I keep getting this error. I don't know what im doing wrong
(qiime2-2021.11) qiime2@qiime2core2021-11:~/Desktop$ qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path metadata.txt
--output-path paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2
There was a problem importing metadata.txt:
metadata.txt is not a file.
Hi @cotomato21,
Welcome to the 
forum!
From your command above, you are attempting to import a file of type SampleData[PairedEndSequencesWithQuality] and the input path for this file is metadata.txt. I cannot see the contents of this file on my end but I assume this is not the file you intend to import, since it is titled as a metadata file. This command would need to be run with the associated sample data in order to successfully import and convert that file to a QIIME 2 Artifact for subsequent downstream analyses within the framework.
If you are actually attempting to import the metadata file itself, that is not a necessary step - metadata files do not need to be imported/converted to QIIME 2 Artifacts.
I'd recommend checking out a couple of resources on our docs page (linked below) that may help further clarify how metadata is handled within QIIME 2, and how to import your sequence data as well.
Metadata in QIIME 2
Importing Data
Hope this helps!
Cheers 
Hey @cotomato21,
Just wanted to circle back on this and provide you with some additional information here - in my original response, I interpreted your commands as being intended for a sequence file import vs. a manifest file import. My apologies if this was incorrect!
Assuming this is a manifest file - it seems as though the issue lies with the metadata.txt file in your --input-path command. The error message you received (below) could mean a couple of things.
metadata.txt is not a file
This could be a directory (vs. a single file), or it may not exist under your current working directory, or be listed under a different file name.
In any case - I'd recommend locating the manifest file on your machine, double checking the name of the file, and that you are including the full path to that file in your command.
More details on manifest files can be found here as well, for your reference.
Hope this helps!
Cheers
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.