Ion Torrent data - trim and quality filter

Hello QIIME2 users,

I beginner working on bioinformatics. I am planning to use QIIME2 for 16S rRNA sequencing analysis (bacterial composition, bacterial diversity, etc.).

I have 15 .fastq sequences files, were obtained from Ion 16S Metagenoimics kit with Ion Torrent machine as following:


Also,
I imported .fastq files to QIIME2 followed the Ion Torrent Importing data by using “Fastq manifest” formats and now I got .qza file.

I have used this command line for import:
qiime tools import
–type SampleData[JoinedSequencesWithQuality]
–input-path manifest_IonXpressBV_ED.txt
–output-path single-end-demux-BV-JoinedSeq.qza
–input-format SingleEndFastqManifestPhred33

After importing data, I checked peek:
qiime tools peek single-end-demux.qza
UUID: f228347a-1913-48c7-b037-a519869e1001
Type: SampleData[JoinedSequencesWithQuality]
Data format: SingleLanePerSampleSingleEndFastqDirFmt

Then I will process to check sequence quality control by using quality-filter q-score-joined but I got an error message. What wrong in this step? and would like some advice?

I have used this for check quality-filter:
qiime quality-filter q-score-joined
–i-demux single-end-demux-BV-JoinedSeq.qza
–o-filtered-sequences BV-demux-joined-filtered.qza
–o-filter-stats BV-demux-joined-filter-stats.qza

In addition, I am trying to denoise with q2-deblur, qiime deblur denoise-16S, followed Ion Torrent data denoise with dada2 but I got error from deblur.

How to proceed further in this case?
Please give more information and suggestion.

Regards,
Auttawit

Can you run the following to check your data?

qiime tools validate single-end-demux-BV-JoinedSeq.qza

Thanks! :qiime2: :t_rex:

Hi @thermokarst,

I checked following your suggestion but it showed some error.

Do you have any suggestion?

Thank you very much for your help.
Regards,
Auttawit

I suspect this might be a locale issue - we can check that by running the following, and pasting the results here:

env

Thanks! :qiime2:

