dada2 no package called "GenomeInfoDbData" after upgrading to 2019.7

Hi! I’m running 2019.7 on a Virtualbox machine. dada2 has worked well for me in the past, but now it’s glitching in a way I’m not sure how to interpret or fix. I recently upgraded from 2018.8 and removed the old 2018.8 environment. I’m guessing that has something to do with the problem.

The main error message is the long one at the end, but here are a couple of others I’ve been getting in case they’re relevant.

When first opening a terminal:

Could not find conda environment: qiime2-2018.8
You can list all discoverable environments with conda info --envs.

bash: tab-qiime: No such file or directory

Easily solved with source activate qiime2-2019.7, though it would be nice to know how to set this as the default environment. I did that somehow when upgrading to 2018.8 a long time ago, but I can’t find instructions now.

I also get the following warning when using quality-filter q-score, but it completes successfully.

qiime quality-filter q-score --i-demux 20190904Popko_MiFish.qza --p-quality-window 0 --p-min-quality 5 --p-min-length-fraction 0.75 --o-filtered-sequences 20190904Popko_MiFish_qual1.qza --o-filter-stats 20190904Popko_MiFish_filterstats1 --verbose
/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_quality_filter/_filter.py:88: YAMLLoadWarning: calling yaml.load() without Loader=… is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
** phred_offset = yaml.load(metadata_view)[‘phred-offset’]**
Saved SampleData[SequencesWithQuality] to: 20190904Popko_MiFish_qual1.qza
Saved QualityFilterStats to: 20190904Popko_MiFish_filterstats1.qza

Here is the main error message from dada2:

(qiime2-2019.7) [email protected]:~/Documents/20190904Popko/MiFish$ qiime dada2 denoise-pyro --i-demultiplexed-seqs 20190904Popko_MiFish_qual2.qza --p-trunc-len 0 --p-max-ee 1 --p-chimera-method consensus --o-table 20190904Popko_MiFish_dereplicated_featuretable --o-representative-sequences 20190904Popko_MiFish_dereplicated_sequences --o-denoising-stats 20190904Popko_MiFish_denoising-stats --verbose
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: run_dada_single.R /tmp/qiime2-archive-dcyqgqco/25cd8461-7eb5-4891-9cc9-6ec751f59c77/data /tmp/tmp5_xrb483/output.tsv.biom /tmp/tmp5_xrb483/track.tsv /tmp/tmp5_xrb483 0 0 1.0 2 Inf consensus 1.0 1 250000 -1 32

R version 3.5.1 (2018-07-02) **
Loading required package: Rcpp
Error: package or namespace load failed for ‘dada2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
** there is no package called ‘GenomeInfoDbData’

Execution halted
Traceback (most recent call last):
** File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 154, in _denoise_single**
** run_commands([cmd])**
** File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands**
** subprocess.run(cmd, check=True)**
** File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/subprocess.py”, line 418, in run**
** output=stdout, stderr=stderr)**
subprocess.CalledProcessError: Command ‘[‘run_dada_single.R’, ‘/tmp/qiime2-archive-dcyqgqco/25cd8461-7eb5-4891-9cc9-6ec751f59c77/data’, ‘/tmp/tmp5_xrb483/output.tsv.biom’, ‘/tmp/tmp5_xrb483/track.tsv’, ‘/tmp/tmp5_xrb483’, ‘0’, ‘0’, ‘1.0’, ‘2’, ‘Inf’, ‘consensus’, ‘1.0’, ‘1’, ‘250000’, ‘-1’, ‘32’]’ returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
** File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call**
** results = action(arguments)
** File “</home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-461>”, line 2, in denoise_pyro**
** File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable**
** output_types, provenance)**
** File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor**
** output_views = self._callable(view_args)
** File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 274, in denoise_pyro**
** band_size=‘32’)**
** File “/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 165, in _denoise_single**
** " and stderr to learn more." % e.returncode)**
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

Plugin error from dada2:

** An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.**

See above for debug info.

Any idea what I can do to sort this out?

Thanks!

