Hi @jwdebelius I have tried and replaced $PWD by actual path home/samrendra/NGS-SEQUENCES/S1-R1.fastq.gz it but its not working. do you have any Idea why i am facing this issue?
Hi @SAMRENDRA01,
You still have a relative path. Absloute paths need to be prefixed by a "/". So, your directory is in /home/etc.
Best,
Justine
Thanks for the reply but I have also tried this command. I think you overlooked that. please see the attached screenshot, mentioning the absolute path by an arrow.
Hi @SAMRENDRA01,
Your file isn't where you say it's located. You need to find it on your system. Go to that directory, print the directory ($pwd
), then use that.
Best,
Justine
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.
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).
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.
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