Alpha Diversity Format Error

User Support
1

I used the down commands to calculate the core-metrics-results especially I am interested in calculating evenness and Shannon index, I only have one sample with depth 10.000 and after i run the down command i had this error"/tmp/q2-AlphaDiversityFormat-rlwh7ghy is not a(n) AlphaDiversityFormat file" and i do not understand where is the problem

qiime diversity core-metrics-phylogenetic \
  --i-phylogeny rooted-tree.qza \
  --i-table table-nonchimeric-wo-borderline.qza \
  --p-sampling-depth 1103 \
  --m-metadata-file metadata.tsv \
  --output-dir core-metrics-results
3

Do not run this command if you only have one sample, because the outputs will not make sense. Most diversity analyses (most importantly those used by this pipeline) are only useful and/or will only compute if you have > 1 sample.

I recommend instead you rarefy your feature table and use qiime diversity alpha to measure alpha diversity of your single sample.

1 Like
4

DearNicholas_Bokulich thank you for your reply, I am new in using qiime could please explain more what you main by measure, there is another way to measure it or you mean use OTU table and do in R ?

5

Use the following commands in sequence
qiime feature-table rarefy
qiime diversity alpha

6

still have the same message:pensive: erorr /tmp/q2-AlphaDiversityFormat-haw7w4av is not a(n) AlphaDiversityFormat file using the recommended commands

7

Have you searched the forum archives for other topics describing this error? It sounds like your rarefaction depth may be too high.

We will need more information to provide support:

  1. what is the exact command that you are running? It is unclear which command is causing this error.
  2. what is the full error message you receive? Add --verbose to your command to see the full message and post it here.
  3. Can you share the feature table summary? (run qiime feature-table summarize on your feature table and post the QZV here).
8

Dear Nicholas,
1- the exact commands is
qiime diversity alpha
--i-table --i-table table-no-mitochondria-no-chloroplast.qza
--p-metric pielou_e
--o-alpha-diversity pielou_e.qza
2-

erorr_screen_shoot
erorr_screen_shoot1295×639 124 KB

3 here with also the screen shot from the feature table summary
table_summary
table_summary1295×639 62.7 KB

thank you so much for your fast reply

9

please share the QZV as I requested. The screenshots do not give me the information that I need.

10

sorry for misunderstood here with attach the summarizetable-no-mitochondria-no-chloroplast.qzv (540.3 KB)

11

would you mind sharing table-no-mitochondria-no-chloroplast.qza ? This will help troubleshoot. Thanks!

15

table-no-mitochondria-no-chloroplast.qza (242.0 KB)
this is the table, as i told you i was trying to run the analysis to calculate both Shanon and pielou but unfortunately. thanks for your fast reply.

20

@Nizar_Goda,
Please install the latest version of QIIME 2 and try again. You appear to be suffering from a format validation bug in older releases of QIIME 2 that has been fixed. I have confirmed that your data work with the latest release.

Good luck!

2 Likes
22

thank you so much now it work, last question how can i visualize the information in the file pielou_e.qza ?

23

Check out the tutorials for examples of how to use the alpha diversity data, e.g., see the moving pictures tutorial. Note, however, that not all visualizations may work since you only have one sample.

You may want to check out the tutorial on exporting data too. Since you have 1 samples, there is nothing to visualize, per se, and you may just want to look at the raw value.

24

An off-topic reply has been split into a new topic: how can I visualize sequence data?

Please keep replies on-topic in the future.

25

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