Error while running QIIME2 - ValueError: Timezone offset does not match system offset: 0 != -25200. Please, check your config files

[chetana]

I get the following error when i follow moving pictures tutorial on importing step

Preformatted text(qiime2-2018.6) ubuntu@final:~/qiime2-moving-pictures-tutorial$ qiime tools import \ –type EMPSingleEndSequences –input-path emp-single-end-sequences –output-path emp-single-end-sequences.qza Traceback (most recent call last): File “/home/ubuntu/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/tools.py”, line 116, in import_data view_type=source_format) File “/home/ubuntu/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/result.py”, li…

Hi @thermokarst, I'm currently running QIIME2 pipeline in a singularity container and I get this ValueError of timezones not matching. Could you please let me know how I can fix it. Thanks.

Chetana

[thermokarst]

Hi @chetana! Did you create the singularity container, or did someone else? We don’t provide a singularity container ourselves, so we don’t have too much experience with this, but my guess is that an environment variable in the container is mis-configured (my guess is the TZ env var). Can you run arbitrary commands inside the container? If so, please run this command:

env

and copy-and-paste the complete results here for us to look at. Thanks!

[chetana]

Hi @thermokarst thanks for the response. Someone else built the container and I’m trying to run qiime2 in it. Please find the ''env" below. Thanks for your help.

CONDA_SHLVL=1

QTINC=/usr/lib64/qt-3.3/include

LC_ALL=C.UTF-8

EBVERSIONSINGULARITY=3.0.3

LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:

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EBROOTBINUTILS=/gstore/apps/binutils/2.28-GCCcore-6.3.0

XDG_CONFIG_HOME=/home/qiime2

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SSH_CONNECTION=128.137.17.10 59469 10.39.54.1 22

GPROF=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gprof

EBDEVELFOSS=/gstore/apps/foss/2017a/gstore/apps/logs/foss-2017a-easybuild-devel

EBVERSIONNUMACTL=2.0.11

EBVERSIONLIBARCHIVE=3.3.3

EBROOTOPENBLAS=/gstore/apps/OpenBLAS/0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0

LANG=C.UTF-8

EBVERSIONSCALAPACK=2.0.2

EBROOTGCC=/gstore/apps/GCCcore/6.3.0

HISTCONTROL=ignoredups

SQUEUE_FORMAT2=jobid:10,arraytaskid:10,partition:10,qos:10,name:20,username:10,state:10,numcpus:6,numnodes:6,gres:8,starttime:22,timeused:12,reasonlist:17

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MODULERCFILE=/system/gredit/lmod/MODULERC

EBVERSIONGOMPI=2017a

GXX=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-g++

EBROOTLIBUUID=/gstore/apps/libuuid/1.0.3-foss-2017a

JAVA_LD_LIBRARY_PATH=/opt/conda/envs/qiime2-2019.7/lib/server

HOSTNAME=nl002

QTDIR=/usr/lib64/qt-3.3

OLDPWD=/gstore/home/macherls

EBDEVELNUMACTL=/gstore/apps/numactl/2.0.11-GCCcore-6.3.0/gstore/apps/logs/numactl-2.0.11-GCCcore-6.3.0-easybuild-devel

__LMOD_REF_COUNT__LMFILES_=/gstore/apps/modulefiles/common/slurm/17.11.11.lua:1;/gstore/apps/modulefiles/common/gredenv.lua:1;/gstore/apps/modulefiles/all/GCCcore/6.3.0.lua:1;/gstore/apps/modulefiles/all/binutils/2.28-GCCcore-6.3.0.lua:1;/gstore/apps/modulefiles/all/GCC/6.3.0-2.28.lua:1;/gstore/apps/modulefiles/all/numactl/2.0.11-GCCcore-6.3.0.lua:1;/gstore/apps/modulefiles/all/hwloc/1.11.6-GCC-6.3.0-2.28.lua:1;/gstore/apps/modulefiles/all/OpenMPI/2.1.0-GCC-6.3.0-2.28.lua:1;/gstore/apps/modulefiles/all/OpenBLAS/0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0.lua:1;/gstore/apps/modulefiles/all/gompi/2017a.lua:1;/gstore/apps/modulefiles/all/FFTW/3.3.6-gompi-2017a.lua:1;/gstore/apps/modulefiles/all/ScaLAPACK/2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0.lua:1;/gstore/apps/modulefiles/all/foss/2017a.lua:1;/gstore/apps/modulefiles/all/squashfs-tools/4.3-foss-2017a.lua:1;/gstore/apps/modulefiles/all/zlib/1.2.11-GCCcore-6.3.0.lua:1;/gstore/apps/modulefiles/all/libxml2/2.9.4-foss-2017a.lua:1;/gstore/apps/modulefiles/all/libarchive/3.3.3-foss-2017a.lua:1;/gstore/apps/modulefiles/all/go/1.11.lua:1;/gstore/apps/modulefiles/all/dep/0.5.0-foss-2017a.lua:1;/gstore/apps/modulefiles/all/libuuid/1.0.3-foss-2017a.lua:1;/gstore/apps/modulefiles/all/singularity/3.0.3-foss-2017a.lua:1

