Error importing Data: Moving pictures tutorial

Hello,

I am new to Qiime and over the past 2 days, I have searched and tried everything possible to import the files to Qiime. I continue to get this error (please see below). Can someone please tell me how to resolve the issue.

[email protected]:~/qiime2-moving-pictures-tutorial$ ls
emp-single-end-sequences sample-metadata.tsv
[email protected]:~/qiime2-moving-pictures-tutorial$ qiime tools import \

–type EMPSingleEndSequences
–input-path emp-single-end-sequences
–output-path emp-single-end-sequences.qza
/usr/bin/qiime: 47: exec: /usr/lib/qiime/bin/tools.py: not found
[email protected]rtual-box:~/qiime2-moving-pictures-tutorial$

1 Like

Hi there @Fabs - looks like you are running QIIME 2 commands in a QIIME 1 environment. QIIME 2 is an entirely different software platform - please check out docs.qiime2.org for more info on how to install and get started. Thanks! :qiime2:

2 Likes

WOW! How I didn't notice >5x's that I was downloading the wrong QIIME file, I do not know, but thank you for pointing this out.

Can I ask you one last question: I tried to run the code for creating a QIIME artifact, and although I downloaded the files to my desktop and saved them as the tutorial states (please see picture below) when I run the code, I get the following error.

There was a problem importing emp-single-end-sequences:
_Missing one or more files for EMPSingleEndDirFmt: 'sequences.fastq.gz'

I saw a previous thread that said that the "emp-single-end-sequence" file needs to contain the 2 files (barcodes and sequences), which they do, on my desktop, not on the directory I created. Would you mind telling me how I can do this?

P.S I know I can use the "wget" code and this actually works, but my data will be on my desktop, so I want to make sure I know how to properly do this for my own work.

Desktop file
image

Virtual Directory file

Sorry, I sent you the picture of the wrong folder, please see attached.

image

just create a directory (on your desktop is fine). Drag and drop in the sequences.fastq.gz and barcodes.fastq.gz files and import that directory rather than the individual files.

I hope that helps!

How do I import the directory? I created the directory w the same name, as per the tutorial, moving pictures, but when I run the code in question, it says missing one or two files. On the desktop, the files are in the directory, on the Qiime directory they are not. So am slightly confused. Could you expand and or send me a more in-depth explanation or a link where it shows how to do this. The tutorials online from QIIME have not worked.

Thanks

Sounds like you are using virtual box and may not have set up the shared folder correctly. Please see these instructions.

You have shown where the barcodes are but not the sequences. Could you show us the full contents of the directory that you are trying to import? It should contain those 2 files and nothing more.

I managed to import the files, but I just downloaded them directly to the virtual box, as opposed to the desktop and this worked properly. Although, I would like to know how I can get them from my desktop (sharedfolder) into my working directory as I have over 216 demultiplexed files that I will eventually need to import.

Please check out the link that I gave above, it provides instructions on setting up the shared folder:

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