problem facing in importing data in WSL

Hi @jwdebelius I have tried and replaced $PWD by actual path home/samrendra/NGS-SEQUENCES/S1-R1.fastq.gz it but its not working. do you have any Idea why i am facing this issue?


You still have a relative path. Absloute paths need to be prefixed by a "/". So, your directory is in /home/etc.


Thanks for the reply but I have also tried this command. I think you overlooked that. please see the attached screenshot, mentioning the absolute path by an arrow.


Your file isn't where you say it's located. You need to find it on your system. Go to that directory, print the directory ($pwd), then use that.


i am not getting how can find the directory.
my home directory is /home/ samrendra and the raw sequences is stored in the NGS-SEQUENCES folder so my absolute forward path is /home/samrendra/NGS-SEQUENCES/S1-R1.fastq.gz and for the reverse absolute reverse path is home/samrendra/NGS-SEQUENCES/S1-R2.fastq.gz. however I have also tried $PWD/NGS-SEQUENCES/S1-R1.fastq.gz for forward path and home/samrendra/NGS-SEQUENCES/S1-R2.fastq.gz for reverse path its showing same error.
for directory I am sharing screen shot please find it.

Try with adding the extension of manifest file. e.g. "--input-path manifest.txt ". Only manifest.txt works for me on WSL2 (Qiime2). .csv does not work. Don't know why.

@kindergarten I TRIED BUT IT NOT WORKED.

That is bummer.
Make a directory c/samrendra/NGS and put your files here.
For absolute path, use /mnt/c/samrendra/NGS
In WSL cd /mnt/c/samrendra/NGS. Run qiime from here.
Manifest file must be manifest.txt
That is how I use Qiime in WSL2 (Windows 11).

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thanks, @kindergarten but how can make a directory c/samrendra/NGS ? could you help me ?

In Windows file explorer, open C drive. Right click to make new folder samrendra. Open c/samrendra. Right click to make folder NGS. Open folder NGS. Copy fastq files here.

Thanks i will try this, after making directory will i write absulte path as cd /mnt/c/samrendra/NGS? right ?

In the manifest file, absolute path will be /mnt/c/samrendra/NGS

thank you one more thing you mentioned in earlier message "In WSL cd /mnt/c/samrendra/NGS" what is this ?

WSL is your Ubuntu terminal. In terminal, cd /mnt/c/samrendra/NGS.

@kindergarten Ok i got it but my question is when I have to use this cd /mnt/c/samrendra/NGS?
I will make directory in c drive as you told me and the manifest file also will make as you suggest.

actually, I am not familiar with WSL, I have used mac os it working fine for me last 2 years but due to space and other issues, I am trying with windows. so I install the QIIME2 with WSL. and facing problems in importing data for the last three days. so if I am asking silly questions please don't mind.

No worries. I had tough time trying to figure out WSL2/Windows11/Ubuntu.

Here is what I have in mind

conda activate qiime2-2022.8
cd /mnt/c/samrendra/NGS (This step is optional. I would run qiime here to keep all input and output files in one place. You can work from any directory you want. On WSL, you must use /mnt/...)
Then run your script.


@kindergarten its working thanks you so much.

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