Accessing data files in WSL

[joaomiranda (João Miranda)]

Hi @lizgehret I have new doubts! Could you help me, please?
I don't know how to import my metadada, I built an .txt file for my metadada like the metadada tutorial in qiime page, but when i try to import this type of data in qiime2 the tutorial shows two ways: download the URL or use the wget command.
My question is: how could I import my file without an URL? Is there any specific command for this?
By the way, I'm using qiime in a WSL system, and I want to import this metadata with an manifest file to begin my sequences analysis.

Thanks in advance

[lizgehret]

Hi @joaomiranda,

@joaomiranda

I don't know how to import my metadada, I built an .txt file for my metadada like the metadada tutorial in qiime page, but when i try to import this type of data in qiime2 the tutorial shows two ways: download the URL or use the wget command.
My question is: how could I import my file without an URL? Is there any specific command for this?

In our Metadata tutorial, we are utilizing a sample metadata file, which is why the URL/wget commands are provided there. You can move through the tutorial with your own .tsv file by simply replacing the filename from the tutorial with your specific metadata file.

@joaomiranda

By the way, I'm using qiime in a WSL system, and I want to import this metadata with an manifest file to begin my sequences analysis.

If you are trying to import your metadata with a .fastq manifest file, you can refer to this tutorial for instructions on how to import that as well.

Hope this helps!

Cheers,
Liz

[joaomiranda (João Miranda)]

Ok @thermokarst , my apologizes, I'm new in qiime2, bioinformatics and texting in English, so I will continue to solve my problem in this new topic.

Hi @lizgehret

About the manifest file and metadata are separated, I've already imported the manifest file, now I'm trying to import my metadata file.
So I tried to use the same wget command replacing the "sample-metadata.tsv" in the tutorial to my metadata's file name: "Metadados.txt".
Here is:

wget
-O "Metadados.txt"
"/mnt/c/users/Joao/desktop/FASTQ_16S/Metadados.txt"

And in the WSL here is the error:
(qiime2-2021.4) joaomiranda@DESKTOP-TH6UO0J:~$ wget
-O "Metadados.txt"
"https://data.qiime2.org/2021.4/tutorials/moving-pictures/Metadados.txt"
--2021-08-05 18:34:30-- https://data.qiime2.org/2021.4/tutorials/moving-pictures/Metadados.txt
Resolving data.qiime2.org (data.qiime2.org)... 54.200.1.12
Connecting to data.qiime2.org (data.qiime2.org)|54.200.1.12|:443... connected.
HTTP request sent, awaiting response... 404 NOT FOUND
2021-08-05 18:34:32 ERROR 404: NOT FOUND.

I think I'm not understanding how could my file that is in my computer can be imported in a command that makes a download directly from web.
Here is my metadada: Metadados.txt (1.9 KB)

Thanks for the attention

[Keegan-Evans]

@joaomiranda,
The wget command in the tutorial is simply so that you can get the sample metadata file that we are providing for the tutorial onto your computer. Since your file is already on your computer, as long as it is correctly constructed, you are ready to use it in your analysis.

For example, if you were trying to run demux, you would use the metadata file by specifying it with -m-barcodes-file ./path/to/your/metadata-file.tsv. To see this in action, you might want to checkout the Moving Pictures tutorial.

You could also check out the metadata visualizer on the "Metadata in QIIME 2" page. This would also give you a chance to inspect your file and make sure that everything is setup correctly.