However, when I run:
conda activate qiime2--2024.10
I get "-bash: distro: No such file or directory"
I am able to run "conda activate qiime2-amplicon-2024.10", "conda activate qiime2-pathogenome-2024.10", etc...
Please see QIIME2_install3 attachment.
Is this because I installed while within qiime2-amplicon-2024.10 and need to deactivate conda in between installations (see ? Why won't "conda activate qiime2--2024.10" work?
As a secondary question...after installing amplicon, I received the following note.
The default QUAST package does not include:
GRIDSS (needed for structural variants detection)
SILVA 16S rRNA database (needed for reference genome detection in metagenomic datasets)
BUSCO tools and databases (needed for searching BUSCO genes) -- works in Linux only!
To be able to use those, please run
quast-download-gridss
quast-download-silva
quast-download-busco
Yet when I run "quast-download-gridss", the "command is not found". How do I run this line?
See QIIME2_install2.
Thanks for providing those screenshots, there's a lot of helpful context in there - from the commands you've run, it looks like there's a bit of confusion regarding your conda environments.
It looks like you're currently operating under a QIIME 2 2024.10 amplicon environment (based on the info shown from your command line - you'll see in parenthesis the current conda environment that you have activated), but are trying to run a command that exists under the metagenomic distribution.
I am seeing that you were able to successfully install the QIIME 2 2024.10 metagenome distribution, so all you need to do is activate it in order to access the functionality that is housed within that environment! In order to do that, you'll want to run the following commands:
Once you've activated this environment, you should be able to run quast-download-gridss as expected - but please feel free to reach back out if you run into any additional issues!
I was able to run the quast commands in the metagenome conda. However when I ran quast-download-busco I received an "HTTP Error 404". I should be able to manually download but I wondered whether other users had experienced this issue (see attachment).
I am still unsure of re-activating QIIME2
conda activate qiime2--2024.10
When I "conda deactivate" and run this line, I see that "no such file or directory exists" (see attachment). I am able to activate each of conda separately (i.e., conda qiime2-tiny-2024.10). Is the issue that I ran the "conda env create..." lines when I was in the amplicon conda?
I thought about trying to re-install the QIIME 2 Metagenome /Pathogenome / and Tiny / Distribution but make sure I was not in the Amplicon Distribution conda (see attached). As expected, I already have these in miniconda (see attachment). What conda environment should I open to begin 16S analyses?
Thank you and apologies as these are likely basic questions.
It looks like this is an issue with some of the existing quast database URLs - this unfortunately isn't a tool that we manage in-house, but I'll reach out to some folks about this and see what we can do to get those URLs updated/fixed.
So from looking at your commands, I can see that you successfully deactivated your qiime2-metagenome-2024.10 environment. You see in your next line that you have (base) listed next to your user account, which indicates you've deactivated your conda environment and are now in the base conda environment.
I think the issue you're running into is when attempting to activate a different environment, you're using the following syntax: conda activate qiime2-<distro>-2024.10
This environment name won't mean anything to your machine, since you don't have any environments with those exact characters. You should be replacing <distro> with whatever QIIME 2 distribution you've created as a conda environment and would like to activate (i.e. qiime2-amplicon-2024.10 or qiime2-metagenome-2024.10).
A helpful command you can use to check on the existing environments you've created and their names is conda env list. Then whenever you'd like to switch between environments, you'll run conda deactivate to exit out of the current environment you're in (unless you're in your base environment), and then run conda activate ENVIRONMENT-NAME with ENVIRONMENT-NAME being replaced with the exact name of the conda environment you wish to switch to.
If you've already installed all of the existing QIIME 2 distributions, you shouldn't need to re-install any of them. I'm seeing from your last screenshot that you do have an amplicon environment, which is what you'll want to use for 16S analysis.
A good starting place for getting familiarized with our 16S analysis workflows in QIIME 2 would be to go through our Moving Pictures tutorial within your amplicon environment (qiime2-amplicon-2024.10). This should help you better understand the tools available at your disposal, and what your best plan of attack should be for your particular dataset!
Yes, thank you @lizgehret! I was able to analyze my data. This was my misunderstanding, I thought the was a command to open all the conda environments.
No worries at all, I'm glad you got things sorted!
I have more info regarding the QUAST issue (thanks @misialq!):
The bottom line is that QUAST is trying to fetch an older version of BUSCO DB which does not exist anymore. I think the only recommendation here is to not download it through QUAST - we have a dedicated action in q2-moshpit to evaluate using BUSCO (that works for MAGs only, though).
Happy to help out here!
