Help with manifest file

Hello there!

I would apprecciate some help with an error I've gotten while trying to import some paired-end files from a MiSeq running.
I'm using qiime2-2021.4, which I installed using conda.

I have used the following command:
qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path Unmerged/manifest_PE_file.tsv --output-path 16S-paired-end.qza --input-format PairedEndFastqManifestPhred33V2

Then I got the following error:

There was a problem importing Unmerged/manifest_PE_file.tsv:

Unmerged/manifest_PE_file.tsv is not a(n) PairedEndFastqManifestPhred33V2 file:

Filepath on line 1 and column "forward-absolute-filepath" could not be found (~/Documents/MiSeq_16S/Unmerged/ANT001003_S58_L001_R1_001.fastq.gz) for sample "ANT001003".

My manifest file is available here: Manifest - Google Sheets

Thank you in advance!

Hi there @RayanaFeltrin!

The main part of the error message is here:

What it is telling you is that there is no file in ~/Documents/MiSeq_16S/Unmerged/ called ANT001003_S58_L001_R1_001.fastq.gz - you can double-check that by running:

ls ~/Documents/MiSeq_16S/Unmerged/ANT001003_S58_L001_R1_001.fastq.gz

You'll need to make sure you have spelled everything correctly in your manifest file, and pay extra close attention to things like spaces and letter capitalization.

Keep us posted!

:qiime2:

1 Like

Thank you so much, @thermokarst !
I have just changed ~ by my complete home path and it worked!

Cheers,
Rayana

1 Like