I just downloaded qiime2 on Windows Subsystem for Linux. I have previously used qiime2 on docker/galaxy as shown in many of the YouTube tutorials available online. I am attempting to go through the Moving Pictures Tutorial, but using my own files to familiarize myself with this version of Qiime2 on linux. I am using the same metadata file that I had worked with previously, which worked fine with Qiime2 docker to run everything I needed in docker. I have checked the read permissions and the metadata file with keemei - both of which should not be an issue. I have checked the forum for issues similar to this and it seems as though most other issues users have run into have been due to path errors, so I am assuming that is the same issue that I have. However, I directly copied the path from the file on my computer. When I copied the file path from my computer it reads "C:\Users\NGreenberg\Documents\FMT Sequencing Files\ubuntu test stuff\FMT-metadata - Sheet1.tsv". I have attached a screenshot of the issue to this post.
Thank you very much for your reply. I tried running:
I tried running this command in both my WSL terminal and in my ubuntu terminal.
When running in WSL this opened "C:\Windows\System32..." path. I pasted in my metadata and the path reads "C:\Windows\System32\Metadata_FMT.txt". I tried running the metadata tabulate command using this data and received the same error as before (screenshots attached).
When running in Ubuntu this path opened: "\wsl.localhost\Ubuntu-22.04\home\nagr4657". I pasted in my metadata and the path reads "\wsl.localhost\Ubuntu-22.04\home\nagr4657\Metadata_FMT.txt". I tried running the metadata tabulate command using this data and received the same error as before (screenshots attached).
Any ideas why this might be happening or do you have another file upload strategy that might work better?
It looks like you are still inside your Windows paths, not the Linux-y paths of WSL.
You can run cd ~ to return to your home directory, then open that using explorer.exe . in WSL and try moving files there. (My guess is that Qiime2 does not like the Windows-y paths from your host OS and I'm hoping sticking to the Linux paths of the WSL home directory will solve this problem.)
Just to check, are you running WSL locally on a Windows machine, or on a remote server / cloud machine?
Thanks again for responding. I am running WSL/Ubnutu locally on my windows laptop. I am running the qiime 2 metadata tabulate command in Ubuntu not WSL. I tried following the instructions you provided.
Restarted computer and opened Ubuntu. Ran explorer.exe .