I am following the q2-fragment-insertion tutorial.
qiime fragment-insertion sepp
But there was a problem with the command: (1/1?) no such option: --i-reference-database
in the script help, --i-representative-sequences doesn't exist!
--i-representative-sequences ARTIFACT FeatureData[Sequence]
The sequences to insert [required]
--i-reference-alignment ARTIFACT FeatureData[AlignedSequence]
The reference multiple nucleotide alignment used to
construct the reference phylogeny. [optional]
Phylogeny[Rooted] The rooted reference phylogeny. Must be in sync with
reference-alignment, i.e. each tip name must have
exactly one corresponding record. [optional]
following de pd-mice tutorial in qiime2's page the same error occurs
Ist he command you typed here the exact command you used where ever you’re running your code?
If so, please try
qiime fragment-insertion sepp \
--i-representative-sequences rep-seqs.qza \
--i-reference-database sepp-refs-gg-13-8.qza \
\ wraps the line in bash, which may be the source of your problem here.
thanks, but in practice, I write it all together,
qiime fragment-insertion sepp --i-representative-sequences rep-seqs.qza --i-reference-database sepp-refs-gg-13-8.qza --o-tree insertion-tree.qza --o-placements insertion-placements.qza
I separated it to be readable
“” aren’t the source
Okay. I’d suggest double checking your spaces then (only one between each flag and command). Then, have you tried copying and pasting the flag names exactly? I can’t find the spelling mistake, but I’m notoriously bad at finding spelling errors in my own work and other people’s. However, copying and pasting the flags gets me around that because then I don’t have to spell or see spelling mistakes in very long flags. (You could also try tab-complete here if you have it set up.)
in both tutorials use the option
but in the scrip help, this option (–i-reference-database) is not listed
Thanks for your patience with vacation.
The tutorial is up to date for qiime2-2019.10, but it looks like you’re working with an older version. So, try updating qiime2-2019.10 or following the documentation for your current version.
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