and the problem actually is a server-side problem with the tool, there is no way to move to a correction at this forum.

Did you check at the other forum? Or are you not working at that server?