Importing From Local files

Hello, I am extremely new to bioinformatics and Qiime2. I followed the tutorials for installing ubuntu and conda then qiime2. I checked that I could run commands then followed the moving picture tutorial. Following that, I started on my own data which is on my local drive. I had some errors occur such as:
(1/1) Invalid value for '--input-path': Path 'MiseqTickRunsSample_Run' does
not exist.
I found some support in another post on the forum but the solution there did not help me. I tried this command:
(qiime2-2021.11) [email protected]:~$ qiime tools import \

--type type EMPPairedEndSequences
--input-path MiseqTickRuns/Sample_Run
--output-path MiseqTickRuns/Sample_Run
and got:
(1/2) Invalid value for '--input-path': Path 'MiseqTickRuns/Sample_Run' does
not exist.
(2/2) Got unexpected extra argument (EMPPairedEndSequences).

I then attempted:
(qiime2-2021.11) [email protected]:~$ qiime tools import \

--type type EMPPairedEndSequences
--input-path C/Users/Austin Brown/Desktop/MiseqTickRuns
--output-path C/Users/Austin Brown/Desktop/MiseqTickRuns
and got:
(1/2) Invalid value for '--input-path': Path 'C/Users/Austin' does not exist.
(2/2) Got unexpected extra arguments (EMPPairedEndSequences
Brown/Desktop/MiseqTickRuns Brown/Desktop/MiseqTickRuns)

My question is: Have I messed up my directories somewhere or is the fact that my C/Users/Austin Brown has a space causing the issues?

Hi @Waldo,

Welcome to the :qiime2: forum!

I'm seeing about 4 possible problems with your command that might explain the issue.

First, can you confirm the system you're running on. Your paths look like microsoft paths (C://Austin would be a windows path; a linux/osx path might look like /Users/Austin/Desktop)

Second, please double check the format of the command, you're getting a second error (I usually find it easiest ot reference to the import tutorial for this

(2/2) Got unexpected extra argument (EMPPairedEndSequences).

Finally, in your first command, are you actually on the desktop? It looks like it, but I would suggest double checking. Is your MiseqTickRuns/Sample_Run file actually located there? (Try pwd, ls and cd to check your current directory, file contents, and change directory. I found a quick command line tutorial really helpful when I was starting!)

Finally, you need a \ character to to wrap every line. So, the command would be

qiime tools import \
--type 'EMPPairedEndSequences' \
--input-path MiseqTickRuns/Sample_Run \
--output-path MiseqTickRuns/Sample_Run \

Finally, are you sure your data is in the EMP format? If you're not sure, read about import formats and check with your sequencing center about how the data was handled.



Thank you for the response! Sorry for the delay, but the holiday season got crazy. I managed to fix the issues and am progressing in the analysis. Thank you for the suggestions, they really helped.