manifest file and importing demultiplex paired ended data

Hi There,

I am using qiime2-2021.8
I followed the tutorial for PairedEndFastqManifestPhred33V2
code used:
unzip -q

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path pe-33-manifest
--output-path paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2

I get the following message:
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path pe-33-manifest
--output-path paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2error: invalid response [unzip -q ]
replace pe-33/2020Colon16forward.fastq.gz? [y]es, [n]o, [A]ll, [N]one, [r]ename:

what should be my answer to the above question Y, No, All, None or rename?
Please let me know.

Thank you very much in advance, Paula.

Hi @pazevedo1! The message asking you to answer yes or no isn't coming from QIIME 2, its actually coming from this command:

Is your manifest inside of a zip file? If so, unzip it, then you can skip including this command each time.

1 Like

Hi Mathew
Thank you for your email.
My manifest file in not in a zip file. Manifest file is named pe-33.manifest
The fastq.gz files are in a folder labelled that need to be unzipped. So not sure what to do.
Please advise.
Thank you

Great, then there is no need to run that unzip ... command!

Then that is what you'll want you --input-path to be specified as.

Keep us posted!