Hi @thermokarst,

I followed your suggestion, the results as below

(qiime2-2019.7) [email protected]:/media/sf_sf_Desktop/Raw Data$ env
CLUTTER_IM_MODULE=xim
CONDA_SHLVL=1
LC_ALL=C.UTF-8
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:.zst=01;31:.tzst=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:.wim=01;31:.swm=01;31:.dwm=01;31:.esd=01;31:.jpg=01;35:.jpeg=01;35:.mjpg=01;35:.mjpeg=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:
CONDA_EXE=/home/qiime2/miniconda/bin/conda
LESSCLOSE=/usr/bin/lesspipe %s %s
GPROF=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gprof
XDG_MENU_PREFIX=gnome-
LANG=C.UTF-8
MANAGERPID=2147
DISPLAY=:0
GXX=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-g++
JAVA_LD_LIBRARY_PATH=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/server
INVOCATION_ID=9c5d5976dcc1413185ae99b4481d470f
LD_GOLD=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ld.gold
GNOME_SHELL_SESSION_MODE=ubuntu
DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og
DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe
COLORTERM=truecolor
GCC_NM=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
USERNAME=qiime2
CONDA_PREFIX=/home/qiime2/miniconda/envs/qiime2-2019.7
JAVA_HOME=/home/qiime2/miniconda/envs/qiime2-2019.7
GCC_RANLIB=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
GCC_AR=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
R_LIBS_USER=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/R/library/
XDG_VTNR=2
SSH_AUTH_SOCK=/run/user/1001/keyring/ssh
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
_CE_M=
CC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-cc
READELF=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-readelf
XDG_SESSION_ID=2
ARBHOME=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/arb
USER=qiime2
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
ARBHOME_BACKUP=
DESKTOP_SESSION=ubuntu
STRIP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-strip
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
OBJCOPY=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-objcopy
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
QT4_IM_MODULE=xim
TEXTDOMAINDIR=/usr/share/locale/
PYTHONNOUSERSITE=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python*/site-packages/
GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/2e5ca721_d48f_4948_a3c4_95c73537d65f
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
PWD=/media/sf_sf_Desktop/Raw Data
HOME=/home/qiime2
ADDR2LINE=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-addr2line
CONDA_PYTHON_EXE=/home/qiime2/miniconda/bin/python
JOURNAL_STREAM=9:28872
TEXTDOMAIN=im-config
SSH_AGENT_PID=2314
HOST=x86_64-conda_cos6-linux-gnu
QT_ACCESSIBILITY=1
XDG_SESSION_TYPE=x11
F77=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop
RANLIB=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ranlib
OBJDUMP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-objdump
AS=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-as
AR=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ar
GFORTRAN=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
CONDA_BACKUP_HOST=x86_64-conda_cos6-linux-gnu
_CE_CONDA=
XDG_SESSION_DESKTOP=ubuntu
DBUS_STARTER_ADDRESS=unix:path=/run/user/1001/bus,guid=f543adef1306121403a62e1d5dcc1dcd
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
FC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
NM=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-nm
CONDA_PROMPT_MODIFIER=(qiime2-2019.7)
GTK_MODULES=gail:atk-bridge
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
CXX=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-c++
WINDOWPATH=2
TERM=xterm-256color
SHELL=/bin/bash
VTE_VERSION=5202
CXXFILT=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-c++filt
QT_IM_MODULE=xim
[email protected]=ibus
MPLBACKEND=Agg
IM_CONFIG_PHASE=2
DBUS_STARTER_BUS_TYPE=session
XDG_CURRENT_DESKTOP=ubuntu:GNOME
GPG_AGENT_INFO=/run/user/1001/gnupg/S.gpg-agent:0:1
GNOME_TERMINAL_SERVICE=:1.71
ELFEDIT=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-elfedit
XDG_SEAT=seat0
SHLVL=1
LANGUAGE=en_US:
FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2
STRINGS=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-strings
F90=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
F95=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-f95
GDMSESSION=ubuntu
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
LOGNAME=qiime2
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1001/bus,guid=f543adef1306121403a62e1d5dcc1dcd
JAVA_HOME_CONDA_BACKUP=
XDG_RUNTIME_DIR=/run/user/1001
XAUTHORITY=/run/user/1001/gdm/Xauthority
RSTUDIO_WHICH_R=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/R
LDFLAGS=-Wl,-O2 -Wl,–sort-common -Wl,–as-needed -Wl,-z,relro -Wl,-z,now -Wl,–disable-new-dtags -Wl,–gc-sections
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/etc/xdg
PATH=/home/qiime2/miniconda/envs/qiime2-2019.7/bin:/home/qiime2/miniconda/condabin:/home/qiime2/miniconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/snap/bin
GCC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc
CONDA_DEFAULT_ENV=qiime2-2019.7
SIZE=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-size
SESSION_MANAGER=local/qiime2core2019-7:@/tmp/.ICE-unix/2179,unix/qiime2core2019-7:/tmp/.ICE-unix/2179
CPP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-cpp
LD=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ld
LESSOPEN=| /usr/bin/lesspipe %s
JAVA_LD_LIBRARY_PATH_BACKUP=
GTK_IM_MODULE=ibus
_=/usr/bin/env
(qiime2-2019.7) [email protected]:/media/sf_sf_Desktop/Raw Data$

Thank you very much for your help.
Regards,
Auttawit

Thanks @auttawit_s!

These two lines jumped out at me:

Can you try the suggestion listed here, and let us know how it goes?

