Alpha and beta diversity analysis error

Dear Qiime2 forum communities.
I got stuck in the Alpha and beta diversity analysis.
I ran the below:

qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table table.qza
--p-sampling-depth 12386 \
--m-metadata-file sample-metadata.tsv
--output-dir core-metrics-results

After that, I got an error
--m-metadata-file sample-metadata.tsv \

--output-dir core-metrics-results
--m-metadata-file: command not found

I confirmed my metadata file in the same working path and the file was validated using Keemei. My Qiime2 version is a 2022.8.
I also checked "--m-metadata-file" is listed in the parameter of qiime diversity core-metrics-phylogenetic \

I would like to ask you for troubleshooting. Your assistance is highly appreciated.

Hello,

In bash every line should be finished with \ if you want to continue the command in the nextline. Without it bash executes the command.
Please rewrite the command with \ in every line except the last one.

Cheers
Valentyn

1 Like

Thank you, that helps. :slight_smile:

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