Issue with feature-table rename-ids

Technical Support
1

Hi,

I'm trying to change my sample names with command feature-table rename-ids. I need to change them because feature-table summarize is not accepting my metadata file, which I think is due to the long file names. I did make sure that they match the encoded file names, so I don't think that's the issue. For context this is a meta-analysis with all samples recently merged. My code reads as

qiime feature-table rename-ids
--i-table /temp/MetaMerged2.qza
--m-metadata-file /temp/newMetaMerged.tsv
--m-metadata-column newsampleid
--p-axis sample
--o-renamed-table /temp/renamed_MetaMerged.qza

The issue I'm running into is that my original sample ids are not being accepted for this command either, so I'm not really sure where to go from here to change them. I suppose it could be a different issue with my MetaData file, though. It's attached here.

Thanks for your help!

Edit: Sorry, I didn't include the error message.

There was an issue with loading the file newMetaMerged.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): newMetaMerged.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: Metadata in QIIME 2 — QIIME 2 2022.11.1 documentation

When I do use the keemei plugin it's saying my sampleid names are the issue.

newMetaMerged.tsv (55.4 KB)

2

Hello @mkc206,

Please also post the error message.

1 Like
3

oops, edited original post

4

Hello @mkc206,

This is the important part:

Metadata file path doesn't exist

So your metadata file isn't at the path that you specified (/temp/newMetaMerged.tsv). Maybe you meant use a relative filepath temp/newMetaMerged.tsv?

2 Likes
5

I'm actually using apptainer to run qiime on a server and /temp/ is the path I have apptainer set to (with the first and last '/' required), which has worked for all my other commands. ls newMetaMerged.tsv returns correctly in that directory as well.

6

Hello @mkc206,

ls newMetaMerged.tsv returns correctly in that directory as well.

What do you mean by this?

If you have a way to run shell commands where your data is located can you run ls -l /temp/newMetaMerged.tsv and post the output?

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