:crossed_fingers: :qiime2:

HI @thermokarst

Thanks for your response and sorry for late reply. But it didn’t fix the issue. I’m running the following and I got error…

(qiime2-2019.7) [email protected]:~/Raw Data$ echo $LC_ALL
C.UTF-8
(qiime2-2019.7) [email protected]:~/Raw Data$ echo $LANG
C.UTF-8
(qiime2-2019.7) [email protected]:~/Raw Data$ export LC_ALL=en_US.UTF-8
(qiime2-2019.7) [email protected]:~/Raw Data$ export LANG=en_US=UTF-8
(qiime2-2019.7) [email protected]:~/Raw Data$ locale
LANG=en_US=UTF-8
LANGUAGE=en_US:
LC_CTYPE="en_US.UTF-8"
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_COLLATE="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_PAPER="en_US.UTF-8"
LC_NAME="en_US.UTF-8"
LC_ADDRESS="en_US.UTF-8"
LC_TELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=en_US.UTF-8
(qiime2-2019.7) [email protected]:~/Raw Data$ env
CLUTTER_IM_MODULE=xim
CONDA_SHLVL=1
LC_ALL=en_US.UTF-8
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:*.zst=01;31:*.tzst=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:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=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:
CONDA_EXE=/home/qiime2/miniconda/bin/conda
LESSCLOSE=/usr/bin/lesspipe %s %s
GPROF=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gprof
XDG_MENU_PREFIX=gnome-
LANG=en_US=UTF-8
MANAGERPID=2164
DISPLAY=:0
GXX=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-g++
JAVA_LD_LIBRARY_PATH=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/server
INVOCATION_ID=ac274402cc2c4332a675089e81c9adc3
LD_GOLD=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ld.gold
GNOME_SHELL_SESSION_MODE=ubuntu
DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og
DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe
COLORTERM=truecolor
GCC_NM=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
USERNAME=qiime2
CONDA_PREFIX=/home/qiime2/miniconda/envs/qiime2-2019.7
JAVA_HOME=/home/qiime2/miniconda/envs/qiime2-2019.7
GCC_RANLIB=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
GCC_AR=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
R_LIBS_USER=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/R/library/
XDG_VTNR=2
SSH_AUTH_SOCK=/run/user/1001/keyring/ssh
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
_CE_M=
CC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-cc
READELF=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-readelf
XDG_SESSION_ID=2
ARBHOME=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/arb
USER=qiime2
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
ARBHOME_BACKUP=
DESKTOP_SESSION=ubuntu
STRIP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-strip
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
OBJCOPY=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-objcopy
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
QT4_IM_MODULE=xim
TEXTDOMAINDIR=/usr/share/locale/
PYTHONNOUSERSITE=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python*/site-packages/
GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/34d7232b_8a68_4b7b_9f88_41c2aa114b33
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
PWD=/home/qiime2/Raw Data
HOME=/home/qiime2
ADDR2LINE=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-addr2line
CONDA_PYTHON_EXE=/home/qiime2/miniconda/bin/python
JOURNAL_STREAM=9:28635
TEXTDOMAIN=im-config
SSH_AGENT_PID=2333
HOST=x86_64-conda_cos6-linux-gnu
QT_ACCESSIBILITY=1
XDG_SESSION_TYPE=x11
F77=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop
RANLIB=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ranlib
OBJDUMP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-objdump
AS=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-as
AR=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ar
GFORTRAN=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
CONDA_BACKUP_HOST=x86_64-conda_cos6-linux-gnu
_CE_CONDA=
XDG_SESSION_DESKTOP=ubuntu
DBUS_STARTER_ADDRESS=unix:path=/run/user/1001/bus,guid=4b66fc7ae5c811fd947ecfb75dd83296
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
FC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
NM=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-nm
CONDA_PROMPT_MODIFIER=(qiime2-2019.7) 
GTK_MODULES=gail:atk-bridge
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
CXX=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-c++
WINDOWPATH=2
TERM=xterm-256color
SHELL=/bin/bash
VTE_VERSION=5202
CXXFILT=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-c++filt
QT_IM_MODULE=xim
[email protected]=ibus
MPLBACKEND=Agg
IM_CONFIG_PHASE=2
DBUS_STARTER_BUS_TYPE=session
XDG_CURRENT_DESKTOP=ubuntu:GNOME
GPG_AGENT_INFO=/run/user/1001/gnupg/S.gpg-agent:0:1
GNOME_TERMINAL_SERVICE=:1.84
ELFEDIT=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-elfedit
XDG_SEAT=seat0
SHLVL=1
LANGUAGE=en_US:
FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2
STRINGS=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-strings
F90=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
F95=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-f95
GDMSESSION=ubuntu
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
LOGNAME=qiime2
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1001/bus,guid=4b66fc7ae5c811fd947ecfb75dd83296
JAVA_HOME_CONDA_BACKUP=
XDG_RUNTIME_DIR=/run/user/1001
XAUTHORITY=/run/user/1001/gdm/Xauthority
RSTUDIO_WHICH_R=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/R
LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/etc/xdg
PATH=/home/qiime2/miniconda/envs/qiime2-2019.7/bin:/home/qiime2/miniconda/condabin:/home/qiime2/miniconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/snap/bin
GCC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc
CONDA_DEFAULT_ENV=qiime2-2019.7
SIZE=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-size
SESSION_MANAGER=local/qiime2core2019-7:@/tmp/.ICE-unix/2196,unix/qiime2core2019-7:/tmp/.ICE-unix/2196
CPP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-cpp
LD=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ld
LESSOPEN=| /usr/bin/lesspipe %s
JAVA_LD_LIBRARY_PATH_BACKUP=
GTK_IM_MODULE=ibus
_=/usr/bin/env
(qiime2-2019.7) [email protected]:~/Raw Data$ qiime tools import --type SampleData[JoinedSequencesWithQuality] --input-path manifest_IonXpressBV.tsv --output-path single-end-demux-BV-JoinedSeq.qza --input-format SingleEndFastqManifestPhred33
Imported manifest_IonXpressBV.tsv as SingleEndFastqManifestPhred33 to single-end-demux-BV-JoinedSeq.qza
(qiime2-2019.7) [email protected]:~/Raw Data$ qiime tools peek single-end-demux-BV-JoinedSeq.qza
UUID:        c4f22979-2265-46ec-981e-622f634e1795
Type:        SampleData[JoinedSequencesWithQuality]
Data format: SingleLanePerSampleSingleEndFastqDirFmt
(qiime2-2019.7) [email protected]:~/Raw Data$ qiime quality-filter q-score-joined \
>   --i-demux single-end-demux-BV-JoinedSeq.qza \
>   --o-filtered-sequences BV-demux-joined-filtered.qza \
>   --o-filter-stats BV-demux-joined-filter-stats.qza
Plugin error from quality-filter:

  'utf-8' codec can't decode byte 0xa3 in position 3: invalid start byte

Debug info has been saved to /tmp/qiime2-q2cli-err-m0qhan5f.log
(qiime2-2019.7) [email protected]:~/Raw Data$ qiime demux summarize \
>   --i-data single-end-demux-BV-JoinedSeq.qza \
>   --o-visualization demux-summary-BV-JoinedSeq.qzv
Plugin error from demux:

  'utf-8' codec can't decode byte 0xa3 in position 3: invalid start byte

Debug info has been saved to /tmp/qiime2-q2cli-err-60jnjsj8.log
(qiime2-2019.7) [email protected]:~/Raw Data$ 

Do you have any suggestions?

Thank you so so much for your help
Regards,
Auttawit

You have a typo here, this should be:

export LANG=en_US.UTF-8

Note the second = has been replaced with a .

Hi @thermokarst,

I edited, but it still not working as same error.

(qiime2-2019.7) [email protected]:~/Raw Data$ export LC_ALL=en_US.UTF-8
(qiime2-2019.7) [email protected]:~/Raw Data$ export LANG=en_US.UTF-8
(qiime2-2019.7) [email protected]:~/Raw Data$ locale
LANG=en_US.UTF-8
LANGUAGE=en_US:
LC_CTYPE="en_US.UTF-8"
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_COLLATE="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_PAPER="en_US.UTF-8"
LC_NAME="en_US.UTF-8"
LC_ADDRESS="en_US.UTF-8"
LC_TELEPHONE="en_US.UTF-8"
LC_MEASUREMENT="en_US.UTF-8"
LC_IDENTIFICATION="en_US.UTF-8"
LC_ALL=en_US.UTF-8
(qiime2-2019.7) [email protected]:~/Raw Data$ env
CLUTTER_IM_MODULE=xim
CONDA_SHLVL=1
LC_ALL=en_US.UTF-8
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:*.zst=01;31:*.tzst=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:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=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:
CONDA_EXE=/home/qiime2/miniconda/bin/conda
LESSCLOSE=/usr/bin/lesspipe %s %s
GPROF=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gprof
XDG_MENU_PREFIX=gnome-
LANG=en_US.UTF-8
MANAGERPID=2164
DISPLAY=:0
GXX=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-g++
JAVA_LD_LIBRARY_PATH=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/server
INVOCATION_ID=ac274402cc2c4332a675089e81c9adc3
LD_GOLD=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ld.gold
GNOME_SHELL_SESSION_MODE=ubuntu
DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og
DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe
COLORTERM=truecolor
GCC_NM=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
USERNAME=qiime2
CONDA_PREFIX=/home/qiime2/miniconda/envs/qiime2-2019.7
JAVA_HOME=/home/qiime2/miniconda/envs/qiime2-2019.7
GCC_RANLIB=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
GCC_AR=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
R_LIBS_USER=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/R/library/
XDG_VTNR=2
SSH_AUTH_SOCK=/run/user/1001/keyring/ssh
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
_CE_M=
CC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-cc
READELF=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-readelf
XDG_SESSION_ID=2
ARBHOME=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/arb
USER=qiime2
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
ARBHOME_BACKUP=
DESKTOP_SESSION=ubuntu
STRIP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-strip
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
OBJCOPY=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-objcopy
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
QT4_IM_MODULE=xim
TEXTDOMAINDIR=/usr/share/locale/
PYTHONNOUSERSITE=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python*/site-packages/
GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/34d7232b_8a68_4b7b_9f88_41c2aa114b33
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
PWD=/home/qiime2/Raw Data
HOME=/home/qiime2
ADDR2LINE=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-addr2line
CONDA_PYTHON_EXE=/home/qiime2/miniconda/bin/python