LD_GOLD=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ld.gold

LMOD_CASE_INDEPENDENT_SORTING=yes

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

EBVERSIONOPENMPI=2.1.0

GCC_NM=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-nm

EBVERSIONFOSS=2017a

EBDEVELSQUASHFSMINTOOLS=/gstore/apps/squashfs-tools/4.3-foss-2017a/gstore/apps/logs/squashfs-tools-4.3-foss-2017a-easybuild-devel

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CONDA_PREFIX=/opt/conda/envs/qiime2-2019.7

JAVA_HOME=/opt/conda/envs/qiime2-2019.7

GCC_RANLIB=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-ranlib

EBROOTGOMPI=/gstore/apps/gompi/2017a

CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe

EBROOTOPENMPI=/gstore/apps/OpenMPI/2.1.0-GCC-6.3.0-2.28

LMOD_RC=/system/gredit/lmod/lmodrc.lua

__LMOD_REF_COUNT_LD_LIBRARY_PATH=/gstore/apps/libuuid/1.0.3-foss-2017a/lib:1;/gstore/apps/go/1.11/lib:1;/gstore/apps/libarchive/3.3.3-foss-2017a/lib:1;/gstore/apps/libxml2/2.9.4-foss-2017a/lib:1;/gstore/apps/zlib/1.2.11-GCCcore-6.3.0/lib:1;/gstore/apps/ScaLAPACK/2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0/lib:1;/gstore/apps/FFTW/3.3.6-gompi-2017a/lib:1;/gstore/apps/OpenBLAS/0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0/lib:1;/gstore/apps/OpenMPI/2.1.0-GCC-6.3.0-2.28/lib:1;/gstore/apps/hwloc/1.11.6-GCC-6.3.0-2.28/lib:1;/gstore/apps/numactl/2.0.11-GCCcore-6.3.0/lib:1;/gstore/apps/binutils/2.28-GCCcore-6.3.0/lib:1;/gstore/apps/GCCcore/6.3.0/lib/gcc/x86_64-pc-linux-gnu/6.3.0:1;/gstore/apps/GCCcore/6.3.0/lib64:1;/gstore/apps/GCCcore/6.3.0/lib:1;/cm/shared/apps/slurm/17.11.11/lib64/slurm:1;/cm/shared/apps/slurm/17.11.11/lib64:1

__LMOD_REF_COUNT_PKG_CONFIG_PATH=/gstore/apps/libuuid/1.0.3-foss-2017a/lib/pkgconfig:1;/gstore/apps/libarchive/3.3.3-foss-2017a/lib/pkgconfig:1;/gstore/apps/libxml2/2.9.4-foss-2017a/lib/pkgconfig:1;/gstore/apps/zlib/1.2.11-GCCcore-6.3.0/lib/pkgconfig:1;/gstore/apps/FFTW/3.3.6-gompi-2017a/lib/pkgconfig:1;/gstore/apps/OpenMPI/2.1.0-GCC-6.3.0-2.28/lib/pkgconfig:1;/gstore/apps/hwloc/1.11.6-GCC-6.3.0-2.28/lib/pkgconfig:1

