Hi everyone!
I'm a bit puzzled about training the classifier, and I'd really appreciate your help.
I followed the "Training feature classifiers with q2-feature-classifier" tutorial to train an ITS classifier.
I should note that I chose the resource file from the UNITE (fungal ITS) section of the QIIME release.
Did I do the training correctly, or should I be using the "Fungal ITS analysis tutorial"?
Hello @Beh_Yaad,
There's an even newer tutorial for building an ITS classifier using RESCRIPt.
This is how I do it:
If you are looking for full length ITS UNITE, I have files already trained that you can download here: GitHub - colinbrislawn/unite-train: 🍄 Qiime2 ITS classifiers for the UNITE database
I'm interested in the UNITE database, so let me know if there is some other way you wanted to use these resources.
Hi Colin,
Thanks a lot for your solution.
When I ran the command 'Evaluate the classifier', I got the following error:
Plugin error from rescript:
A plugin named 'longitudinal' could not be found.
First, I'd appreciate it if you could demonstrate how to resolve the error.
Next, should I run the command using the 'qiime2-shotgun-2023.9' or 'rescript' environment?
Third, if I intend to use your pre-trained ITS classifier, should I apply and follow the 'Training feature classifiers with q2-feature-classifier' tutorial?
Thanks ahead of time!
Sure, I'm happy to help.
Can you post the full command you ran, along with the conda environment you ran it in?
Uh... I run these right in qiime2-amplicon-2023.9, so maybe the shotgun env is the issue?
The classifiers I distribute on GitHub are pre-trained, so you can skip directly to using them with
qiime feature-classifier classify-sklearn
(Just wanted to let you know that I've installed the latest Conda update.
WARNING: A newer version of conda exists. <==
current version: 23.7.3
latest version: 24.1.0)
1- Sure, here is the full command I ran:
(qiime2-shotgun-2023.9) uw-user@V74RMK29HK qiime2-shotgun-2023.9 % qiime rescript evaluate-fit-classifier
--i-sequences uniteDB/sequences-filtered.qza
--i-taxonomy uniteDB/taxonomy-no-SH.qza
--p-n-jobs 2
--o-classifier uniteDB/classifier.qza
--o-evaluation uniteDB/classifier-evaluation.qzv
--o-observed-taxonomy uniteDB/predicted-taxonomy.qza
qiime rescript evaluate-taxonomy
--i-taxonomies uniteDB/taxonomy-no-SH.qza uniteDB/predicted-taxonomy.qza
--p-labels ref-taxonomy predicted-taxonomy
--o-taxonomy-stats uniteDB/both-taxonomy-evaluation.qzv
Plugin error from rescript:
A plugin named 'longitudinal' could not be found.
Debug info has been saved to /var/folders/d1/l587ml155pq01sd8nm1f9d2r0000gr/T/qiime2-q2cli-err-4crrzeki.log
2- So, what's your opinion? Should I go with the "QIIME 2 Amplicon Distribution" for updating QIIME2, or could I achieve what I need using the "QIIME 2 Shotgun Distribution" option?
I think installing a new conda env with the amplicon distribution is probably the easiest option. Let's try that first!
We can also reach out to the rescript devs if that does not solve the problem
I installed 'QIIME 2 Amplicon Distribution' and ran the first command based on your tutorial 'How to train a UNITE ITS classifier using RESCRIPt':
(qiime2-amplicon-2023.9) uw-user@V74RMK29HK qiime2-amplicon-2023.9 % qiime rescript get-unite-data
--p-version 9.0
--p-taxon-group eukaryotes
--p-cluster-id dynamic
--p-no-singletons
--verbose
--output-dir uniteDB
and I got the following error:
Error: QIIME 2 has no plugin/command named 'rescript'.
But if I'm not mistaken, the 'QIIME 2 Shotgun Distribution' environment already comes with rescript installed, doesn't it!?!
You are doing everything right! It looks like there are dependency conflicts so q2-longitudinal is not installed by default in all distributions.
Try installing RESCRIPt in the amplicon distro following the instructions on GitHub:
Thanks for using RESCRIPt, especially while we work to streamline the install process.
I installed RESCRIPt using the link you provided and following Nicholas's tutorial, as shown in the command below:
"conda create -y -n rescript
conda activate rescript
conda install
-c https://packages.qiime2.org/qiime2/{ENV_VERSION}/shotgun/passed/
-c https://packages.qiime2.org/qiime2/{ENV_VERSION}/amplicon/passed/
-c conda-forge -c bioconda -c qiime2 -c defaults
qiime2 q2cli q2templates q2-types q2-types-genomics q2-longitudinal q2-feature-classifier
"pandas>=0.25.3" xmltodict ncbi-datasets-pylib rescript
qiime rescript --help"
This time, I ran into this error:
Error: QIIME 2 plugin 'rescript' has no action 'get-unite-data'. Did you mean 'get-ncbi-data'?
When I set up RESCRIPt, I noticed these commands got installed and showed up:
get-gtdb-data Download, parse, and import GTDB referencedata.
get-ncbi-data Download, parse, and import NCBI sequences and taxonomies
get-ncbi-data-protein Download, parse, and import NCBI protein sequences and taxonomies
get-ncbi-genomes Fetch entire genomes and associated taxonomies and metadata using NCBI Datasets.
get-silva-data Download, parse, and import SILVA database.
