Iteration over a 0-d array

User Support
1

I am trying to get evenness data using QIIME2-v2023.2. Apologies in advance as I am new to QIIME2. I am using a filtered table to filter out only the samples I want and there may be low numbers in some of them.

I tried the following command:
qiime diversity alpha-group-significance
--i-alpha-diversity core-metrics-results/evenness_vector.qza
--m-metadata-file cleanmetadata2.tsv
--o-visualization evenness-group-significance.qzv

I got the error:

Plugin error from diversity: iteration over a 0-d array

I read from this post where they multiplied the OTUs by 10^6. Is this the correct way to handle this? If yes, how do I multiply the OTUs by 10^6?
filtered-table.qza (140.9 KB)
filtered-table.qzv (516.4 KB)
filtered-table.qzv (516.4 KB)
cleanmetadata2.tsv (4.5 KB)

Thanks!

2

Hello,
It seems like your case is different. I don't see any problems with the data you provided.
Could you please attach an evenness vector, so we could reproduce the error?

Cheers,
V

1 Like
3

Thank you @crusher083!

Please find below:
evenness_vector.qza (128.3 KB)

5

Hello,
your evenness vector is empty. Please look for the bugs upstream. .qza is an archive, so you can always unzip the file and check the raw data. That should help you find the step, where something went wrong.

Cheers,
V

6

Thanks.

The parent command that lead to these results was:

qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table filtered-samples.qza 
--p-sampling-depth 1
--m-metadata-file cleanmetadata2.tsv 
--output-dir core-metrics-results

Is it because of the sampling depth? I chose 1 because I did not want to lose any samples and had filtered my samples previously.

7

I see! Samples were rarefied to a single read by using --p-sampling-depth parameter. That means, that there is only single 16S copy in every sample, we can't calculate statistics on that. Please, review “Moving Pictures” tutorial — QIIME 2 2023.5.1 documentation to learn how to choose the appropriate sampling depth. That should help the problem.

Cheers,
V

15

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