GCC_AR=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc-ar

R_LIBS_USER=/opt/conda/envs/qiime2-2019.7/lib/R/library/

EBROOTGCCCORE=/gstore/apps/GCCcore/6.3.0

SINGULARITY_APPNAME=

EBROOTSCALAPACK=/gstore/apps/ScaLAPACK/2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0

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EBVERSIONGCC=6.3.0

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TINI_VERSION=v0.16.1

EBDEVELHWLOC=/gstore/apps/hwloc/1.11.6-GCC-6.3.0-2.28/gstore/apps/logs/hwloc-1.11.6-GCC-6.3.0-2.28-easybuild-devel

CC=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-cc

READELF=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-readelf

EBROOTZLIB=/gstore/apps/zlib/1.2.11-GCCcore-6.3.0

XDG_SESSION_ID=232946

ARBHOME=/opt/conda/envs/qiime2-2019.7/lib/arb

USER_PATH=/gstore/apps/singularity/3.0.3-foss-2017a/bin:/gstore/apps/dep/0.5.0-foss-2017a/bin:/gstore/apps/go/1.11/bin:/gstore/apps/libarchive/3.3.3-foss-2017a/bin:/gstore/apps/libxml2/2.9.4-foss-2017a/bin:/gstore/apps/FFTW/3.3.6-gompi-2017a/bin:/gstore/apps/OpenBLAS/0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0/bin:/gstore/apps/OpenMPI/2.1.0-GCC-6.3.0-2.28/bin:/gstore/apps/hwloc/1.11.6-GCC-6.3.0-2.28/sbin:/gstore/apps/hwloc/1.11.6-GCC-6.3.0-2.28/bin:/gstore/apps/numactl/2.0.11-GCCcore-6.3.0/bin:/gstore/apps/binutils/2.28-GCCcore-6.3.0/bin:/gstore/apps/GCCcore/6.3.0/bin:/cm/shared/apps/slurm/17.11.11/sbin:/cm/shared/apps/slurm/17.11.11/bin:/gstore/apps/utils/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:~/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/sbin

USER=macherls

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

EBDEVELLIBXML2=/gstore/apps/libxml2/2.9.4-foss-2017a/gstore/apps/logs/libxml2-2.9.4-foss-2017a-easybuild-devel

ARBHOME_BACKUP=

EBVERSIONHWLOC=1.11.6

STRIP=/opt/conda/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

LMOD_REDIRECT=yes

OBJCOPY=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-objcopy

_ModuleTable012_=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

EBVERSIONGCCCORE=6.3.0

_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu

EBROOTLIBARCHIVE=/gstore/apps/libarchive/3.3.3-foss-2017a

SINGULARITY_CONTAINER=/gstore/data/genomics/pipeline_resources/containers/qiime2-2019.7.sif

EBROOTSINGULARITY=/gstore/apps/singularity/3.0.3-foss-2017a

__LMOD_REF_COUNT_MODULEPATH=/gstore/apps/modulefiles/all:1;/gstore/apps/modulefiles/common:1;/gstore/apps/modulefiles/bioinfo:1;/gstore/apps/modulefiles/cdd:1

PYTHONNOUSERSITE=/opt/conda/envs/qiime2-2019.7/lib/python*/site-packages/

EBDEVELLIBARCHIVE=/gstore/apps/libarchive/3.3.3-foss-2017a/gstore/apps/logs/libarchive-3.3.3-foss-2017a-easybuild-devel

__LMOD_REF_COUNT_LOADEDMODULES=slurm/17.11.11:1;gredenv:1;GCCcore/6.3.0:1;binutils/2.28-GCCcore-6.3.0:1;GCC/6.3.0-2.28:1;numactl/2.0.11-GCCcore-6.3.0:1;hwloc/1.11.6-GCC-6.3.0-2.28:1;OpenMPI/2.1.0-GCC-6.3.0-2.28:1;OpenBLAS/0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0:1;gompi/2017a:1;FFTW/3.3.6-gompi-2017a:1;ScaLAPACK/2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0:1;foss/2017a:1;squashfs-tools/4.3-foss-2017a:1;zlib/1.2.11-GCCcore-6.3.0:1;libxml2/2.9.4-foss-2017a:1;libarchive/3.3.3-foss-2017a:1;go/1.11:1;dep/0.5.0-foss-2017a:1;libuuid/1.0.3-foss-2017a:1;singularity/3.0.3-foss-2017a:1

