Manifest file does not exist error

[suetli19]

Hi, I have trouble importing manifest file into qiime2.

This is the manifest file I created:
manifest.csv (9.2 KB)
This is the command line I input:

However, it gives me this error.

Please help. Thank you!

[jwdebelius (Justine Debelius)]

Hi @suetli19,

Welcome to the forum!

Your error is telling you that qiime2 cannot find the file. If you know the file exists, it may mean youre in the wrong directory. Try pwd to check your current working directory and ls to list the files. If the manifest isnt in your current folder, you'll need to change directories to get to where the manifest is, or provide the correct path.

Best,
Justine

[suetli19]

I got these after putting in the commands, but not sure what it means?

[suetli19]

Hi @jwdebelius ,

I have moved the manifest.csv file into the current working directory and input the same command as just now.

But this time, it gave me another error as shown in the screenshot here:

I don't really understand what this means. Is there anything that I should change?

Regards,
Suet Li

[jwdebelius (Justine Debelius)]

Hi @suetli19,

This new message is telling you thaat you have a non UTF-8 character somewhere. This means that you have some kind of special character (maybe like a ä, ø, or ñ) in your file. There was a pretty extensive thread discussing how to fix tis a while back:

metadata problem utf-8 codec can't decode byte invalid start byte

Hi @mudbugecology, It appears that the error: is being caused by special characters (i.e. †) in your data files. When I open your file n Excel I see: [excel_ss] Which looks like this in my Raw Text Editor BBEdit. I am also showing the invisible text like tabs (triangles) and spaces (dots): [bbedit_ss] I would highly recommend that you always use a raw text editor like NotePad, Atom, BBEdit, etc... to view the files prior to importing them. Tools like MS Word & Excel can sometimes hide th…

Best,
Justine

[suetli19]

Based on this discussion, I viewed the manifest.csv file using Notepad and this is what I saw:

I'm not sure how to fix this in Excel?

Regards,
Suet Li

[jwdebelius (Justine Debelius)]

Hi @suetli19,

That looks like an excel file that was renamed and saved as a CSV. How did you generate your manifest file?

Best,
Justine

[suetli19]

Yes. It was an excel file and I renamed it as CSV.
manifest.csv (9.2 KB)

[suetli19]

I think I will need to save the excel file as CSV instead of renaming.

After saving it as CSV, this is what I've got:

Is this what we are supposed to see?

[jwdebelius (Justine Debelius)]

Hi @suetli19,

That looks like a CSV! However, I’d double check the import tutorial to make sure that’s the right file format for your command.

I’d also double check your paths. It looks like you might be on a virtual machine; are your files in that location on the VM?

Best,
Justine

[suetli19]

Hi @jwdebelius ,
The files are not in the VM.
However, I finally figured out that I just needed to change the manifest file formats into this:

And, the command line should be 'Phred33' instead of 'Phred33V2' if I'm importing a CSV file.

Thanks a lot!

Regards,
Suet Li