ITS 1 and 2 Analysis

I try to install q2-itspress on qiime2. I used the following command and it was installed. I refreshed and test the installation but it not working.
Can you advise how to go about this?
I am working on processing of ITS 1 and 2 data from illumina sequence facility.

conda install -c bioconda itsxpress

Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 4.9.2
latest version: 4.10.1

Please update conda by running

$ conda update -n base -c defaults conda

Package Plan

environment location: /home/qiime2/miniconda/envs/qiime2-2020.11

added / updated specs:
- itsxpress

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
bbmap-38.18                |                0         7.2 MB  bioconda
biopython-1.78             |   py36h7b6447c_0         2.2 MB
ca-certificates-2021.5.25  |       h06a4308_1         112 KB
certifi-2021.5.30          |   py36h06a4308_0         139 KB
itsxpress-1.8.0            |             py_1         968 KB  bioconda
openssl-1.1.1k             |       h27cfd23_0         2.5 MB
------------------------------------------------------------
                                       Total:        13.1 MB

The following NEW packages will be INSTALLED:

bbmap bioconda/noarch::bbmap-38.18-0
biopython pkgs/main/linux-64::biopython-1.78-py36h7b6447c_0
itsxpress bioconda/noarch::itsxpress-1.8.0-py_1

The following packages will be UPDATED:

ca-certificates conda-forge::ca-certificates-2020.12.~ --> pkgs/main::ca-certificates-2021.5.25-h06a4308_1
certifi conda-forge::certifi-2020.12.5-py36h5~ --> pkgs/main::certifi-2021.5.30-py36h06a4308_0
openssl conda-forge::openssl-1.1.1h-h516909a_0 --> pkgs/main::openssl-1.1.1k-h27cfd23_0

Proceed ([y]/n)? Invalid choice: pip install q2-itsxpress
Proceed ([y]/n)?

Downloading and Extracting Packages
bbmap-38.18 | 7.2 MB | #################################### | 100%
itsxpress-1.8.0 | 968 KB | #################################### | 100%
biopython-1.78 | 2.2 MB | #################################### | 100%
openssl-1.1.1k | 2.5 MB | #################################### | 100%
ca-certificates-2021 | 112 KB | #################################### | 100%
certifi-2021.5.30 | 139 KB | #################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(qiime2-2020.11) [email protected]:~/Desktop/shared/qiime2-ITS1$ 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.
(qiime2-2020.11) [email protected]:~/Desktop/shared/qiime2-ITS1$ qiime itsxpress
Error: QIIME 2 has no plugin/command named 'itsxpress'.
(qiime2-2020.11) [email protected]:~/Desktop/shared/qiime2-ITS1$ q2-itsxpress --help
q2-itsxpress: command not found

Hi Betty,

I’ve moved this post over to our Community Plugin Support category, as q2-itsxpress is not included in the QIIME 2 core distribution. A couple of things that may help you here:

Here is the installation tutorial for q2-itsxpress. I’d recommend following the instructions provided there, and if you are still having trouble you can ping Adam_ Rivers (the developer who created q2-itsxpress) and he may be able to help you troubleshoot from there.

Hope this helps!

1 Like

Hi
Thank you, it actually help. I contacted Dr Rivers on the ITS trim tutorial.
I am still waiting for his response, I hope he will respond.
Regards.

Betty

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