EBDEVELGO=/gstore/apps/go/1.11/gstore/apps/logs/go-1.11-easybuild-devel

PWD=/gstore/home/macherls/gne_qiime2/singularity

EBDEVELOPENBLAS=/gstore/apps/OpenBLAS/0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0/logs/OpenBLAS-0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0-easybuild-devel

HOME=/home/qiime2

GOROOT=/gstore/apps/go/1.11

EBROOTFOSS=/gstore/apps/foss/2017a

ADDR2LINE=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-addr2line

CONDA_PYTHON_EXE=/opt/conda/bin/python

HOST=x86_64-conda_cos6-linux-gnu

SSH_CLIENT=128.137.17.10 59469 22

EBDEVELSCALAPACK=/gstore/apps/ScaLAPACK/2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0/gstore/apps/logs/ScaLAPACK-2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0-easybuild-devel

LMOD_VERSION=7.7.34

CPATH=/gstore/apps/libuuid/1.0.3-foss-2017a/include:/gstore/apps/libarchive/3.3.3-foss-2017a/include:/gstore/apps/libxml2/2.9.4-foss-2017a/include:/gstore/apps/zlib/1.2.11-GCCcore-6.3.0/include:/gstore/apps/ScaLAPACK/2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0/include:/gstore/apps/FFTW/3.3.6-gompi-2017a/include:/gstore/apps/OpenBLAS/0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0/include:/gstore/apps/OpenMPI/2.1.0-GCC-6.3.0-2.28/include:/gstore/apps/hwloc/1.11.6-GCC-6.3.0-2.28/include:/gstore/apps/numactl/2.0.11-GCCcore-6.3.0/include:/gstore/apps/binutils/2.28-GCCcore-6.3.0/include:/gstore/apps/GCCcore/6.3.0/include:/cm/shared/apps/slurm/17.11.11/include

SINGULARITY_CACHEDIR=/gstore/scratch/u/macherls

F77=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran

KRB5CCNAME=FILE:/tmp/krb5cc_751380_IcjozQ

FORTRANFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe

BASH_ENV=/gstore/apps/Lmod/default/lmod/lmod/init/bash

EBVERSIONSQUASHFSMINTOOLS=4.3

RANLIB=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ranlib

OBJDUMP=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-objdump

AS=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-as

AR=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ar

EBVERSIONLIBUUID=1.0.3

GFORTRAN=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran

CONDA_BACKUP_HOST=x86_64-conda_cos6-linux-gnu

_CE_CONDA=

EBROOTLIBXML2=/gstore/apps/libxml2/2.9.4-foss-2017a

__LMOD_REF_COUNT_LIBRARY_PATH=/gstore/apps/libuuid/1.0.3-foss-2017a/lib:1;/gstore/apps/go/1.11/lib:1;/gstore/apps/libarchive/3.3.3-foss-2017a/lib:1;/gstore/apps/libxml2/2.9.4-foss-2017a/lib:1;/gstore/apps/zlib/1.2.11-GCCcore-6.3.0/lib:1;/gstore/apps/ScaLAPACK/2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0/lib:1;/gstore/apps/FFTW/3.3.6-gompi-2017a/lib:1;/gstore/apps/OpenBLAS/0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0/lib:1;/gstore/apps/OpenMPI/2.1.0-GCC-6.3.0-2.28/lib:1;/gstore/apps/hwloc/1.11.6-GCC-6.3.0-2.28/lib:1;/gstore/apps/numactl/2.0.11-GCCcore-6.3.0/lib:1;/gstore/apps/binutils/2.28-GCCcore-6.3.0/lib:1;/gstore/apps/GCCcore/6.3.0/lib64:1;/gstore/apps/GCCcore/6.3.0/lib:1;/cm/shared/apps/slurm/17.11.11/lib64/slurm:1;/cm/shared/apps/slurm/17.11.11/lib64:1

