Multiple errors in importing data into QIIME2 2021.11

Hi all, I experienced some problems when importing data into QIIME2. I have gone through the tutorials with no difficulties, but the error happens when it comes to my dataset.
I intended to import multiple demultiplexed, paired-end, fastq.gz files into .qza file. According to my understanding, I need to create a manifest file, and choose "PairedEndFastqManifestPhred33V2" as input format.
Here is the code I used:

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path manifest.txt \
  --input-format PairedEndFastqManifestPhred33V2 \
  --output-path amp_seq.qza

And I received the following errors:

It looks like I am experiencing multiple errors, in both input format, and output path.
In addition, I attached some screen shots of different layouts, hope they are useful:
The manifest file:

The file layout:

The fastq layout:

I suspect I am choosing the wrong input format, but not sure how to select the correct one.
I tried multiple options in the --show-importable-formats list, but none of them work.

Any help would be highly appreciate!

1 Like

My understanding is that for paired-end-read imports, manifest file should have three columns.
sample-id forward-absolute-filepath reverse-absolute-filepath

I think you just have an extra whitespace character in your command between the end of PairedEndManifestPhred33V2 and the beginning of --output-path, it is most likely a space after the slash you are using to extend your line. You should go to the --input-format line, use the right arrow key to go as far as you can to the right, then use backspace to get rid of any whitespace characters past the \.

Thanks for the advice, there are indeed extra white spaces on the line.
Never expect it is the cause!

Thanks for the advice, maybe I am looking at the wrong manifest file format.
With the help of @Keegan-Evans ,the code works after using a new manifest format as suggested!
Thanks to both of you.



It can be a bit surprising! It has nothing to do with QIIME 2 but is caused by the fact that the command line itself only interprets a \ as a continuation if it is the very last character in the line.


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