JOURNAL_STREAM=9:28635
TEXTDOMAIN=im-config
SSH_AGENT_PID=2333
HOST=x86_64-conda_cos6-linux-gnu
QT_ACCESSIBILITY=1
XDG_SESSION_TYPE=x11
F77=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop
RANLIB=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ranlib
OBJDUMP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-objdump
AS=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-as
AR=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ar
GFORTRAN=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
CONDA_BACKUP_HOST=x86_64-conda_cos6-linux-gnu
_CE_CONDA=
XDG_SESSION_DESKTOP=ubuntu
DBUS_STARTER_ADDRESS=unix:path=/run/user/1001/bus,guid=4b66fc7ae5c811fd947ecfb75dd83296
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
FC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
NM=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-nm
CONDA_PROMPT_MODIFIER=(qiime2-2019.7) 
GTK_MODULES=gail:atk-bridge
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
CXX=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-c++
WINDOWPATH=2
TERM=xterm-256color
SHELL=/bin/bash
VTE_VERSION=5202
CXXFILT=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-c++filt
QT_IM_MODULE=xim
[email protected]=ibus
MPLBACKEND=Agg
IM_CONFIG_PHASE=2
DBUS_STARTER_BUS_TYPE=session
XDG_CURRENT_DESKTOP=ubuntu:GNOME
GPG_AGENT_INFO=/run/user/1001/gnupg/S.gpg-agent:0:1
GNOME_TERMINAL_SERVICE=:1.84
ELFEDIT=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-elfedit
XDG_SEAT=seat0
SHLVL=1
LANGUAGE=en_US:
FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2
STRINGS=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-strings
F90=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
F95=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-f95
GDMSESSION=ubuntu
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
LOGNAME=qiime2
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1001/bus,guid=4b66fc7ae5c811fd947ecfb75dd83296
JAVA_HOME_CONDA_BACKUP=
XDG_RUNTIME_DIR=/run/user/1001
XAUTHORITY=/run/user/1001/gdm/Xauthority
RSTUDIO_WHICH_R=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/R
LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/etc/xdg
PATH=/home/qiime2/miniconda/envs/qiime2-2019.7/bin:/home/qiime2/miniconda/condabin:/home/qiime2/miniconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/snap/bin
GCC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc
CONDA_DEFAULT_ENV=qiime2-2019.7
SIZE=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-size
SESSION_MANAGER=local/qiime2core2019-7:@/tmp/.ICE-unix/2196,unix/qiime2core2019-7:/tmp/.ICE-unix/2196
CPP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-cpp
LD=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ld
LESSOPEN=| /usr/bin/lesspipe %s
JAVA_LD_LIBRARY_PATH_BACKUP=
GTK_IM_MODULE=ibus
_=/usr/bin/env
(qiime2-2019.7) [email protected]:~/Raw Data$ qiime tools import \
> --type SampleData[JoinedSequencesWithQuality] \
> --input-path manifest_IonXpressBV.tsv \
> --output-path single-end-demux-BV-JoinedSeq.qza \
> --input-format SingleEndFastqManifestPhred33
Imported manifest_IonXpressBV.tsv as SingleEndFastqManifestPhred33 to single-end-demux-BV-JoinedSeq.qza
(qiime2-2019.7) [email protected]:~/Raw Data$ 
(qiime2-2019.7) [email protected]:~/Raw Data$ qiime tools peek single-end-demux-BV-JoinedSeq.qza
UUID:        f6f0dd5c-21eb-4cfb-8d47-6e656cea6557
Type:        SampleData[JoinedSequencesWithQuality]
Data format: SingleLanePerSampleSingleEndFastqDirFmt
(qiime2-2019.7) [email protected]:~/Raw Data$ 
(qiime2-2019.7) [email protected]:~/Raw Data$ qiime quality-filter q-score-joined \
>   --i-demux single-end-demux-BV-JoinedSeq.qza \
>   --o-filtered-sequences BV-demux-joined-filtered.qza \
>   --o-filter-stats BV-demux-joined-filter-stats.qza
Plugin error from quality-filter:

