Hi @taf1g17,
I noticed that you are within the share
folder you set up based on the instructions I provided. Note this was only meant to have a place for you to easily access all of your files. However, you should make another folder, perhaps within the share
folder that is labelled seqs-to-import
or something. Copy only the *.fastq.qz
files into the folder. It also appears that you have extra files other in that folder, i.e. .Zone.Identifier
. I am not sure what these are…
Also, To keep things simple do not run the command from within the directory in which your sequences are located. I’d do the following:
For example, lets say we are in you home folder within WSL:
taf1g17$: cd share
taf1g17:~/share$
taf1g17:~/share$ mkdir seqs-to-import
taf1g17:~/share$ cp *.fastq.gz seqs-to-import/
taf1g17:~/share$ qiime tools import \
> --type 'SampleData[PariedEndSequencesWithQuality]' \
> --input-path seqs-to-import \
> --input-format CasavaOneEightSingleLanePerSampleDirFmt \
> --output-path imported-seqs.qza
Note: you do not need to provide the full file path, which is incorrect anyway as it is using backward-slashes. For more information see here. Also note that I simply provide a relative path.
Keep in mind the Windows Command Prompt does not work the same way as WSL Terminal. I’d recommend reading a few tutorials, like this one, about unix / linux systems.
I also noticed that you seemed to have installed QIIME 2 into your base environment. I would highly advise against this as you may create potential issues. I’d follow the instructions as outlined for the WSL install and use the naming convention we describe there.
-I hope this helps!
-Mike