Alpha and Beta Diversity Analyses

Technical Support
1

I am trying to do alpha and beta diversity analysis but encountered this problem:
Plugin error from diversity:

Command '['faithpd', '-i', '/tmp/qiime2/jaishi452/data/44bca6e8-93e2-4ead-9cc4-d42de18ce15f/data/feature-table.biom', '-t', '/tmp/qiime2/jaishi452/data/8a309405-362f-422e-8254-4ee04bcb9c5e/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-f1hf0kh4']' returned non-zero exit status 126.

Debug info has been saved to /tmp/qiime2-q2cli-err-i9b4b_26.log

I am using qiime2-amplicon-2024.5 and updated conda as well. Can anyone help?

2

Hello @Namraj_Jaishi,

Welcome to the forums! :qiime2:

Can you post the full command you ran and also the rest of the error message?

3

This is the code
qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table table.qza
--p-sampling-depth 6
--m-metadata-file metadata.tsv
--output-dir core-metrics-results
The error it shows :
--output-dir core-metrics-results
/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)
Plugin error from diversity:

Command '['faithpd', '-i', '/tmp/qiime2/jaishi452/data/44bca6e8-93e2-4ead-9cc4-d42de18ce15f/data/feature-table.biom', '-t', '/tmp/qiime2/jaishi452/data/8a309405-362f-422e-8254-4ee04bcb9c5e/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-f1hf0kh4']' returned non-zero exit status 126.

Debug info has been saved to /tmp/qiime2-q2cli-err-i9b4b_26.log

4

That's very helpful! Looks like you found an issue numpy on WSL:

Can you tell us more about the computer on which you are running Qiime? Is this a Mac with OSX or Windows with WSL?

5

I am using Ubuntu in Windows 10 via WSL. It's intel core I3 7th gen.
I am not sure what to do next.

While importing the file and generating the phylogenetic tree, I encountered this issue every time. Still, the code gets executed. But while doing alpha and beta diversity analysis code doesn't execute.
I tried removing conda, qiime and re-installing and re-updating all.
/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)"

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