I just install qiime2-2021.11 and all my commands are "not found"

Hi, I used qiime2 two years ago in my former lab and know how to write commands as split_otu_table.py, summarize_taxa_through_plots.py or alpha_diversity.py
now I do not find this command on the new qiime2 version I downloaded in my new lab (all are "not found") and when I do "qiime feature-table --help" I only see new command names that I cannot use (how to write them? are they the old ones with new names?)
thank you for your help

HI @franz,

The commands you are referencing are only available from QIIME 1. You've likely seen the notice that support for QIIME 1 has been discontinued since 2018.

QIIME 2 is entirely re-written from scratch. I suggest you work through the tutorials, and our accompanying YouTube videos. You'll find a video playlist from one of our workshops, that highlight many of the most common QIIME 2 commands.



Thank you very much for your answer. I will try.


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Thank you very much Mike, the tutorials are very helpful (is there a error in the fist one?, I cannot open the data and was stopped soon after the beginning).
Qiime2 seems still a bit complex for me in comparison to qiime1 but I will be soon familiarized with the new scripts and tools.
Naive question: we do not need anymore to write paths as soon as we download your data, but what about our own files? Do we need to keep everything in Home.
Best regards,

The tutorials should work as they are compiled and tested for each release. Can you provide the exact command and error you are observing?

FIle paths are no different that in QIIME 1. Just provide the relative or full file-paths to the data you'd like to process.

You'll have to import your data into QIIME 2, i.e. as a QZA file. Note, this is often the more tricky part of the process. But once your data is imported you'll be good to go.

You can work within any directory you wish. I often make a directory for each project and work from within that.


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Hi Mike,
Here is the error I have when I run the scripts of the first tutorial:

(qiime2-2021.11) [email protected]:~/qiime2-moving-pictures-tutorial$ qiime tools import
--type EMPSingleEndSequences
--input-path emp-single-end-sequences
--output-path emp-single-end-sequences.qza
There was a problem importing emp-single-end-sequences:

Missing one or more files for EMPSingleEndDirFmt: 'sequences.fastq.gz'

I assume you are working through the this part of the Moving Pictures tutorial? or this part of the Importing tutorial? I ask, because this error:

tells me that the sequences.fastq.gz file could not be found where it was expected to be.

DId you run the prior commands to make the specified folders and download the sequence data to the specified locations? Hint, checkout the download path which appears after the wget -O portion of the command. If using the browser to download the files, then you must place the fastq files within the specified folder emp-single-end-sequences. The tutorial expects you to run each command in the order presented. Otherwise you'll have to modify the commands based on where you placed the files and folders.


Hi Mike,
Thank you for your answer. I will redo the first tutorial tomorrow, following your suggestions.

I just redo the first Tutorial (working nicely). QIIME2 is really amazing and the two tutorials are very useful, thank you. I will now work with our own data and come back to you when I will have problems.
Is there a possibility to visualize a phylogenetic tree in QIIME2?


Yep, you can install the q2-empress plugin. Another option (external to :qiime2:), is to use iTOL as outlined in our q2-phylogeny tutorial.


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