QIIME 2 2017.9 release is now live!


(Matthew Ryan Dillon) #1

The QIIME 2 2017.9 release is now live! There are lots of exciting new changes packed into this release that are described below. Through the end of 2017 we will have monthly releases. 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 monthly release of QIIME 2 as these monthly releases continue through the end of 2017.

QIIME 2 will succeed QIIME 1 on January 1, 2018. QIIME 1 will no longer be supported at that time, as development and support effort for QIIME will be focused entirely on QIIME 2. We recommend that existing QIIME users begin transitioning from QIIME 1 to QIIME 2 now.

Check out the QIIME 2 2017.9 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. 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
    • Artifacts and Visualizations now record their output-name in provenance. This can help consumers of provenance disambiguate multiple artifacts produced by the same Action (e.g. qiime diversity core-metrics). :tada:
    • FileFormats and DirectoryFormats can now implement a validate method which may raise a ValidationError to explain what part of a given file/directory makes it invalid.
    • Added additional validation and cleanup to TSV-format metadata files - rows made entirely of whitespace will be ignored (like they are with a comment line).
  • docs
    • Updated the Sample Classifier tutorial to include an example of maturity-index, as well as replaced the Atacama dataset with ECAM.
    • Updated the Longitudinal tutorial to include an example of volatility, as well as using the ECAM dataset now.
  • q2-vsearch
    • This new plugin wraps several vsearch methods, allowing for dereplication as well as de novo and closed-reference OTU picking! :balloon:
    • A Community Tutorial for de novo and closed-reference OTU picking with q2-vsearch is now available. This will be transitioned to the QIIME 2 docs in a future release.
  • q2-longitudinal
    • Warnings are now displayed in a collapsible section in the visualization instead of stdout.
    • Fixed a bug in linear-mixed-effects that caused it to fail when only one variable was provided as input.
    • LME now fails gracefully when singular matrix error is raised.
    • Added volatility visualizer, which lets you plot a control chart of a single dependent variable across multiple groups contained in a sample metadata column.
    • Fixed a bug that caused a misleading HTML title to be displayed in visualizations produced by this plugin.
    • Added nmit method, which performs nonparametric microbial interdependence test to determine longitudinal sample similarity as a function of temporal microbial composition. Thanks Yilong Zhang! :balloon:
  • q2-sample-classifier
    • Added the ability to collapse the (sometimes lengthy) “Feature Importance” table of the classify-samples visualizer.
    • Fixed a bug that caused a misleading HTML title to be displayed in visualizations produced by this plugin.
  • q2-feature-classifier
    • Added optional class_weight input to sklearn classifier fitting.
    • Fixed a bug for classifiers that don’t support confidence calculations.
    • Added parameter descriptions to classify-sklearn.
    • Renamed the chunk-size parameter of classify-sklearn to reads-per-batch.
  • q2-composition
    • The statistical-test parameter has been removed from ancom. This parameter did not generally work (resulted in an immediate error). It may be added back in the future.
    • ancom now provides a message when no significant features are found instead of an empty table.
    • ancom will now display a message if a volcano plot cannot be drawn.
  • q2-types
    • A new semantic type SampleData[Sequences] has been added. This has a default format of QIIME1DemuxFormat (and is the analogue to seqs.fna from split_libraries.py).
    • DNAFASTAFormat now supports empty files (zero FASTA records).
    • Fixed a bug in the pd.Series to DNAFASTAFormat transformer :bug:.
    • CasavaOneEightSingleLanePerSampleDirFmt and related formats have been made significantly more robust and will now report issues such as missing forward/reverse reads, duplicate sample IDs, and unusual directory structures at import time.
  • q2-feature-table
    • Added qiime feature-table heatmap visualizer for visualizing a feature table as a heatmap, optionally in the context of sample metadata and sample/feature axes clustering.
    • Added y-axis labels to the frequency plots in the summarize visualizer!
    • Added qiime feature-table filter-seqs to support filtering FeatureData[Sequences].
    • Added a new merge method: sum. This allows for both overlapping Sample IDs and Feature IDs when merging two tables.
  • q2-phylogeny
    • fasttree method now supports an n-threads parameter for running FastTree in multi-threaded mode (uses FastTreeMP to accomplish this).
  • q2-diversity
    • core-metrics now computes only non-phylogenetic metrics (so a phylogenetic tree is not required as input). Added core-metrics-phylogenetic which computes both phylogenetic and non-phylogenetic metrics and requires a tree as input.
    • core-metrics and core-metrics-phylogenetic now output the rarefied table in addition to the other outputs.
    • Fixed a bug in alpha-rarefaction that caused visualizations produced with optional metadata to display the sum of the various metrics, instead of the median.
    • A new method beta-phylogenetic-alt has been added. Notably, this method is faster and uses much less memory while producing identical results to beta-phylogenetic, making it ideal for large datasets. This method also includes support for Generalized UniFrac and Variance Adjusted UniFrac. At a later date, this may be merged with beta-phylogenetic.
    • alpha-rarefaction now ignores metadata columns that contain entirely “null” values and provides a warning indicating which columns those were.
  • q2cli
    • Fixed a bug where --help text labeled output visualizations as both Artifacts and Visualizations.
    • qiime tools import error messages are now formatted in a more user-friendly way.
    • Input options are now ordered to match the signature of the registered action, this means that required options will appear first in the help text followed by optional options and then outputs.
    • Provide prettier errors when attempting to use invalid metadata (either TSV or QZA format).
  • q2-emperor
    • Upgraded to the latest version of Emperor, which includes the following changes:

      Opacity Tab (new):

      • Add the ability to modify the opacity of the elements on screen, see the Opacity tab. This tab works very much the same way as the Scale tab, the opacity of the objects can be set on a per-category basis, globally (all at once), or based on a numeric metadata category.

      Axes Tab:

      • Add the ability to hide axes lines and axes labels. Go to the Axes tab, click on the color for the tab and then select the X on the top right of the color selector.
      • The bars in the scree plot (under the Axes tab) will now display the percentage explained by each dimension.
      • Add the ability to create 2D plots. To do this, go to the Axes tab, click on the dropdown menu for “Axes 3” and then select Hide (make 2D plot).

      The animated gif below shows the tooltips for the scree plot, then how to hide the axes lines and finally how to convert the 3D plot into a 2D plot:

      Bug Fixes:

      • Fix a bug where the background and axes color controllers would stop working after loading a settings file.
      • Fix a bug where after setting the background color to a value that is not black, the background would no longer change back to black.
      • Fix a bug where attribute editors would sometimes need to be double or tripled clicked for the editors to show.


      • The tabs have been reordered, from [Color, Visibility, Shape, Axes, Scale] to [Color, Visibility, Opacity, Scale, Shape, Axes]
      • Most elements on the UI now display a tooltip whenever the mouse hovers over them.
      • Add a counter of visible samples on the top left of the plot.

Happy QIIME-ing! :sun_with_face:

Core-metrics without phylogeny
Visualization for Paired-end Demultiplexed Fastq Imports
MOCK sample and PCR blanks
Core matrix command Error: no such option: --i-phylogeny
Filtering representative sequences
Catching duplicate ID's, redux
Error without a display
Plugin Error: list index out of range for qiime demux summarize
Filtering and then merging 2 different runs- same barcodes used in both runs
Working with ITS data on a supercomputer/server
Feature Table / Metadata Index Mismatch
Save emperor plot and legend as .png
Import Paired End Illumina Data
Error in command for generating PCoA plot
Importing clean FASTA files from Illumina
Is it available to Make 2D PCoA Plots?
Memory Error using the pretrained silva 119 classifier
Multiple Regions of 16s Sequenced

I can’t find the url for QIIME2 2017.9 virtual machine, thanks.

(Matthew Ryan Dillon) #65

Hi @asr17!

We haven’t gotten the VMs out the door just yet:

but hopefully in the next few days! Stay tuned here for a follow-up! :t_rex: :tada:

(Matthew Ryan Dillon) #67

An off-topic reply has been split into a new topic: Filter Seqs (feature table)

Please keep replies on-topic in the future.

QIIME 2 plugin 'diversity' has no action 'core-metrics-phylogenetic'
(Jai Ram Rideout) #68

The QIIME 2 Virtual Machines are now available! We have QIIME 2 2017.9 available on AWS, Docker, and VirtualBox, please see the docs for more information. Thanks!

(M. Nazmul Huda) #69

Adding tool for maturity-index calculation is a cool idea. Thank you so much for adding this tool.

(Evan Bolyen) #70

An off-topic reply has been split into a new topic: Save emperor plot and legend as .png

Please keep replies on-topic in the future.