Erin

Hi @Erin_dfo,

Sounds like there is something wrong with your QIIME 2 installation

How did you upgrade? By downloading a new VB image? Or by attempting to install 2019.7 from within virtualbox?

See the support questions here. Please let us know the answers to these questions and we can try to diagnose the issue:

Thanks!

Hi Nicholas,

You are correct, I did update from within virtualbox, following the instructions here:

https://docs.qiime2.org/2019.7/install/native/

When I run the command env, this is what I get:

env
AS=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-as
XDG_VTNR=7
AR=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ar
LDFLAGS=-Wl,-O2 -Wl,–sort-common -Wl,–as-needed -Wl,-z,relro -Wl,-z,now -Wl,–disable-new-dtags -Wl,–gc-sections
RSTUDIO_WHICH_R=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/R
XDG_SESSION_ID=c2
JAVA_LD_LIBRARY_PATH=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/server
GCC_NM=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/qiime2
CLUTTER_IM_MODULE=xim
SESSION=ubuntu
GPG_AGENT_INFO=/home/qiime2/.gnupg/S.gpg-agent:0:1
HOST=x86_64-conda_cos6-linux-gnu
TERM=xterm-256color
VTE_VERSION=4205
XDG_MENU_PREFIX=gnome-
SHELL=/bin/bash
NM=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-nm
PYTHONNOUSERSITE=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python*/site-packages/
CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2
CONDA_SHLVL=1
QT_LINUX_ACCESSIBILITY_ALWAYS_ON=1
CONDA_PROMPT_MODIFIER=(qiime2-2019.7)
SIZE=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-size
WINDOWID=62914570
OLDPWD=/home/qiime2/Documents/20190904Popko/Fish16S
UPSTART_SESSION=unix:abstract=/com/ubuntu/upstart-session/1001/1777
GNOME_KEYRING_CONTROL=
GTK_MODULES=gail:atk-bridge:unity-gtk-module
GFORTRAN=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
LC_ALL=C.UTF-8
ARBHOME=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/arb
USER=qiime2
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:.tar=01;31:.tgz=01;31:.arc=01;31:.arj=01;31:.taz=01;31:.lha=01;31:.lz4=01;31:.lzh=01;31:.lzma=01;31:.tlz=01;31:.txz=01;31:.tzo=01;31:.t7z=01;31:.zip=01;31:.z=01;31:.Z=01;31:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=01;31:.bz2=01;31:.bz=01;31:.tbz=01;31:.tbz2=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=01;31:.war=01;31:.ear=01;31:.sar=01;31:.rar=01;31:.alz=01;31:.ace=01;31:.zoo=01;31:.cpio=01;31:.7z=01;31:.rz=01;31:.cab=01;31:.jpg=01;35:.jpeg=01;35:.gif=01;35:.bmp=01;35:.pbm=01;35:.pgm=01;35:.ppm=01;35:.tga=01;35:.xbm=01;35:.xpm=01;35:.tif=01;35:.tiff=01;35:.png=01;35:.svg=01;35:.svgz=01;35:.mng=01;35:.pcx=01;35:.mov=01;35:.mpg=01;35:.mpeg=01;35:.m2v=01;35:.mkv=01;35:.webm=01;35:.ogm=01;35:.mp4=01;35:.m4v=01;35:.mp4v=01;35:.vob=01;35:.qt=01;35:.nuv=01;35:.wmv=01;35:.asf=01;35:.rm=01;35:.rmvb=01;35:.flc=01;35:.avi=01;35:.fli=01;35:.flv=01;35:.gl=01;35:.dl=01;35:.xcf=01;35:.xwd=01;35:.yuv=01;35:.cgm=01;35:.emf=01;35:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.m4a=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.oga=00;36:.opus=00;36:.spx=00;36:.xspf=00;36:
QT_ACCESSIBILITY=1
CONDA_BACKUP_HOST=x86_64-conda_cos6-linux-gnu
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0
UNITY_HAS_3D_SUPPORT=false
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
SSH_AUTH_SOCK=/run/user/1001/keyring/ssh
DEBUG_FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe
CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
SESSION_MANAGER=local/qiime2core2018-2:@/tmp/.ICE-unix/2188,unix/qiime2core2018-2:/tmp/.ICE-unix/2188
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
LD_GOLD=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ld.gold
STRINGS=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-strings
CPP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-cpp
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/usr/share/upstart/xdg:/etc/xdg
UNITY_DEFAULT_PROFILE=unity-lowgfx
CXXFILT=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-c++filt
ARBHOME_BACKUP=
DESKTOP_SESSION=ubuntu
