MetaData Duplicate Column label

Hello Everyone,

I am trying to validate my metadata file using Keemi. I have a column labeled pH and a column labeled width but each have a value of 7.3 for a particular sample. When I try and validate, Keemi output says that those values are “Duplicate Column labels”. Am I unable to have same number in two separate columns or am I doing something wrong? Attached is the metadata file I’m working with.

Biofilm_MetaData.tsv (2.7 KB)

Thanks for the help,
Danny

Hi @Stream_biofilm, thanks for reporting this issue! It looks like Keemei isn’t up-to-date with how QIIME 2 interprets metadata files coming from QIIME 1 (i.e. where the header starts with #SampleID). Right now Keemei will treat any lines starting with # as a comment, so it needs to be updated to notice #SampleID as a special-case QIIME 1-style file.

So with your data, Keemei is ignoring the header line (because it thinks it is a comment line) and treating the next line in the file as the header. This is why you’re seeing an error about duplicate column names, since 7.3 is repeated in the second row.

You can safely ignore those errors. If you’d like to see Keemei successfully validate your file, as a workaround you could rename the first column to something like SampleID, and that’ll also fix it (just drop the # character). But again, this is totally optional and won’t affect how QIIME 2 interprets your metadata file.

I’m planning a Keemei release within the next few weeks to fix this issue and to make other updates to match QIIME 2’s latest metadata file format spec. We’ll follow up here when this bug fix is available in a Keemei release!

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The latest version of Keemei supports the new Metadata file format included in the QIIME 2 2018.2 release, and the reported bug has been fixed.

Note: if you have Keemei installed already, you’ll automatically be updated to the latest version.

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. :sun_with_face: