Are those sample ids listed in exactly the same way in the metadata file and your table? ID matching is exact, so if you have hyphens versus underscores, or upper/lowercase letters, those will be read as different IDs (please note, the metadata behavior described here might not be applicable in future releases of QIIME 2 - we are currently overhauling the metadata handling in the framework).
Some ways you can make sure your IDs match:
Run feature-table summarize on your feature table, without your metadata, you will have a list of sample IDs in there.
Run feature-table summarize on your feature table, with your metadata. Compare the sample IDs in this step with the sample IDs in the previous step.
Hi @Restuadi! Thanks for the files - that was super helpful!
You have extra spaces (' ') after the listed sample IDs in your metadata file ('R4286 ' instead of 'R4286' & 'R2406 ' instead of 'R2406'). If you delete those spaces in your metadata file, you should be good to go.
We are currently in the middle of overhauling metadata handling in QIIME 2 --- once those changes land, one important change is that leading and trailing whitespace will not be significant --- it will be stripped off, so this wouldn't have even been an issue for you. We will let you know when this is made available in a future release - stay tuned!
Thanks
PS - you can attach files by clicking this icon in the edit menu bar:
In the QIIME 2 2018.2 release, Metadata ignores any leading or trailing whitespace characters in cells, avoiding the issue reported in this topic.
There are a number of other changes to QIIME 2 Metadata in the 2018.2 release. See this forum announcement for details on what changed, as well as the updated Metadata tutorial.
