PairedEndFastqManifestPhred33 file error

I am trying to import data in Qiime2 (2019.4). I get the error:

There was a problem importing manifest.csv:

manifest.csv is not a(n) PairedEndFastqManifestPhred33 file:

File referenced on line 2 could not be found ($PWD/sequence_files/SRR7629764_R1.fastq.gz).

I’ve checked the manifest.csv file, and even reduced it to one sample to trouble shoot. It contains only comma separated columns sample-id,absolute-filepath,direction

and the two sample lines are:

I’ve checked using TextWrangler and there is no other column, lines or formatting apparent for this file, so I cant work out why its not being recognised as the manifest file.

Any suggestions welcome!

Hi @apreston243,

I think the issue comes here:

So, you’ve got a path issue. Can you check where you are ($pwd) and that you have a folder called sequence_files which contains the files you’re listing? I (embarrassingly) often have the problem where I’ve misspelled something in my path, and then run into issues. My guess is that if its a systematic issue, it might be because your overall path is wrong.




Many thanks. The issue turned out to be the space in ‘sequence files’ folder name. Removing that fixed the problem.

Thanks again,

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