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