Output from MaAsLin

Dear Galaxy team,

I’m using MaAsLin for the gut microbiota analysis. Instead of filtering output by FDR, I’d like to get the p-values of all taxa. Therefore, I set the FDR threshold to 1.

However, the output seems always neglect several taxa. For example, I import 20 taxa for the analysis, and I only get the analysis result for 15 taxa. I’ve tried several times with different taxa table. But I never get the whole result.

Would you please kindly tell me how I can get p-values for all taxa?

Thanks a lot in advance!


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PS: No taxa are filtered by the prevalence and abundance.

Welcome, @clairexu!

Are you using the tool at this public Galaxy server? http://huttenhower.sph.harvard.edu/galaxy/

The tool was custom wrapped for this particular public Galaxy server and is not available in the ToolShed (the Galaxy “app store”) for review. So, we can’t help to troubleshoot what, if any, output limitations or input/parameter formatting problems you might be encountering at this forum. And if a server-side issue, the administrators of the server would need to get involved.

I would suggest asking this question at the Google forum for this tool. Contact for help is noted on the tool form and will reach the developers that created/support the tool wrapper.

Contacting the administrators of this public Galaxy server is also a choice (for potential technical issues). Please see:


Dear Jennaj,

Thank you so much for your prompt reply. You’re right. I’m using the Galaxy server. I will contact the Huttenhower’s lab instead. Thanks for the information.

Best regard,

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Hi clairexu,
have you solve the problem yet? thanks a lot.

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ping @clairexu re ^^^^