Manifest file import failed

Hello I am using qiime2-2020.11 and have a problem importing manifest file (demultipled data). Any help is much appreciated.

the error return is bellow.

zsh: no matches found: ‘SampleData[PairedEndSequencesWithQuality]’ --input-path

Here is the script I used:

qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path ManifesFile.tsv
–output-path demux.qza
–source-format PairedEndFastqManifestPhred33

Hi @baronhabtom,

Welcome to the :qiime2: forum!

I think the issue, based on what you're showing here, is possibly that you didn't wrap your text correctly. You need to use the \ character between lines, so your re-formatted command would look like this:

qiime tools import \
 --type 'SampleData[PairedEndSequencesWithQuality]' \
 --input-path ManifesFile.tsv \
 --output-path demux.qza \
 --source-format PairedEndFastqManifestPhred33

if this isn't correct, could you please copy and paste the command from the terminal? You can format it like text using the (`) symbol.


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Hi Justine, thank you for your kind support. I get two different errors: one is when the code is in one line and there is when the code is wrapped.

(qiime2-2020.11) [email protected] bioner % qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path ManifestFile.tsv --output-path demux.qza --source-format PairedEndFastqManifestPhred33
Usage: qiime tools import [OPTIONS]

Import data to create a new QIIME 2 Artifact. See
for usage examples and details on the file types and associated semantic
types that can be imported.

–type TEXT The semantic type of the artifact that will be
created upon importing. Use --show-importable-types
to see what importable semantic types are available
in the current deployment. [required]
–input-path PATH Path to file or directory that should be imported.
–output-path ARTIFACT Path where output artifact should be written.
–input-format TEXT The format of the data to be imported. If not
provided, data must be in the format expected by the
semantic type provided via --type.
–show-importable-types Show the semantic types that can be supplied to
–type to import data into an artifact.
Show formats that can be supplied to --input-format
to import data into an artifact.
–help Show this message and exit.

                There was a problem with the command:                     

(1/1?) no such option: --source-format
(qiime2-2020.11) [email protected] bioner %

(qiime2-2020.11) [email protected] bioner % qiime tools import\

–type ‘SampleData[PairedEndSequencesWithQuality]’\

–input-path ManifestFile.tsv\

–output-path demux.qza\

–source-format PairedEndFastqManifestPhred33

Usage: qiime tools [OPTIONS] COMMAND [ARGS]…

Try ‘qiime tools --help’ for help.

Error: No such command ‘import–type’.

zsh: command not found: --input-path

zsh: command not found: --output-path

zsh: command not found: --source-format

(qiime2-2020.11) [email protected] bioner %

Hi @baronhabtom,

If you check the output error, you’ll find the problem with the first command in the docs:

Is there a --source-format flag in for this command? (Note that I reformmated above based on the command verses going in depth wtih the help docs. I recommend checking the docs for pretty much any command you run and (--help will print them for you.)

In your second error, it looks like you didn’t prefix the “” with a space. So, qiime tools import\ should be qiime tools import \, etc fo the rest of the commands.


Hi Justine,
Thank you for your quick and kind support. I found my mistake. It was the apostrophe mark around the command, –type ‘SampleData[PairedEndSequencesWithQuality]’
In my macbook I have three types of these and wasn’t aware that they are so different.

Thank you,

Hi @baronhabtom,

I’m glad you sorted it out! And yeah, depending on the keyboard and language it can be hard. I have a non-english keyboard, and there is a way to change the layout on a macbook (you can switch your preferred languages if you need to be multi-regional), which semi helps. You can also use double quotes (") in place of the single quote there.


The no-space between the command and backslash noticed in the second error was also another problem.
Thank you

1 Like