QIIME 2 2018.2 release is now live!

release

(Q2-D2) #1

The QIIME 2 2018.2 release is now live! There are lots of exciting new changes packed into this release that are described below.

As a reminder, QIIME 2 has succeeded QIIME 1 as of January 1, 2018. QIIME 1 is no longer officially supported at this time, as development and support effort for QIIME are focused entirely on QIIME 2. To assist with this transition, we have been working toward “feature parity” with QIIME 1 over the last year. We have made a huge amount of progress toward this goal, but there may still be some things that you want to do with QIIME 1 that are not possible with QIIME 2. If you identify things that you did with QIIME 1 but can’t do with QIIME 2, please get in touch about them on the QIIME 2 forum. We’ll be happy to help with work-arounds as we wrap up loose ends.

Because we still anticipate a lot of new features going into QIIME 2 over the next few months, we plan to have bi-monthly releases for at least the first quarter of 2018. We were previously on a monthly release cycle, but we feel that at the moment a slightly longer development cycle will help us get some exciting new features out the door. We highly recommend staying up-to-date with the latest releases to get access to new features, bug fixes, documentation, etc. We will only provide user support for the latest release of QIIME 2 as these bi-monthly releases continue. Later in 2018, we expect to develop and implement a strategy for “long-term support” releases that we will support for longer periods of time. Our next planned QIIME 2 release is tentatively scheduled for April 2018 (QIIME 2 2018.4), but please stay tuned.

Check out the QIIME 2 2018.2 docs for details on installing the latest QIIME 2 release, as well as tutorials and other resources. Get in touch on the QIIME 2 forum if you run into any issues!

We will provide official conda builds on release day for native QIIME 2 installations. Virtual machine builds such as AWS and Docker will be released within the following week. We will post a follow-up announcement here when those builds become available.


Here’s the highlights of the release:

  • QIIME 2 Framework
    • There are large changes to Metadata in QIIME 2, including a new file format and Metadata API. See this forum announcement for details on what changed, as well as the updated Metadata tutorial.
    • Improved the error reporting for all methods that support filtering with a SQL where clause.
  • docs
  • Keemei
  • q2cli
    • Some CLI option names related to Metadata have changed in a backwards-incompatible way. Previously, any QIIME 2 action accepting a metadata column as input would have an option name ending with -category. The new option names end with -column, so previous commands will not work with the new naming scheme. For example, if a command previously used an option called --m-metadata-category, the new option name will be --m-metadata-column. If the CLI detects usage of the older option names, it will error and describe how to update your command to use the new option names. See this forum announcement for details on other Metadata-related changes in this release.
    • Added a new subcommand: qiime tools inspect-metadata! This will let you interrogate metadata, allowing you to learn about the available columns, their declared or inferred type, and the dimensions of the metadata. :cool:!
  • q2-metadata
    • Metadata column types (e.g. numeric or categorical) are now displayed in the tabulate visualization. The column types are included in the exported TSV/CSV files using the #q2:types comment directive. See this forum announcement for details on the new Metadata column typing support in this release.
    • Fixed a bug when tabulating metadata with single quotes (') in metadata values.
    • Added more robust error handling when qiime metadata tabulate can’t display metadata in the interactive table. If the metadata can’t be displayed interactively, users still have an option to download the metadata as a TSV file (e.g. to load in Excel/Google Sheets, or for further use with QIIME 2).
    • qiime metadata tabulate now has a simple progress indicator while loading the interactive table. Note: there isn’t any meaningful representation of loading progress at this point, just a binary “loading” / “not loading” type of indicator.
  • q2-feature-table
    • Changed the behind-the-scenes mechanism responsible for merging feature tables — this should reduce the amount of time required to merge large feature tables.
  • q2-demux
    • @mahermassoud added the ability to download the backing quality score stats from the summarize visualization. Thanks @mahermassoud! :tada: :balloon:
  • q2-cutadapt
    • Updated the adapter parameter descriptions to hint at cutadapt's ability to handle linked primers.
  • q2-gneiss
    • The boxplots produced by qiime gneiss balance-taxonomy are now displayed regardless of the number of the groups within the categorical metadata column.
  • q2-diversity
    • Fixed a bug (:bug:) in alpha-rarefaction that caused visualizations to break when using metadata with column names that contained spaces (' ').
    • Upgraded the scatterplot symbols in the alpha-rarefaction plot to display boxplots instead of dots. The boxplots help convey the distribution of a particular metric at a given depth, which is useful for understanding these data with more context than just the dots on their own.
  • q2-quality-filter
    • Fixed a bug (:butterfly:) that caused a confusing error message when providing incompatible metadata to evaluate-composition.
  • q2-emperor
    • --p-custom-axis has been renamed to --p-custom-axes and is now a List[Str] type, meaning it can be provided multiple times.
  • q2-dada2
    • Fixed a bug that caused denoise-single and denoise-paired to fail when specifying 'none' as the chimera removal method.

Happy QIIME-ing! :sun_with_face:


Import multiplexed R1.fastq and R2.fastq with mixed forward and reverse reads + truncate reverse primer
Raw quality data
[Preview] QIIME 2 2018.2 development changelog
Failure when attempting to filter samples
Error message of "qiime diversity core-metrics-phylogenetic" step
Getting error when performing "diversity core-metrics-phylogenetic"
Alpha Rarefaction Feedback
Export demux interactive quality plots as csv
Problems with fastq files paired end without barcode file
Taxonomy visualization does not load
I have an error message in denoise-paired commands
DADA2 error running without chimera checking
Gneiss balances boxplot doesn't show up
Alpha rarefaction
Beta Diversity Trees
Error involving temporary file (?) in de-noise DADA2 step
Error with metadata tabulate in qiime2 view
"Group" not accepted as metadata category
(Q2-D2) #9

The QIIME 2 Virtual Machines are now available! We have QIIME 2 2018.2 available on AWS, Docker, and VirtualBox, please see the docs for more information. Thanks! :tada:


(Tom Hu) #10

Is it possible to update to the newest one from version 2017.12?


(Junfei Guo) #11

I am not sure, I just downloaded the latest version. I have two versions in my laptop now:)


(Aleksey) #13

Hi @hzh0005,
You ‘update’ by creating a new conda environment with the new QIIME distribution. So if you follow the installation instructions on the main qiime2 page, you’ll have an updated version. You can then remove the old environment with: conda remove --name myenv --all , where myenv is the old version of qiime (e.g. qiime2-2017.12).