Qiime diversity core-metrics-phylogenetic error

[mly (L.Ma)]

Hi when i follow the “Moving Pictures” tutorial — QIIME 2 2018.2.0 documentation , 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

[colinbrislawn (Colin J Brislawn)]

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