Hi @Beh_Yaad,
I think you skipped a very important part of the instructions:
Note: update
{ENV_VERSION}in the commands below to match the QIIME 2 release.
That is, replace {ENV_VERSION} with 2023.9.
Hi Mike, big thanks for your instructions!
I followed the steps in your GitHub tutorial precisely, yet I'm still missing the "get-unite-data" as per Colin's tutorial on 'How to train a UNITE classifier using RESCRIPt'.
How can I go about installing the "get-unite-data" plugin?
Alternatively, is there a specific location within my conda environments where I can find this plugin?
Did you run qiime dev refresh-cache and then qiime rescript --help? After running those commands.
For the sake of clarity can you please, in your reply, paste all the commands you ran. That is, from activating your environment through installing RESCRIPt?
That is, you should be running the commands stated here for 2023.9.
Also, I realized my comment about replacing {ENV_VERSION} with 2023.9, was incorrect. That was for other RESCRIPt install options. 
Did you run
qiime dev refresh-cacheand thenqiime rescript --help? After running those commands.
No, but now I ran it and got the same output as the following command:
conda activate qiime2-amplicon-2023.9
conda install -c conda-forge -c bioconda -c qiime2 \
-c https://packages.qiime2.org/qiime2/2023.9/shotgun/passed/ \
-c defaults xmltodict 'q2-types-genomics>2023.5' ncbi-datasets-pylib rescript
qiime rescript --help
the commands:
cull-seqs
degap-seqs
dereplicate
edit-taxonomy
evaluate-classifications
evaluate-cross-validate
evaluate-fit-classifier
evaluate-seqs
evaluate-taxonomy
extract-seq-segments
filter-seqs-length
filter-seqs-length-by-taxon
filter-taxa
get-gtdb-data
get-ncbi-data
get-ncbi-data-protein
get-ncbi-genomes
get-silva-data
merge-taxa
orient-seqs
parse-silva-taxonomy
reverse-transcribe
subsample-fasta
trim-alignment
*******************************************
activating my environment:
# conda environments:
#
base * /Users/uw-user/miniconda3
qiime2-2023.7 /Users/uw-user/miniconda3/envs/qiime2-2023.7
qiime2-amplicon-2023.9 /Users/uw-user/miniconda3/envs/qiime2-amplicon-2023.9
qiime2-shotgun-2023.9 /Users/uw-user/miniconda3/envs/qiime2-shotgun-2023.9
rescript /Users/uw-user/miniconda3/envs/rescript
-------------------------------------------------------------------------------------
(base) uw-user@V74RMK29HK ~ % conda activate qiime2-amplicon-2023.9
conda install -c conda-forge -c bioconda -c qiime2 \
-c https://packages.qiime2.org/qiime2/2023.9/shotgun/passed/ \
-c defaults xmltodict 'q2-types-genomics>2023.5' ncbi-datasets-pylib rescript
qiime rescript --help
(qiime2-amplicon-2023.9) uw-user@V74RMK29HK ~ %
My apologies if things seem unclear! I was a bit mixed up myself. Should you require any additional information, please provide specifics, and I'll make sure to get it to you.
Thank you @Beh_Yaad.
Note, I edited your post using some simple markdown to make the commands stand out more clearly.
You commands should look like this:
(base) user % conda activate qiime-amplicon-2023.9
(qiime2-amplicon-2023.9) user % conda install -c conda-forge -c bioconda -c qiime2 \
-c https://packages.qiime2.org/qiime2/2023.9/shotgun/passed/ \
-c defaults xmltodict 'q2-types-genomics>2023.5' ncbi-datasets-pylib rescript
(qiime2-amplicon-2023.9) user % qiime dev refresh-cache
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
(qiime2-amplicon-2023.9) user % qiime rescript --help
You should see get-unite-data in the resscript output? If not, I'd suggest removing qiime2-amplicon-2023.9 and reinstalling that version of QIIME 2. Then install RESCRIPt. Or you can wait until the next QIIME 2 release (2024.2) comes out, as RESCRIPt will be part of both the amplicon and shotgun releases.
Great, thank you!
As I mentioned earlier, I need to train a UNITE ITS classifier with RESCRIPt. The tutorial starts off with this command:
qiime rescript get-unite-data \
--p-version 9.0 \
--p-taxon-group eukaryotes \
--p-cluster-id dynamic \
--p-no-singletons \
--verbose \
--output-dir uniteDB
And Colin said that he ran this command within the qiime2-amplicon-2023.9 environment.
I'm wondering, if 'qiime2-shotgun-2023.9' comes with RESCRIPt pre-installed, does that mean I can use the shotgun version without having to switch between different environments?
Hi @Beh_Yaad,
I realized, with the help of the other devs, that the get-unite-data action is flagged for the next QIIME 2 "amplicon" release. Therefore the only way to obtain the get-unite-data action is with the developer version. That is, running the following command:
pip install git+https://github.com/bokulich-lab/RESCRIPt.git
after running the conda install command for the 'amplicon' distribution. Which you've already done.
Once 2024.2 is released you'll not need to run the pip install command.
Let us know if this works.
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