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"…

[image] Nizar_Goda: I only have one sample with depth 10.000 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…

Dear Nicholas_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 ?

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

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

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: what is the exact command that you are running? It is unclear which command is causing this error. what is the full…

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] 3 here with also the screen shot from the feature table summary [table_summary] thank you…

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

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

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

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.

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