  'utf-8' codec can't decode byte 0xa3 in position 3: invalid start byte

Debug info has been saved to /tmp/qiime2-q2cli-err-ti9_2_iu.log
(qiime2-2019.7) [email protected]:~/Raw Data$ 
(qiime2-2019.7) [email protected]:~/Raw Data$ qiime demux summarize \
>   --i-data single-end-demux-BV-JoinedSeq.qza \
>   --o-visualization demux-summary-BV-JoinedSeq.qzv
Plugin error from demux:

  'utf-8' codec can't decode byte 0xa3 in position 3: invalid start byte

Debug info has been saved to /tmp/qiime2-q2cli-err-2qatsj80.log
(qiime2-2019.7) [email protected]:~/Raw Data$ 

Regards,
Auttawit

Hi @auttawit_s!
This is a long shot, but some systems use different conventions for locale strings, and that can impact Python packages. Can you try these options with the hyphen removed from ‘utf-8’:

export LC_ALL=en_US.utf8
If that doesn’t work, try export LC_ALL=en_US.UTF8

Thanks for your patience! No guarantee this will work, but it may help us rule out locale as the issue.

Hi @ChrisKeefe,

Thank you for your help and suggestion.

I either used export LC_ALL=en_US.utf8 or export LC_ALL=en_US.UTF8 but it doesn’t work as showed the same error.

