Hello All
I wanna predict the functional profile of my metagenome (16s) samples. For that I tried to install the picrust via qiime 2 plugin and following the tutorial. First I ran this command
conda install -c bioconda -c conda-forge picrust2 and it successfully ran then following the tutorial I downloaded the q2-picrust plugin and enter into it by typing cd
Then trying to pip install -e I am getting some options here I am not sure what to do.
pip install [options] [package-index-options] …
pip install [options] -r [package-index-options] …
pip install [options] [-e] …
pip install [options] [-e] …
pip install [options] <archive url/path> …
I am not able to run them properly.
And secondly I have my feature.otu.biom and seq.fna obtained from closed reference otu clustering and I have exported them. Are these the right files to play with them so as to predict the functional profiles.
please guide and help out
Is there a reason you need to install from source using pip install? It looks to me like you are attempting to install q2-picrust2 twice using two different methods. Since you said the first command was succesful, you should be good to go and don’t need to run pip install. As the installation instructions state, you can type qiime picrust2 --help to see if you have the plugin installed.
Thank You Sir
For your quick response
I just opened the system and it gave this information Could not find conda environment: qiime2-2020.8 You can list all discoverable environments with conda info --envs.
bash: tab-qiime: No such file or directory qiime2@qiime2core2020-8:~ conda activate picrust2**
**(picrust2) qiime2@qiime2core2020-8:~ qiime picrust2 --help
Command ‘qiime’ not found, but can be installed with:
I suggest running conda env list to list your conda environments and then using conda env remove --name env-name to remove the QIIME 2 environment(s) you have previously created. Then I suggest creating a brand new QIIME 2 environment before installing q2-picrust2. Note that q2-picrust2 seems to suggest installing a specific version of QIIME 2 (2019.10). You can find instructions for installing that specific version of QIIME 2 here. Then follow these instructions to install q2-picrust2. If you run into issues, you will find several discussions on the forum about problems and solutions installing q2-picrust2.
I should also add that I mispoke above when I said
this was in response to:
Your first command was trying to install picrust2 (not q2-picrust2). This is unnecessary because when you install q2-picrust2, picrust2 is installed automatically (as is noted here.)
Thank You
For your responses, I installed a specific version of QIIME 2 (2019.10), as mentioned by you. Now visiting to .q2-picrust2 web page to follow the installation instructions. The first instruction is to
These instructions assume you have a conda environment named qiime2-2019.10 installed.
Activate this environment:
conda activate qiime2-2019.10
If I have already (qiime2-2019.10) qiime2@qiime2core2019-10:~$ installed, do I need to activate the Conda activate qiime2-2019.10.
That is my query and point of misconception, as I am not a hardcore bioinformatician and a computer trainee.
Thanking You
Good questions, @divyaprince321. After you create a new conda environment, you will need to manually activate it. Creating an environment and activating it are two different steps. After you create an environemnt, conda will print a message telling you how to activate it. Depending on how your shell is configured, the (qiime2-2019.10) may indicate that a specific environment is activated. Another way to check this is simply to type qiime info to see which version of QIIME 2 you are using, if it's available at all, and where it is installed.
Regarding your other question: please create a new topic on the forum since this question is a new, unrelated question.