EBVERSIONLIBXML2=2.9.4

LIBRARY_PATH=/gstore/apps/libuuid/1.0.3-foss-2017a/lib:/gstore/apps/go/1.11/lib:/gstore/apps/libarchive/3.3.3-foss-2017a/lib:/gstore/apps/libxml2/2.9.4-foss-2017a/lib:/gstore/apps/zlib/1.2.11-GCCcore-6.3.0/lib:/gstore/apps/ScaLAPACK/2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0/lib:/gstore/apps/FFTW/3.3.6-gompi-2017a/lib:/gstore/apps/OpenBLAS/0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0/lib:/gstore/apps/OpenMPI/2.1.0-GCC-6.3.0-2.28/lib:/gstore/apps/hwloc/1.11.6-GCC-6.3.0-2.28/lib:/gstore/apps/numactl/2.0.11-GCCcore-6.3.0/lib:/gstore/apps/binutils/2.28-GCCcore-6.3.0/lib:/gstore/apps/GCCcore/6.3.0/lib64:/gstore/apps/GCCcore/6.3.0/lib:/cm/shared/apps/slurm/17.11.11/lib64/slurm:/cm/shared/apps/slurm/17.11.11/lib64

LMOD_sys=Linux

_ModuleTable010_=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

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

_ModuleTable001_=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

EBDEVELGOMPI=/gstore/apps/gompi/2017a/gstore/apps/logs/gompi-2017a-easybuild-devel

LOADEDMODULES=slurm/17.11.11:gredenv:GCCcore/6.3.0:binutils/2.28-GCCcore-6.3.0:GCC/6.3.0-2.28:numactl/2.0.11-GCCcore-6.3.0:hwloc/1.11.6-GCC-6.3.0-2.28:OpenMPI/2.1.0-GCC-6.3.0-2.28:OpenBLAS/0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0:gompi/2017a:FFTW/3.3.6-gompi-2017a:ScaLAPACK/2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0:foss/2017a:squashfs-tools/4.3-foss-2017a:zlib/1.2.11-GCCcore-6.3.0:libxml2/2.9.4-foss-2017a:libarchive/3.3.3-foss-2017a:go/1.11:dep/0.5.0-foss-2017a:libuuid/1.0.3-foss-2017a:singularity/3.0.3-foss-2017a

GRED_SREGISTRY_DATABASE=/system/containers/registry/sregistry.db

LMOD_AVAIL_STYLE=system:<gred_hpc>

EBROOTGO=/gstore/apps/go/1.11

FC=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran

__LMOD_REF_COUNT_ACLOCAL_PATH=/gstore/apps/libxml2/2.9.4-foss-2017a/share/aclocal:1

EBDEVELOPENMPI=/gstore/apps/OpenMPI/2.1.0-GCC-6.3.0-2.28/gstore/apps/logs/OpenMPI-2.1.0-GCC-6.3.0-2.28-easybuild-devel

__LMOD_REF_COUNT_MANPATH=/gstore/apps/libarchive/3.3.3-foss-2017a/share/man:1;/gstore/apps/libxml2/2.9.4-foss-2017a/share/man:1;/gstore/apps/zlib/1.2.11-GCCcore-6.3.0/share/man:1;/gstore/apps/FFTW/3.3.6-gompi-2017a/share/man:1;/gstore/apps/OpenMPI/2.1.0-GCC-6.3.0-2.28/share/man:1;/gstore/apps/hwloc/1.11.6-GCC-6.3.0-2.28/share/man:1;/gstore/apps/numactl/2.0.11-GCCcore-6.3.0/share/man:1;/gstore/apps/binutils/2.28-GCCcore-6.3.0/share/man:1;/gstore/apps/GCCcore/6.3.0/share/man:1;/cm/shared/apps/slurm/17.11.11/man:1;/gstore/apps/Lmod/default/lmod/lmod/share/man:1;/usr/local/share/man:1;/usr/share/man/overrides:1;/usr/share/man:1;/opt/ibutils/share/man:1;/cm/local/apps/environment-modules/current/share/man:1

_ModuleTable006_=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

SCRATCH=/gstore/scratch/u/macherls

EBVERSIONZLIB=1.2.11

_ModuleTable003_=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

NM=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-nm

CONDA_PROMPT_MODIFIER=(qiime2-2019.7) 