(qiime2-2019.7) [email protected]:~/Raw Data$ export LC_ALL=en_US.utf-8
(qiime2-2019.7) [email protected]:~/Raw Data$ locale
LANG=C.UTF-8
LANGUAGE=en_US:
LC_CTYPE="en_US.utf-8"
LC_NUMERIC="en_US.utf-8"
LC_TIME="en_US.utf-8"
LC_COLLATE="en_US.utf-8"
LC_MONETARY="en_US.utf-8"
LC_MESSAGES="en_US.utf-8"
LC_PAPER="en_US.utf-8"
LC_NAME="en_US.utf-8"
LC_ADDRESS="en_US.utf-8"
LC_TELEPHONE="en_US.utf-8"
LC_MEASUREMENT="en_US.utf-8"
LC_IDENTIFICATION="en_US.utf-8"
LC_ALL=en_US.utf-8
(qiime2-2019.7) [email protected]:~/Raw Data$ 
(qiime2-2019.7) [email protected]:~/Raw Data$ env
CLUTTER_IM_MODULE=xim
CONDA_SHLVL=1
LC_ALL=en_US.utf-8
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:*.zst=01;31:*.tzst=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:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=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:
CONDA_EXE=/home/qiime2/miniconda/bin/conda
LESSCLOSE=/usr/bin/lesspipe %s %s
GPROF=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gprof
XDG_MENU_PREFIX=gnome-
LANG=C.UTF-8
MANAGERPID=2236
DISPLAY=:0
GXX=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-g++
JAVA_LD_LIBRARY_PATH=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/server
INVOCATION_ID=755d9fc498f64de9b09380ee90dda7bf
LD_GOLD=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ld.gold
GNOME_SHELL_SESSION_MODE=ubuntu
DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og
DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe
COLORTERM=truecolor
GCC_NM=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-nm
USERNAME=qiime2
CONDA_PREFIX=/home/qiime2/miniconda/envs/qiime2-2019.7
JAVA_HOME=/home/qiime2/miniconda/envs/qiime2-2019.7
GCC_RANLIB=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib
CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
GCC_AR=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-ar
R_LIBS_USER=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/R/library/
XDG_VTNR=2
SSH_AUTH_SOCK=/run/user/1001/keyring/ssh
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
_CE_M=
CC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-cc
READELF=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-readelf
XDG_SESSION_ID=3
ARBHOME=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/arb
USER=qiime2
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
ARBHOME_BACKUP=
DESKTOP_SESSION=ubuntu
STRIP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-strip
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
OBJCOPY=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-objcopy
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
QT4_IM_MODULE=xim
TEXTDOMAINDIR=/usr/share/locale/
PYTHONNOUSERSITE=/home/qiime2/miniconda/envs/qiime2-2019.7/lib/python*/site-packages/
GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/915b6f94_1f0b_48bc_8941_9ea46416fd9c
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
PWD=/home/qiime2/Raw Data
HOME=/home/qiime2
ADDR2LINE=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-addr2line
CONDA_PYTHON_EXE=/home/qiime2/miniconda/bin/python
JOURNAL_STREAM=9:29413
TEXTDOMAIN=im-config
SSH_AGENT_PID=2406
HOST=x86_64-conda_cos6-linux-gnu
QT_ACCESSIBILITY=1
XDG_SESSION_TYPE=x11
F77=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop
RANLIB=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ranlib
OBJDUMP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-objdump
AS=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-as
AR=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ar
GFORTRAN=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
CONDA_BACKUP_HOST=x86_64-conda_cos6-linux-gnu
_CE_CONDA=
XDG_SESSION_DESKTOP=ubuntu
DBUS_STARTER_ADDRESS=unix:path=/run/user/1001/bus,guid=aeb87d1206e1b3cc75a4242c5ddc28da
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
FC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
NM=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-nm
CONDA_PROMPT_MODIFIER=(qiime2-2019.7) 
