Hi @Stephanieorch,
Looks like ggq2.qza is a TaxonomicClassifier, not a FeatureData[Sequences] artifact. This is not the file that you want to use. Instead, use the reference sequences that you used to train ggq2.qza.
I got the taxonomic classifier online from greengenes. Is there a way to go backwards? As in from a TaxanomicClassifier to FeatureData[sequences]? Thank you for all of your help!
Ah, thanks for clarifying — I thought perhaps you trained this file yourself, but it sounds like maybe you downloaded one of the classifiers from here?
No, there is no way to go backwards, but you just need to download a different file. You can download the full Greengenes 13_8 release (linked to on this page) and find an appropriate reference sequence fasta file (in the rep_set directory of the zipped directory that you will download)
It looks like the parameter flag has a single em-dash (—i-table) instead of two hyphens (--i-table) preceding the parameter name. Same with all other parameters. This often happens (the text is usually auto-corrected) if writing the commands in microsoft word or some other text programs. Typing in the correct parameter names into your terminal should fix this.
It looks like you are still using a trained classifier, not the representative sequences fasta file. You should download this archive, unzip, and look for the rep_set directory, which will contain a number of sequence files clustered at different similarity %s.
When copying from terminal to the qiime2 forum, my 2 hyphens changed to a single em-dash. So I am getting the error when using 2 hyphens.
Regarding the representative sequences fasta file does this file name look correct: 99_otus.fasta?
Hi @Stephanieorch! Thanks for the command, that was really helpful! Since you are trying to write your command across many lines, you need to end all but the last line with a \ — this tells your shell “hey bud, wait just a minute, I still have more stuff to put into this command.”
Alternatively, you could just write the entire command on one line, then you wouldn’t need to “escape your line breaks” (that is the technical term for why you would need to add the trailing slashes). So, pick one option, and give it a shot! Personally I like the multi-line approach, it helps me re-read my commands later so that I know what I did. Good luck!
I was so focused on your line endings that I missed the fact that you weren’t running a qiime command, you were actually running a vsearch command. Besides the line endings, you also need to prepend qiime to your command, in your to actually run the q2-vsearch plugin. I updated my code block above to reflect that change.
