I am a Fresh user here, and would appreciate any help in this error message I had when running "qiime diversity core-metrics-phylogenetic" command:
Plugin error from diversity:
** Ordinations with less than two dimensions are not supported.**
Debug info has been saved to /tmp/qiime2-q2cli-err-lxzrblxo.log
And the exact command I used was:
qiime diversity core-metrics-phylogenetic *
** --i-phylogeny rooted-tree.qza *
** --i-table table.qza **
** --p-sampling-depth 90806 **
** --m-metadata-file sample-metadata.tsv **
** --output-dir core-metrics-results **
** --p-n-jobs-or-threads 15**
I have read through the forum and tried the two checks suggested, but were still unable to resolve the issue. Would be much grateful of any help! Thanks!
Check1: If the number of sample is 1? --> No, I have 14 samples.
Check2: If the sample-id match between the feature table and the metadata? --> Yes, they do match.
Here I post the files that may be needed in debugging:
rooted-tree.qza (87.8 KB)sample-metadata.tsv (917 Bytes) table.qzv (517.7 KB)
Would be very grateful of any pointers to direct me to solve the issue!
Thanks for reaching out! Happy to provide some insight on this error.
I took a look at your table.qza file, and it looks like the maximum sampling depth is 90806 - which leaves you with only one sample at that depth. I’d recommend choosing a smaller depth that will pull in more of your samples.
From view.qiime2.org, you can upload your table.qza file and select the ‘Interactive Sample Detail’ tab in the upper right hand corner of the page to play around with sampling depths and determine a good depth for your dataset.
Hope this helps! Let me know if you are still running into any issues!
Ah, silly me. Sorry, I mixed up “sampling-depth” and “max-depth”. Thanks! I am now able to proceed on.
Fantastic! Glad to hear you’re up and running now. Cheers!
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