Error: qiime diversity bioenv

User Support
1

Hello,

I am getting the following error when executing the below command: Any insights would be greatly appreciated.

Thanks!

qiime diversity bioenv \
  --i-distance-matrix cm7514/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file Canine_metadata.tsv \
  --o-visualization cm7514/unweighted-unifrac-bioenv.qzv

DissimilarityMatrixError("Data must be at least 1x1 in "
skbio.stats.distance._base.DissimilarityMatrixError: Data must be at least 1x1 in size.
2

Hey @Nathan_Stone1,

I suspect your distance matrix is empty. You can check by running qiime tools export on the unweighted_unifrac_distance_matrix.qza artifact to see if the internal file is empty.

(This may have happened because you filtered out all of your samples in the rarefy step.)

3

Thanks. Distance matrix looks good. Any other possibilities? I tried running this on multiple environments with the same result.

4

Do the IDs in the distance matrix match your metadata? I am pretty sure scikit-bio guards against this, but perhaps that is also subsetting (although I don't see a DistanceMatrix constructor in that code so I wouldn't expect your particular error text).

Another option would be the transformer which sits the middle of the artifact and the actual method/visualization execution. Would you be able to post your artifact? I can try messing around with it using some of the internal QIIME 2 APIs which are invoked, I might see something there.

5

@Nathan_Stone1 can you also provide your Canine_metadata.tsv file? I suspect your distance matrix is being filtered within the bioenv visualizer such that the filtered distance matrix is empty.

6

unweighted_unifrac_distance_matrix.qza (61.8 KB)

7

Canine_metadata.tsv (13.9 KB)

8

Hi guys,
I am having the same issue, checked distance matrix, metadata and ids.

Please let me know if my files would be of any use.
Thanks!

9

The issue seems to be where the sample-metadata is filtered to find all numeric categories without N/A values. In @Nathan_Stone1's case it finds these categories as continuous:

Empty DataFrame
Columns: [Latitude, Longitude, Year, Month, Day, SixteenS_CT, Description]
Index: []

But because each of these categoreis has a N/A value somewhere, it drops the entire category, resulting in no samples.

@Nathan_Stone1, try removing samples in your metadata file which have N/A for the categories you are interested in.

@ErikaGanda you may be having the same issue, check if you have N/A values in your continuous categories as well.

1 Like
10

Thanks @ebolyen! Just to clarify, empty cells in a mapping file are treated as N/A values.

11

Thanks! I will give it a try!

12

Thanks all, I'll give it a try.