No --output-dir option when exporting

[usfmicrobiome (microbiome team)]

Hi all,
I am also getting problem while exporting feature table from QIIME 2 after clustering.
Msg come sno option --output-dir.
The code I am writing is:
qiime tools export tbl-cr-97.qza --output-dir .
Pleas suggest what to do?
Thanks in advance.
I tried different ways like output path/ output format etc no luck.

[jwdebelius (Justine Debelius)]

Hi @usfmicrobiome,

Welcome to the forum!

When I check the exporting tutorial, it looks like --output-dir is not an option for this function. (It looks like --output-path is a better option.

https://docs.qiime2.org/2021.11/tutorials/exporting/

In general, I highly recommend checking the docs with any function using the --help flag.

So, in your case:

qiime tools export --help

Best,
Justine

[usfmicrobiome (microbiome team)]

Thanks Justine, I will check.
best,
Shalini