qiime diversity core-metrics-phylogenetic error


(Castle) #1

Hello, I’m getting an error message with qiime diversity core-metrics-phylogenetic. It seems that issue isn’t the input files or the sample names.

This is my code:
-bash-4.2$ qiime diversity core-metrics-phylogenetic \

–i-phylogeny rooted-tree.qza
–i-table table.qza
–p-sampling-depth 11000
–m-metadata-file sample-metadata.tsv
–output-dir core-metrics-results
–verbose

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.

Thanks for your help!
Sarah


QIIME diversity core-metrics-phylogenetic error
(Menachem Sklarz) #2

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.


(Castle) #3

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.


(Matthew Ryan Dillon) #4

Can you please share you “feature-table summarize” visualization? This will help us understand the situation a bit more. Thanks! :t_rex: :qiime2:


#5

@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)


(Nicholas Bokulich) #6

(Matthew Ryan Dillon) #7

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! :t_rex:


(Matthew Ryan Dillon) #8

#9

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!


(Matthew Ryan Dillon) #10

(Matthew Ryan Dillon) #11

Cool!

I’m not sure - that is why I asked above for your data, to dig into this a bit more myself!

Please give that a go and let us know how it goes! :qiime2: :t_rex:


(Matthew Ryan Dillon) #12

(Matthew Ryan Dillon) #13

An off-topic reply has been split into a new topic: Errors when running alpha-div

Please keep replies on-topic in the future.


(Matthew Ryan Dillon) #14

An off-topic reply has been merged into an existing topic: Errors when running alpha-div

Please keep replies on-topic in the future.


(Castle) #15

Hi @thermokarst -
I’m running the tutorial on a single sample. Here’s the feature table. Thanks!


#16

Thanks for your reply. I have got the diversity results when I used 60 samples. Thanks again