I want to train my classifier using the new SILVA 138 release. I checked SILVA database, but the available formats are different from those of the previous releases. In other word, in 128, and 132, I downloaded a package of files from which I use silva_132_97_16S.fna by converting to qza, then consensus_taxonomy_7_levels.txt to generate a reference taxonomy.
I have attached the link of the new SILVA release and need to know which files should I download to train the classifier.
Everything you need is on the Data Resources page, which was updated to reflect the 2020.6 release.
Specifically, the pre-made SILVA 138 classifiers are here, and the files used to make them are here. If you’d like a little more control preparing a SILVA database in your own way, feel free to make use of our new tool: RESCRIPt. This was used to make the current QIIME 2 compatible SILVA 138 release.
Thank you! I checked Data resource page, but I felt uncomfortable when reading the warning message. I will try the new tool and keep the forum updated.
Thanks again
Eman
RESCRIPt an external plugin that you need to install. The very first link in the tutorial links you to the github page with the instructions. All you need to do is activate your qiime environment and skip right to the pip install command step, and go from there.
I've copied and pasted the command you posted earlier into my terminal and it worked without issue. Did you run the command any differently from what you initially posted?
This implies you are using combinations of --p-version and --p-target that are not allowed. That is you can only run
Good to know! So, that means no worries and it is recommended to use the posted files. Actually, I am just curious to try the updates in Qiime2 and SILVA.
Thanks so much
I am wondering if there is something wrong with the install? One last test you can try is to not set the parameters, and use the defaults (with and without the --p-include-species-labels option). That is, if you run the following:
It will download and parse the SILVA 138 NR 99 files (w/o species labels), as these are set by default. This will ensure the problem is not coming from some odd hidden characters that are being entered in on the command line (that is, try typing the commands rather than pasting them). That’s all I can think of at the moment.
One more thing that I forgot to mention, I created an environment within qiime environment to install rescript and other plugins (as in the noted website). That means every time I use these plugins, I have to activate both qiime, then rescript environment. Is that correct?
No need to have it set up that way. As I mentioned earlier:
This is also mentioned this on the github page:
First create a conda environment and install relevant dependencies (you can skip this step and install RESCRIPt in a conda environment containing QIIME 2 2020.2+, which should contain the necessary dependencies/versions)
That is, once you install QIIME 2 as outlined here, do the following:
conda activate qiime2-2020.2 # or later version, 2020.6
pip install git+https://github.com/bokulich-lab/RESCRIPt.git
qiime dev refresh-cache
qiime rescript --help
