Trouble importing data: "There was a problem importing Manifest.txt"

Hi all, I am having some trouble importing my data into Qiime2. Attached is some screenshots of the output I get and my Manifest file. Any help would be greatly appreciated!

Hello Chris,

Looks like you are using WSL (just like me!) and also Windows style file paths to get to your files

I bet that Linux style file paths will work better. To get these paths, run pwd, see how that compares, and update your paths.

(base) [email protected]:~$ pwd

I bet this will be something like /home/chris/processed_1_S1_L001_R1_001.fastq.gz
Note that it uses /forward/slashes/ instead of the wsl$\backwards\slashes use in Windows.

Thanks for the advice! I gave it a try with several different versions. None of them worked (as shown in the screenshot). Is there something else I should try? I am very new to Qiime2 and using command line so sorry if the solution is obvious!

I am using Qiime2-2021.11 in WSL2 (Windows 11).
I keep my fastq.gz and other files in a folder on drive "H". My file path is /mnt/h/myrun/R1.fastq.gz. I have successfully imported files using this approach. Hope it helps.


Hi Kindergarten, thanks for the advice! I dont have an H drive. would an external hard drive work? If so how would I link it to Ubuntu?

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You can use the letter for which ever drive you have. It can be c drive.
On Windows side, just make a folder in c drive. put all your files there (fastq.gz, manifest.txt, metadat.txt).
On Ubuntutu side, change to folder where you have the files. e.g. /mnt/c/myrun

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Whenever I try to access the mnt\c folder I get this error. Any idea on how to get past this?

Please see my screen shot. At the command prompt type
cd /mnt/c/yourfolder.


Awesome! thank you very much!

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