Interactive Quality Plot : Danger: Some of the PHRED quality values are out of range

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You will need to define a manifest file that lists out all of your demultiplexed sequence files:

sample-id,absolute-filepath,direction
sample-1,$PWD/some/filepath/sample1_R1.fastq.gz,forward
sample-2,$PWD/some/filepath/sample2_R1.fastq.gz,forward
...

and save that to a new file (for this example, I will name it se-64-manifest).

Then, you can import the sequences by running something like:

qiime tools import \
  --type SampleData[SequencesWithQuality] \
  --input-path se-64-manifest \
  --output-path demux.qza \
  --source-format SingleEndFastqManifestPhred64

One shortcut to make it easier to do this is to take the QZA that has your first attempt at importing, and export the data from it to get a starter template for the manifest. In your exported directory would be a file called MANIFEST (please ignore all the other files that are exported with it), which you could then copy and use as your new manifest file. You would need to edit the second column and rename it to absolute-filepath, and then edit the entries in that column to become absolute filepaths. Then, you could use this manifest in the import command I provided above.

Hope that helps and good luck! Feel free to write back if you get stuck on anything.

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