SSH_TTY=/dev/pts/27

_ModuleTable013_=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

MAIL=/var/spool/mail/macherls

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

EBROOTSQUASHFSMINTOOLS=/gstore/apps/squashfs-tools/4.3-foss-2017a

CXX=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-c++

QTLIB=/usr/lib64/qt-3.3/lib

EBROOTFFTW=/gstore/apps/FFTW/3.3.6-gompi-2017a

_ModuleTable009_=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

SHELL=/bin/bash

TERM=xterm-256color

LMOD_ADMIN_FILE=/system/gredit/lmod/admin.list

QT_GRAPHICSSYSTEM_CHECKED=1

SINGULARITY_NAME=qiime2-2019.7.sif

CXXFILT=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-c++filt

MPLBACKEND=Agg

EBDEVELGCCCORE=/gstore/apps/GCCcore/6.3.0/gstore/apps/logs/GCCcore-6.3.0-easybuild-devel

EBROOTHWLOC=/gstore/apps/hwloc/1.11.6-GCC-6.3.0-2.28

SIF=/gstore/data/genomics/pipeline_resources/containers/qiime2-2019.7.sif

_ModuleTable_Sz_=14

__LMOD_REF_COUNT_CPATH=/gstore/apps/libuuid/1.0.3-foss-2017a/include:1;/gstore/apps/libarchive/3.3.3-foss-2017a/include:1;/gstore/apps/libxml2/2.9.4-foss-2017a/include:1;/gstore/apps/zlib/1.2.11-GCCcore-6.3.0/include:1;/gstore/apps/ScaLAPACK/2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0/include:1;/gstore/apps/FFTW/3.3.6-gompi-2017a/include:1;/gstore/apps/OpenBLAS/0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0/include:1;/gstore/apps/OpenMPI/2.1.0-GCC-6.3.0-2.28/include:1;/gstore/apps/hwloc/1.11.6-GCC-6.3.0-2.28/include:1;/gstore/apps/numactl/2.0.11-GCCcore-6.3.0/include:1;/gstore/apps/binutils/2.28-GCCcore-6.3.0/include:1;/gstore/apps/GCCcore/6.3.0/include:1;/cm/shared/apps/slurm/17.11.11/include:1

EBDEVELBINUTILS=/gstore/apps/binutils/2.28-GCCcore-6.3.0/gstore/apps/logs/binutils-2.28-GCCcore-6.3.0-easybuild-devel

SACCT_FORMAT=jobid%-12,partition%-9,jobname%-32,user%-10,state%-10,nodelist%-12,ncpus%-5,nnodes%-5,allocgres%-6,maxrss%-8,start%-20,end%-20,elapsed%-12,cputimeraw%-9,exitcode%-4

ELFEDIT=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-elfedit

SHLVL=2

EBDEVELLIBUUID=/gstore/apps/libuuid/1.0.3-foss-2017a/gstore/apps/logs/libuuid-1.0.3-foss-2017a-easybuild-devel

ACLOCAL_PATH=/gstore/apps/libxml2/2.9.4-foss-2017a/share/aclocal

FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe

MANPATH=/gstore/apps/libarchive/3.3.3-foss-2017a/share/man:/gstore/apps/libxml2/2.9.4-foss-2017a/share/man:/gstore/apps/zlib/1.2.11-GCCcore-6.3.0/share/man:/gstore/apps/FFTW/3.3.6-gompi-2017a/share/man:/gstore/apps/OpenMPI/2.1.0-GCC-6.3.0-2.28/share/man:/gstore/apps/hwloc/1.11.6-GCC-6.3.0-2.28/share/man:/gstore/apps/numactl/2.0.11-GCCcore-6.3.0/share/man:/gstore/apps/binutils/2.28-GCCcore-6.3.0/share/man:/gstore/apps/GCCcore/6.3.0/share/man:/cm/shared/apps/slurm/17.11.11/man:/gstore/apps/Lmod/default/lmod/lmod/share/man:/usr/local/share/man:/usr/share/man/overrides:/usr/share/man:/opt/ibutils/share/man:/cm/local/apps/environment-modules/current/share/man

EBDEVELGCC=/gstore/apps/GCC/6.3.0-2.28/gstore/apps/logs/GCC-6.3.0-2.28-easybuild-devel

CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2

EBDEVELSINGULARITY=/gstore/apps/singularity/3.0.3-foss-2017a/gstore/apps/logs/singularity-3.0.3-foss-2017a-easybuild-devel

EBVERSIONFFTW=3.3.6

STRINGS=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-strings

F90=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gfortran

F95=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-f95

MODULEPATH=/gstore/apps/modulefiles/all:/gstore/apps/modulefiles/common:/gstore/apps/modulefiles/bioinfo:/gstore/apps/modulefiles/cdd

EBVERSIONDEP=0.5.0

EBDEVELFFTW=/gstore/apps/FFTW/3.3.6-gompi-2017a/gstore/apps/logs/FFTW-3.3.6-gompi-2017a-easybuild-devel

LOGNAME=macherls

JAVA_HOME_CONDA_BACKUP=

XDG_RUNTIME_DIR=/run/user/751380

RSTUDIO_WHICH_R=/opt/conda/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

EBVERSIONBINUTILS=2.28

MODULEPATH_ROOT=/gstore/apps/modulefiles

LMOD_PACKAGE_PATH=/system/gredit/lmod

EBDEVELZLIB=/gstore/apps/zlib/1.2.11-GCCcore-6.3.0/gstore/apps/logs/zlib-1.2.11-GCCcore-6.3.0-easybuild-devel

PATH=/opt/conda/envs/qiime2-2019.7/bin:/opt/conda/condabin:/opt/conda/envs/qiime2-2019.7/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

_ModuleTable014_=ZWZpbGVzL2NkZCIsfQ==

_LMFILES_=/gstore/apps/modulefiles/common/slurm/17.11.11.lua:/gstore/apps/modulefiles/common/gredenv.lua:/gstore/apps/modulefiles/all/GCCcore/6.3.0.lua:/gstore/apps/modulefiles/all/binutils/2.28-GCCcore-6.3.0.lua:/gstore/apps/modulefiles/all/GCC/6.3.0-2.28.lua:/gstore/apps/modulefiles/all/numactl/2.0.11-GCCcore-6.3.0.lua:/gstore/apps/modulefiles/all/hwloc/1.11.6-GCC-6.3.0-2.28.lua:/gstore/apps/modulefiles/all/OpenMPI/2.1.0-GCC-6.3.0-2.28.lua:/gstore/apps/modulefiles/all/OpenBLAS/0.2.19-GCC-6.3.0-2.28-LAPACK-3.7.0.lua:/gstore/apps/modulefiles/all/gompi/2017a.lua:/gstore/apps/modulefiles/all/FFTW/3.3.6-gompi-2017a.lua:/gstore/apps/modulefiles/all/ScaLAPACK/2.0.2-gompi-2017a-OpenBLAS-0.2.19-LAPACK-3.7.0.lua:/gstore/apps/modulefiles/all/foss/2017a.lua:/gstore/apps/modulefiles/all/squashfs-tools/4.3-foss-2017a.lua:/gstore/apps/modulefiles/all/zlib/1.2.11-GCCcore-6.3.0.lua:/gstore/apps/modulefiles/all/libxml2/2.9.4-foss-2017a.lua:/gstore/apps/modulefiles/all/libarchive/3.3.3-foss-2017a.lua:/gstore/apps/modulefiles/all/go/1.11.lua:/gstore/apps/modulefiles/all/dep/0.5.0-foss-2017a.lua:/gstore/apps/modulefiles/all/libuuid/1.0.3-foss-2017a.lua:/gstore/apps/modulefiles/all/singularity/3.0.3-foss-2017a.lua

PS1=(qiime2-2019.7) Singularity qiime2-2019.7.sif:\w> 

GCC=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-gcc

MODULESHOME=/gstore/apps/Lmod/7.7.34-foss-2017a/lmod/lmod

CONDA_DEFAULT_ENV=qiime2-2019.7

LMOD_SETTARG_FULL_SUPPORT=no

PKG_CONFIG_PATH=/gstore/apps/libuuid/1.0.3-foss-2017a/lib/pkgconfig:/gstore/apps/libarchive/3.3.3-foss-2017a/lib/pkgconfig:/gstore/apps/libxml2/2.9.4-foss-2017a/lib/pkgconfig:/gstore/apps/zlib/1.2.11-GCCcore-6.3.0/lib/pkgconfig:/gstore/apps/FFTW/3.3.6-gompi-2017a/lib/pkgconfig:/gstore/apps/OpenMPI/2.1.0-GCC-6.3.0-2.28/lib/pkgconfig:/gstore/apps/hwloc/1.11.6-GCC-6.3.0-2.28/lib/pkgconfig

