Faith's phylogeny diversity and evenness command error

Technical Support
1

Hi,

I'm having trouble to get faiths_pd .qzv output when I ran the command:
qiime diversity alpha-group-significance
--i-alpha-diversity ./faith_pd_vector.qza
--m-metadata-file ./metadata.tsv
--o-visualization ./faiths_pd_statistics.qzv

And error says: "(1/1) Invalid value for '--i-alpha-diversity': './faith_pd_vector.qza' is not a QIIME 2 Artifact (.qza)", same issue with evenness command, my working directory has core-metrics artifact "faith_pd_vector.qza".

I would be very grateful for any help, many thanks,

Regards,

2

Hello!
Most probably you misspelled the name of the artifact, or indicated a wrong path.
Usually, diversity metrics are located in a separate subfolder named something like "core-diversity-metrics", ot whatever name you gave as output directory, when run core diversity plugin.
So, check if you wrote everything correctly, including the path to the artifact.

2 Likes
3

Hi Timur,

Thanks so much for your prompt response, all diversity metrics are saved in the main folder, not in a subfolder of "core-diversity-metrics" so, I can see core-metrics artifact "faith_pd_vector.qza" when check with ls, and looks command spelled correctly but the error remained same, I'm using WLS in Ubuntu 20.04 LTS

Many thanks,

Regards,

4

Hello!
That's a little bit strange then.
Could you perform a sanity check by running exactly this command?

qiime diversity alpha-group-significance \
    --i-alpha-diversity faith_pd_vector.qza \
    --m-metadata-file metadata.tsv \
    --o-visualization faiths_pd_statistics.qzv

Just wondering if plugin do not like './'. If the error still persist, could you provide as with screenshots of your terminal command and ls as well?

1 Like
5

Hi Timur,

Thanks so much, I tried command without './' but the error still continues to exist, attached are ls and error message, many thanks for your help,

ls
ls1891×169 76.7 KB
faith_pd_vector error
faith_pd_vector error687×509 55.5 KB

Regards,

7

Hi Timur, the error still continues to exist, would be grateful if could hear any advice, thank you,

Best,

8

Hi @Microbiome
I am not sure why you are getting this error since everything looks fine to me. I left your question queued for other moderators to see if they can help you with this issue.
The only thing I can suggest you now while waiting is to copy the complete the full name of the artifact and insert it to the command instead of typing it in case if there are some issues with characters.

1 Like
9

Thanks so much Timur, hope to get it's solution,

Best,

13

Hi @Microbiome
Could you share your metadata and .qza file in question with me?

2 Likes
14

Thanks so much Timur for your help, I fixed the problem,

Best,

1 Like