Permission denied when importing FASTQ files

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$: cd share
taf1g17:~/share$ 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. :man_teacher:

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! :slight_smile:

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