mly
(L.Ma)
1
Hi when i follow the https://docs.qiime2.org/2018.2/tutorials/moving-pictures/ , doing the phylogenetic diversity analysis, commands are exactly same as the tutorial, as following:
qiime diversity core-metrics-phylogenetic \
–i-phylogeny rooted-tree.qza
–i-table table.qza \
–p-sampling-depth 1109
–m-metadata-file sample-metadata.tsv
–output-dir core-metrics-results
but got error.
Usage: qiime diversity core-metrics-phylogenetic [OPTIONS]
Error: Got unexpected extra arguments (1109 sample-metadata.tsv core-metrics-results)
anybody has the same “unexpected extra arguments”?
Thank you
Good morning,
I think I know what’s going on!
So, most linux commands are on a single line. Like this:
mkdir emp-single-end-sequences
But you have probably noticed that some of the commands in the tutorial are over many lines.
qiime tools import \
--type EMPSingleEndSequences \
--input-path emp-single-end-sequences \
--output-path emp-single-end-sequences.qza
Notice how the \
is used to show that this command it going to continue on the next line.
Your command is missing the \
backslash, so qiime is getting confused. Try running this:
qiime diversity core-metrics-phylogenetic \
--i-phylogeny rooted-tree.qza \
--i-table table.qza \
--p-sampling-depth 1109 \
--m-metadata-file sample-metadata.tsv \
--output-dir core-metrics-results
Colin
1 Like
system
(system)
Closed
5
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