And the error:
Traceback (most recent call last):
qiime2.core.exceptions.ValidationError: /tmp/q2-AlphaDiversityFormat-r8_sbbjk is not a(n) AlphaDiversityFormat file
Plugin error from diversity: /tmp/q2-AlphaDiversityFormat-r8_sbbjk is not a(n) AlphaDiversityFormat file See above for debug info.
I got this same error when setting the --p-sampling-depth in diversity core-metrics-phylogenetic to a value larger than the largest sample. I assume that creates an empty rarefied table which causes the error.
Check you feature table summary for the sample sizes.
Thanks @Menachem_Sklarz - I had also thought that might be the issue, but I get the same error message when I set the sampling depth to a very low number.
@thermokarst i got this same error. Plugin error from diversity: /tmp/q2-AlphaDiversityFormat-key3df63 is not a(n) AlphaDiversityFormat file
the following is my code: qiime diversity core-metrics-phylogenetic --i-phylogeny root_tree.qza --i-table table.qza --p-sampling-depth 26000 --output-dir diversity_26000 --m-metadata-file metadata.txt table_summary.qzv (387.4 KB)
Hi @whitewind - are you sure this is the summary of the same table you are using in the core-metrics-phylo command above? The table here has two samples, one with 30539 sequences and the other with 27898. I wonder if you could send me the files necessary to re-run this command on my machine, that way I can do a bit of in-depth debugging… If so, please send me a download link in a direct message. Thanks!
Thanks for your response. I am sure the table_summary is the same table using in the core-metrics-phylo command above. I am a newbie, so I only used two samples to understand the qiime2 environment. I only have the data of the two samples. Other samples have not been processed. Can the sample size affect the results? If so, I will process the all my samples. Thanks!