Importing manifest file error


I am running Qiime2 version 2022.11. I am familiar with Qiime 1 but new to Qiime 2. I have been experiencing an error for several weeks in importing my data using manifest format. I succesfully completed the tutorials and haven't experienced any problem in importing data using the sample manifest file, however I have run into some trouble while importing my fastq files. For my dataset, I only pick 2 of my samples paired end sequences to a separate file as an example. I would be grateful if somebody can tell me the problem in the below steps!

-The raw sequence files were provided from a seq facility called Novogene and I put the raw data fastq files into 'Help' folder. The F and R read formats are: A_1_1.fq.gz, A_1_2.fq.gz
2023-01-03 14.33.10

-Here is my manifest file in .txt format
Help-manifest.txt (157 Bytes)

-I tried too many options, path modifications etc. However I always get the same error when I ran the below command in my home path in Terminal

qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path Help-manifest.txt
--output-path paired-end-demux.qza
--input-format PairedEndFastqManifestPhred64V2

Since the data is from a seq facility and I am not sure about the Phred scores I also tried 33V2, 64 versions but none of them have worked.

The error message is: Help-manifest.txt is not a(n) PairedEndFastqManifestPhred64V2 file:

And also, the appearance of my fq files are also pretty different from that in the tutorials (too many FFFFF in QC line), I would be grateful if you can also check this!

Thank you very much for your precious time!!!

Welcome to the forum!
Looks like you have a typo in the manifest file:

Please try to correct files extension from ".qz" to ".gz" as in the file names.


Dear Timur,

Thank you very much for your time and help! I cant believe that I haven't noticed this!

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