PATH=/home/qiime2/miniconda/envs/qiime2-2019.7/bin:/home/qiime2/bin:/home/qiime2/miniconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games
QT_IM_MODULE=ibus
QT_QPA_PLATFORMTHEME=appmenu-qt5
LD=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ld
DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe
CONDA_PREFIX=/home/qiime2/miniconda/envs/qiime2-2019.7
F90=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
XDG_SESSION_TYPE=x11
PWD=/home/qiime2/Documents/20190904Popko/MiFish
JOB=unity-settings-daemon
STRIP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-strip
JAVA_HOME=/home/qiime2/miniconda/envs/qiime2-2019.7
[email protected]=ibus
ELFEDIT=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-elfedit
MPLBACKEND=Agg
F95=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-f95
GCC_RANLIB=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
GNOME_KEYRING_PID=
LANG=C.UTF-8
GDM_LANG=en_US
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
DEBUG_FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe
COMPIZ_CONFIG_PROFILE=ubuntu
IM_CONFIG_PHASE=1
F77=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
GDMSESSION=ubuntu
CXX=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-c++
OBJCOPY=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-objcopy
SESSIONTYPE=gnome-session
GTK2_MODULES=overlay-scrollbar
SHLVL=1
HOME=/home/qiime2
XDG_SEAT=seat0
LANGUAGE=en_US:
FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og
CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
LIBGL_ALWAYS_SOFTWARE=1
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
FC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
GCC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc
UPSTART_INSTANCE=
ADDR2LINE=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-addr2line
CONDA_PYTHON_EXE=/home/qiime2/miniconda/bin/python
UPSTART_EVENTS=xsession started
XDG_SESSION_DESKTOP=ubuntu
LOGNAME=qiime2
COMPIZ_BIN_PATH=/usr/bin/
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/share/gnome:/usr/local/share:/usr/share:/var/lib/snapd/desktop:/var/lib/snapd/desktop
QT4_IM_MODULE=xim
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-xHUiVxRUfe
JAVA_HOME_CONDA_BACKUP=
CONDA_DEFAULT_ENV=qiime2-2019.7
LESSOPEN=| /usr/bin/lesspipe %s
RANLIB=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ranlib
DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe
INSTANCE=
UPSTART_JOB=unity7
CC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-cc
XDG_RUNTIME_DIR=/run/user/1001
DISPLAY=:0
READELF=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-readelf
JAVA_LD_LIBRARY_PATH_BACKUP=
XDG_CURRENT_DESKTOP=Unity
GTK_IM_MODULE=ibus
OBJDUMP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-objdump
R_LIBS_USER=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/R/library/
GCC_AR=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
LESSCLOSE=/usr/bin/lesspipe %s %s
GPROF=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gprof
FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
GXX=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-g++
XAUTHORITY=/home/qiime2/.Xauthority
_=/usr/bin/env

I installed everything from scratch on a new computer, and the analysis ran fine there. But I’d rather not have to reinstall everything every time there’s an update, so if there’s another solution, that would be great.

Thanks!

Erin

The Virtualbox machines aren’t designed to be upgraded - it is certainly possible, but it involves a few steps, and is (in my opinion) not worth it. If you set up a data directory mount and keep the analysis files on the host computer, the process of installing a new vbox machine is usually significantly less work. With that in mind, my guess is that this is not working for you because you have more than one QIIME 2 environment in your PATH, which will lead to problems. You can edit the .bashrc file in the home directory to point to your new QIIME 2 environment, or, you can create a new user in the old virtualbox machine. Keep us posted!

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