GTK_MODULES=gail:atk-bridge
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
CXX=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-c++
WINDOWPATH=2
TERM=xterm-256color
SHELL=/bin/bash
VTE_VERSION=5202
CXXFILT=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-c++filt
QT_IM_MODULE=xim
[email protected]=ibus
MPLBACKEND=Agg
IM_CONFIG_PHASE=2
DBUS_STARTER_BUS_TYPE=session
XDG_CURRENT_DESKTOP=ubuntu:GNOME
GPG_AGENT_INFO=/run/user/1001/gnupg/S.gpg-agent:0:1
GNOME_TERMINAL_SERVICE=:1.80
ELFEDIT=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-elfedit
XDG_SEAT=seat0
SHLVL=1
LANGUAGE=en_US:
FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe
CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2
STRINGS=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-strings
F90=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran
F95=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-f95
GDMSESSION=ubuntu
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
LOGNAME=qiime2
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1001/bus,guid=aeb87d1206e1b3cc75a4242c5ddc28da
JAVA_HOME_CONDA_BACKUP=
XDG_RUNTIME_DIR=/run/user/1001
XAUTHORITY=/run/user/1001/gdm/Xauthority
RSTUDIO_WHICH_R=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/R
LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/etc/xdg
PATH=/home/qiime2/miniconda/envs/qiime2-2019.7/bin:/home/qiime2/miniconda/condabin:/home/qiime2/miniconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/snap/bin
GCC=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc
CONDA_DEFAULT_ENV=qiime2-2019.7
SIZE=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-size
SESSION_MANAGER=local/qiime2core2019-7:@/tmp/.ICE-unix/2268,unix/qiime2core2019-7:/tmp/.ICE-unix/2268
CPP=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-cpp
LD=/home/qiime2/miniconda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ld
LESSOPEN=| /usr/bin/lesspipe %s
JAVA_LD_LIBRARY_PATH_BACKUP=
GTK_IM_MODULE=ibus
_=/usr/bin/env
(qiime2-2019.7) [email protected]:~/Raw Data$ 
(qiime2-2019.7) [email protected]:~/Raw Data$ qiime tools import \
> --type SampleData[JoinedSequencesWithQuality] \
> --input-path manifest_IonXpressBV.tsv \
> --output-path single-end-demux-BV-JoinedSeq.qza \
> --input-format SingleEndFastqManifestPhred33
Imported manifest_IonXpressBV.tsv as SingleEndFastqManifestPhred33 to single-end-demux-BV-JoinedSeq.qza
(qiime2-2019.7) [email protected]:~/Raw Data$ 
(qiime2-2019.7) [email protected]:~/Raw Data$ qiime tools peek single-end-demux-BV-JoinedSeq.qza
UUID:        40f4b475-e0a0-42be-988c-1645fa0a2c66
Type:        SampleData[JoinedSequencesWithQuality]
Data format: SingleLanePerSampleSingleEndFastqDirFmt
(qiime2-2019.7) [email protected]:~/Raw Data$ 
(qiime2-2019.7) [email protected]:~/Raw Data$ qiime demux summarize \
>   --i-data single-end-demux-BV-JoinedSeq.qza \
>   --o-visualization demux-summary-BV-JoinedSeq.qzv
Plugin error from demux:

  'utf-8' codec can't decode byte 0xa3 in position 3: invalid start byte

Debug info has been saved to /tmp/qiime2-q2cli-err-bj0qa_88.log
(qiime2-2019.7) [email protected]:~/Raw Data$ 
(qiime2-2019.7) [email protected]:~/Raw Data$ qiime quality-filter q-score-joined \
>   --i-demux single-end-demux-BV-JoinedSeq.qza \
>   --o-filtered-sequences BV-demux-joined-filtered.qza \
>   --o-filter-stats BV-demux-joined-filter-stats.qza
Plugin error from quality-filter:

  'utf-8' codec can't decode byte 0xa3 in position 3: invalid start byte

Debug info has been saved to /tmp/qiime2-q2cli-err-8k_z0mjg.log
(qiime2-2019.7) [email protected]:~/Raw Data$ 
(qiime2-2019.7) [email protected]:~/Raw Data$ 

Thank you very much for your help.
Regards,
Auttawit

Hey @auttawit_s, the LANGUAGE variable also seems to be a problem:

At this point, I would strongly recommend you coordinate with your local IT support team to see if they can help get your environment sorted out.

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