Incorrect results produced by q2-quality-control evaluate-composition

data-integrity-bug

(Q2-D2) #1

Summary

We recently discovered a bug related to the q2-quality-control plugin’s evaluate-composition command that caused TAR and TDR scores to be swapped. Other metrics computed by this method were unaffected.

Impact

This issue impacts all versions of q2-quality-control prior to 2018.6.1. Other implementations of these metrics (e.g., in tax-credit) were not affected.

If you think you may have been impacted please check your provenance at https://view.qiime2.org for the versions listed above.

If data you already generated is impacted, be aware: the scores were computed correctly but are labelled incorrectly in the output. Simply swapping the labels will correct this issue.

Resolution

We have issued an updated release of QIIME 2 2018.6 that fixes this error. Installing with the standard installation instructions will download the patched version of q2-quality-control included in this updated release.

If you already installed the 2018.6 release of QIIME 2 and want to check if you have the patched version of q2-quality-control installed, use the following command (be sure to activate the environment in question first):

qiime info | grep 'quality-control'

If you have the patch installed, you will see the following:

quality-control: 2018.6.1

Please note, at the time this is posted we have not reissued the VMs with the latest release — please watch for an announcement about that in the next few days.

We apologize for any inconvenience this may have caused, and are happy to discuss further.


Special thanks to @Rocio for bringing this issue to our attention, and for providing a well documented issue report. It made troubleshooting this issue very straightforward. Thanks!


QIIME 2 2018.6 release is now live!
QIIME 2 2018.8 release is now live!
TDR vs TAR Bokulich et al 2018
[Preview] QIIME 2 2018.8 development changelogv
QC/benchmark Qiime2 on Mock community
Question how to evaluate sequence quality
(Matthew Ryan Dillon) #2

(Mel Melendrez) #3

Hi! So then for those of us who need to update, like me, quality-control: 2018.6.0

I then need to redownload per the instructions at Q2 install docs which are currently:

wget https://data.qiime2.org/distro/core/qiime2-2018.6-py35-linux-conda.yml
conda env create -n qiime2-2018.6 --file qiime2-2018.6-py35-linux-conda.yml

So do we just need to update -n qiime2-2018.6 to -n qiime2-2018.6.1 ?

Or will using the directions as stated download the latest release?

Also is it then recommended to clean out version 2018.6.0? via
conda env remove -n qiime2-2018.6.0 ? or
conda env remove -n qiime2-2018.6?

Thanks!
Mel


(Matthew Ryan Dillon) #4

(Matthew Ryan Dillon) #5

Hey there @mmelendrez!

That could work, although you would only need to do that if you want to keep your old environment around.

The only difference between those two commands is the name of the environment - so it totally depends on what you named the env when you created it! If you followed our install guide, the name would be qiime2-2018.6.


Here is what I would do, personally. I would remove the old env — I don’t want it around anymore!

source deactivate  # make sure I am not in an active env
conda env remove -n qiime2-2018.6  # update the name if you used a different name when installing
wget $URL_TO_ENV_FILE  # get this file again, to make sure you have the patched version
conda env create -n qiime2-2018.6 --file $ENV_FILE

Again, this is just what I would do, but, the beauty of conda is that you have all the flexibility to do what is right for you, right there! Hope that helps - keep us posted!


(Q2-D2) #7

New VMs are available that include q2-quality-control 2018.6.1.