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:
sequence1,$PWD/sequence_files/SRR7629764_R1.fastq.gz,forward
sequence1,$PWD/sequence_files/SRR7629764_R2.fastq.gz,reverse

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.

Best,
Justine

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Justine,

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

Thanks again,
Andy

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