LMOD_CACHED_LOADS=yes

_ModuleTable011_=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

EBROOTNUMACTL=/gstore/apps/numactl/2.0.11-GCCcore-6.3.0

EBVERSIONGO=1.11

HISTSIZE=1000

SIZE=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-size

LMOD_PKG=/gstore/apps/Lmod/7.7.34-foss-2017a/lmod/lmod

CPP=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-cpp

LD=/opt/conda/envs/qiime2-2019.7/bin/x86_64-conda_cos6-linux-gnu-ld

_ModuleTable005_=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

LMOD_CMD=/gstore/apps/Lmod/7.7.34-foss-2017a/lmod/lmod/libexec/lmod

EBDEVELDEP=/gstore/apps/dep/0.5.0-foss-2017a/gstore/apps/logs/dep-0.5.0-foss-2017a-easybuild-devel

CVS_RSH=ssh

LESSOPEN=||/usr/bin/lesspipe.sh %s

JAVA_LD_LIBRARY_PATH_BACKUP=

LMOD_DIR=/gstore/apps/Lmod/7.7.34-foss-2017a/lmod/lmod/libexec

_=/usr/bin/env

[chetana]

And I do see tzlocal v2.0.0 defined in the config file of the container. I’m not sure if its the issue with qiime or the container

[thermokarst]

Can you please provide the error you observed? You mentioned above:

@chetana

I get this ValueError of timezones not matching

But, the post you linked to is not about mismatched timezones, it is about unknown timezones (which I think is different). Either way, this is almost certainly going to be easiest to fix in the definition of the singularity container, I would have a chat with whoever created the container (but, please share the error message that you saw, and the command you ran, and the version of QIIME 2 you are running).

[SetaPark]

Hello
In case this is useful…
I was getting error
ValueError: Timezone offset does not match system offset: 0 != 43200. Please, check your config files.
An inhouse expert asked me to add in
export TZ=‘Pacific/Auckland’
which helped.

Thanks

[chetana]

Hi @SetaPark, thanks for your response. I’m not sure where to add it in, could you please let me know?

Thanks,
Chetana

[chetana]

Hi @thermokarst, the version of qiime2 used for the singularity container is 2019.7. Here is the command that I used -

"qiime metadata tabulate --m-input-file /gstore/home/macherls/gne_qiime2/trial_qiime2_wdl/Demultiplex_Sheet.txt --o-visualization /gstore/home/macherls/gne_qiime2/trial_qiime2_wdl/visualizations/MQ2121_mapping.qzv"

and the error I see is -

"Plugin error from metadata:

Timezone offset does not match system offset: 0 != -25200. Please, check your config files.

Debug info has been saved to /tmp/qiime2-q2cli-err-bryq9rg_.log"

And find the debug info in the logfile qiime2_sig_logfile.txt (2.5 KB) attached to the post here.

Thanks for your help.

Chetana

[SetaPark]

Hi @chetana

I added it before the script like so…
export TZ=‘Pacific/Auckland’
qiime phylogeny align-to-tree-mafft-fasttree
–i-sequences $FILTER/filt-rep-seqs-dada2-7.qza
–o-alignment $PHYLOGENY/filt-aligned-rep-seqs-7.qza
–o-masked-alignment $PHYLOGENY/filt-masked-aligned-rep-seqs-7.qza
–o-tree $PHYLOGENY/filt-unrooted-tree-7.qza
–o-rooted-tree $PHYLOGENY/filt-rooted-tree-7.qza

Of course, you will have to add the timezone relevant to you? And I had to do it only once when running a workflow. So not required for subsequent commands.

Hope this helps.
Regards

[chetana]

Hi @SetaPark,

Thanks for the comment. It worked. Now I don’t get the timezone error anymore. I guess it’s with the singularity container, adding this tz environmental variable to the container fixed it as well.

Thanks,
Chetana