problem facing in importing data in WSL

[SAMRENDRA01 (SAMRENDRA SINGH)]

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?

[jwdebelius (Justine Debelius)]

Hi @SAMRENDRA01,

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

Best,
Justine

[SAMRENDRA01 (SAMRENDRA SINGH)]

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.

[jwdebelius (Justine Debelius)]

Hi @SAMRENDRA01,

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.

Best,
Justine

[SAMRENDRA01 (SAMRENDRA SINGH)]

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.

[kindergarten]

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.

[SAMRENDRA01 (SAMRENDRA SINGH)]

@kindergarten I TRIED BUT IT NOT WORKED.

[kindergarten]

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).

[SAMRENDRA01 (SAMRENDRA SINGH)]

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

[kindergarten]

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.

[SAMRENDRA01 (SAMRENDRA SINGH)]

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

[kindergarten]

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

[SAMRENDRA01 (SAMRENDRA SINGH)]

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

[kindergarten]

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

[SAMRENDRA01 (SAMRENDRA SINGH)]

@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.

[SAMRENDRA01 (SAMRENDRA SINGH)]

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.

[kindergarten]

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.

[SAMRENDRA01 (SAMRENDRA SINGH)]

@kindergarten

cd /mnt/c/samrendra/NGS

@kindergarten its working thanks you so much.