qiime2 manifest file ubuntu

I recently switched from a mac to pc and now i am trying to run qiime2 in wsl ubuntu.
I have major problems with creating the manifest file... seems like it might be the wrong format or something. I tried saving it as a tab deliminated .txt file.

Here is my code
qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path manifest10.txt --output-path demux.qza --input-format PairedEndFastqManifestPhred33

This is the error i keep getting;
There was a problem importing manifest10.txt:

manifest10.txt is not a(n) PairedEndFastqManifestPhred33 file:

Found header on line 1 with the following labels: ['sample-id\tabsolute-filepath\tdirection'], expected: ['sample-id', 'absolute-filepath', 'direction']

this is an example file path in my manifest:

Please help!

Hello @justh and welcome to :qiime2:!

First of all, please read Code of Conduct - QIIME 2 Forum. This post does not comply with forum rules.

There is a lot of information on this topic in the Forum, please see: How to create a proper manifest file and how to import it?


Hi @justh and @crusher083,
I don't agree that this post constitutes a code of conduct violation. I apologize if this created any confusion. @cherman2 is sitting next to me and mentioned that she'll be happy to help with this @justh, so she will follow up with you here.

Thank you! When i transfer the raw reads to my old mac, create a manifest file there, and import data as demux.qza it works no problem. But when i do the same on PC then i have some weird formatting issue with my manifest file

1 Like

Hi @justh!
Welcome to the :qiime2: forum!
It looks like your issue is here:

It is expecting a comma separated file and it looks like yours is tab separated. If you changed the tabs to comma's this should work.

Also, This is the original version of a manifest file but this v1 manifest was a bit more error prone so we now have switched to a v2 manifest. Here is our tutorial about how to make that v2 manifest. Importing data — QIIME 2 2023.2.0 documentation

I hope that helps! Let me know if you run into any errors while importing! Importing your data into :qiime2: is always the hardest part!



Thank you Chloe! It worked!

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