Metadata loading error

metadata

(Vivianna Sanchez) #1

Hello,

I’m trying to run alpha and beta diversity analyses with data I’ve downloaded from Qiita and
I’m receiving a metadata loading error. Along with the Qiita artifacts, I also downloaded the QIIME map and using that as my metadata file for QIIME2. I’m running QIIME2 version 2018.11 and installed it using conda.
Here is the command I’m trying to run:

qiime diversity core-metrics-phylogenetic
–i-phylogeny rooted-tree.qza
–i-table table.qza
–p-sampling-depth 12476
–m-metadata-file sample-metadata.tsv
–output-dir core-metrics-results

Here is the error I received:

There was an issue with loading the file sample-metadata.tsv as metadata:
Metadata file path doesn’t exist, or the path points to something other than a file. Please check that the path exists, has read permissions, and points to a regular file (not a directory): metadata.tsv
There may be more errors present in the metadata file. To get a full report, sample/feature metadata files can be validated with Keemei: https://keemei.qiime2.org
Find details on QIIME 2 metadata requirements here: https://docs.qiime2.org/2018.11/tutorials/metadata/

I validated my metadata on keemei, here is my metadata file https://docs.google.com/spreadsheets/d/14L7D1kZtKqf6waCcsZsjJ96oSYlZJ3abkiY_ntI4ilw/edit?usp=sharing

I also checked it to make sure it is following proper metadata format and I’m not sure why it is not working. I’m a beginner, so any advice/explanation would be great.

Thank you!


(Justine) #2

Hi @Vivianna_Sanchez,

It sounds like you’ve done a fair bit of trouble shooting already, and like your metadata is good. My suspecion is that you might have a path problem, which is pretty easy to fix. The last couple times I ran into this particular error, my issue had to do with the path…

First, use the pwd command to check your current location. Then, us ls to list the files in your current directory. If the sample-metadata file is there, then there’s more troubleshooting to be done. If it’s not, you need to specify the path to the file.

Hopefully this helps.

Best,
Justine