Importing error

[walsh0311 (Daniel Walsh)]

Thank you for the input, that was helpful. I ran into some more problems if you wouldn’t mind. I read some of the introductory material and proceeded to the “moving pictures” tutorial ( https://docs.qiime2.org/2018.6/tutorials/moving-pictures/ ).

Under the “obtain and import” section it says to copy and paste the following command:
mkdir emp-single-end-sequences
However, I got an error message. Any ideas?

I decided to keep following the protocol anywas, not expecting it to work. By the tiem I got to the end of the following command lines it gave another error message. Lines:
qiime tools import
–type EMPSingleEndSequences
–input-path emp-single-end-sequences
–output-path emp-single-end-sequences.qza

I wasn’t surprised it didn’t work. But, along the way I came across a problem. The protocl asks me to save files using a “/”. For example: emp-single-end-sequences/barcodes.fastq.gz.
But my computer says files cannot be saved using this character. How will this affect my pipeline?

Thanks in advance!

[colinbrislawn (Colin J Brislawn)]

Hello Daniel,

Thanks for using Qiime 2. Welcome! The tutorials are a great place to start, so let's see if we can get these working for you.

@walsh0311

Under the “obtain and import” section it says to copy and paste the following command:
mkdir emp-single-end-sequences
However, I got an error message. Any ideas?

What was the error message? We are looking for clues about what caused this problem, so any information you found would be helpful. Also, are you using Windows or a Mac? ?

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@walsh0311

I wasn’t surprised it didn’t work. But, along the way I came across a problem. The protocl asks me to save files using a “/”. For example: emp-single-end-sequences/barcodes.fastq.gz.
But my computer says files cannot be saved using this character. How will this affect my pipeline?

I think I can explain this one! So this file
emp-single-end-sequences/barcodes.fastq.gz
is a file in a folder

- folder
  - a_file.txt
  - another_file.txt.gz
- secondfolder
  - aFolderInAFolder
    - a_file.txt
- emp-single-end-sequences
  - barcodes.fastq.gz

So if I want to refer to that last file in the list, I also need to show what folder it's in. So would say
emp-single-end-sequences/barcodes.fastq.gz

I could also say
folder/another_file.txt.gz
or
secondfolder/aFolderInAFolder/a_file.txt

So the folder names and file names are separated/by/slashes, which is why you can't have /slashes/ in the file name itself.

Let me know if that helps!

Colin

[walsh0311 (Daniel Walsh)]

Hi Colin, thanks for the response. I am operating on windows. The error mess age was:
bash: sample-metadata.tsv: command not found.
I still am not sure why this doesn’t work.

Concerning your answer about the saving and slashes, I interpret your explanation:

“save file as emp-single-end-sequences/barcodes.fastq.gz”

means I am supposed to create a file called “emp-single-end-sequences” and create a file in that folder named "barcodes.fastq.gz. Is this correct?

Thanks again for all your help!

[colinbrislawn (Colin J Brislawn)]

Hello Again Daniel,

@walsh0311

I am operating on windows.

There's the problem! Qiime only works on unix based on operating systems (linux or OSX). So you can start by install qiime inside of a VM so you can run Linux on your Windows machine.

Once you have the VM set up, try that tutorial again. Once you are using Linux, those tutorials should work much better. Keep me updated!

---

@walsh0311

means I am supposed to create a file called “emp-single-end-sequences” and create a file in that folder named "barcodes.fastq.gz. Is this correct?

The other way around. You would make a folder called emp-single-end-sequences, then inside that folder you could place a file called barcodes.fastq.gz. The path to the file has to pass through the folder first.

emp-single-end-sequences/barcodes.fastq.gz

firstFolderYouOpen/SecondFolderYouOpen/thefileyouwant.txt 

Colin