I'm trying to run the taxonomy analyses but I found that error: Duplicate semantic type ('RNASequence') defined in plugins: 'rescript' and 'type'. What can I do to solve that? How can I remove the RESCRIPt to try to install it again?
Thanks for bringing this to our attention, would you mind posting a screenshot of the error and output of
qiime info so that we can see the versions of QIIME2 and RESCRIPt that you have running for opening an issue to fix this? Regarding removing RESCRIPt, it is not really trying to remove an individual plugin, it is best to remove the entire environment with
conda env remove -n <the-name-of-your-environment> and then doing a fresh install of QIIME 2 using the instructions in the docs.
Hi Keegan, thanks for your answer!
I think that I install the RESCRIPt in the qiime2 environment since firstly I can't run the taxonomy analyses because I can't download the Silva data. After I've had problems with the xmltodict module and them, when I solve it, the problem is with the duplicate semantic type that I can't solve.
Do I need to deinstall the qiime2 conda environment and create it again? I need to create independent environments to qiime and RESCRIPT?
Yes, I think removing and installing a new QIIME 2 conda environment would be the easiest path forward, I will have to chat with some of the other moderators about how to go about using RESCRIPt, I have not had a chance to dig through the code for it/am not sure why it is producing a duplicate semantic type/I have not heard of this coming up before and I am not sure the best way to deal with that part of your issue currently.
It sounds like you are installing an older version of RESCRIPt into QIIME 2. There was a point in which we added an "RNASequence type" into RESCRIPt, so that we can read and handle RNA sequence data. Eventually, this type was moved into the base QIIME 2 types and subsequently removed from the RESCRIPt plugin.
If trying to install the older version of RESCRIPt, which has its own version of RNASequence, it will cause the error you are seeing, as there is now a version of RNASequence already in the latest version of QIIME 2.
As you appear to be using
qiime2-2022.2, the only way I can see that the "Duplicate semantic type ('RNASequence')" is being raised, is if a local / older version of RESCRIPt is being used to install into QIIME 2. If this is not the case then I suspect the environment is corrupted in some way.
I would proceed with @Keegan-Evans suggestion and remove your current version of QIIME 2 and reinstall a fresh QIIME 2 environment. Then install RESCRIPt as outlined on the github page. I'd highly recommend that you only copy and paste end execute one line at a time. Sometimes pasting multiple commands into the terminal at once can cause problems.
@Patricia_Azevedo I noticed that your "conda activate ..." command ends with a
/. This is why your subsequent commands are not working, as the system is reading everything as one long command.
I'd execute the following one line at a time:
conda activate qiime2-2022.2
conda install -c conda-forge -c bioconda -c qiime2 -c defaults xmltodict
pip install git+https://github.com/bokulich-lab/RESCRIPt.git
qiime dev refresh-cache
Let us know if this works out.
Thanks so much!
I removed the environment conda, make another one and followed your instructions... It's worked.
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