Hello Carli,
As close as I can tell, this error has to do with special characters (not utf-8) in your metadata file. These are often sÿmbõs not commonly found in english.
You can use keemei to validate your metadata, and that should detect any unsuspected characters. https://keemei.qiime2.org/
Let me know what you find!
Colin
Hi Colin,
I validated the metadata file using Keemei and did not find errors or special symbols! In our sample ID column, we have the sample names listed as Sample_1 for example, using an underscore instead of a dash because this is how they are formatted in our manifest file, and this has never caused us issues before even though Keemei gives a warning on this. There were no other errors.
I tried converting our dates from using slashes (ie. 3/26/20) to dashes (ie. 3-26-20) to see if that would help, but it did not and I got the same error.
Best,
Carli
Did you look for hiden characters?
Try open the metadata file with VI or VIM and type :set invlist
That will show you all hiden charac. Maybe there is something.
Cheers
Hi Leo,
Thanks for your reply!! When I try doing that, I get this:
Are the $ a problem? The symbol \u03b2 in the error code refers to a greek beta, which I definitely don't see anywhere...
Thanks,
Carli
Hello Carli,
Thanks for validating with Keemei.
Well, I’m all out of ideas. Let’s see what the devs suggest!
Colin
Hey @colinbrislawn & @cjone228, I think we might be looking at the wrong things here:
Looking at the error traceback (thanks for sharing that, @cjone228!), it looks like the error is cropping up when QIIME 2 is attempting to save the citation data in the QZA’s provenance. That probably means the β is being introduced via the citations, not your input files.
Okay, so taking a closer look at the “meat” of the error message - it sounds like your local computational environment might be set to a latin locale. We can double check that by running the following command:
env
There are a handful of environment variables that we might need to change, but in general QIIME 2 expects you to be using a UTF-8 locale.
Great! That post is actually right in line with where we need to get going towards. Follow up to my previous post with the output of the env command and we will go from there. Thanks!
Hi Matthew!
When I do env, I get the following for the language:
LC_ALL=en_US.utf8
(I followed the instructions from the post I linked to to get this, but before it was UTF8 anyway. I also added this to my .bashrc file)
I got the same error again when running the core metrics analysis - any ideas?
Thanks!!
Oops, sorry about that!! Here’s the full output:
(base) [[email protected]@bc-login03 ~]$ env
MARCC_COMPILER_MAJOR=5
LMOD_FAMILY_COMPILER_VERSION=5.5.0
MANPATH=/software/apps/mpi/openmpi/3.1/gcc/5.5/share/man:/software/apps/compilers/gcc/5.5.0/share/man:/software/apps/slurm/current/share/man:/software/lmod/lmod/share/man
XDG_SESSION_ID=4478
_ModuleTable003_=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
HOSTNAME=bc-login03
MPI_FFLAGS=-I/software/apps/mpi/openmpi/3.1/gcc/5.5/include
MPI_F90FLAGS=-I/software/apps/mpi/openmpi/3.1/gcc/5.5/include
MPICH_HOME=/software/apps/mpi/openmpi/3.1/gcc/5.5
__LMOD_REF_COUNT_MODULEPATH=/software/lmod/modulefiles/mpi_compiler/gcc/5.5:1;/software/lmod/modulefiles/compiler_and_base:1;/software/lmod/modulefiles/apps:1;/software/lmod/modulefiles/holding_apps:1;/software/lmod/modulefiles/compiled_apps/gcc/5.5:1;/software/lmod/modulefiles/mpi_compiled_apps/gcc/5.5/openmpi/3.1:1
TERM=xterm-256color
SHELL=/bin/bash
HISTSIZE=1000
TMPDIR=/home-1/[email protected]/scratch
MODULEPATH_ROOT=/software/lmod/modulefiles
LMOD_SYSTEM_DEFAULT_MODULES=MARCC/summer-2018
SSH_CLIENT=172.16.0.9 34964 22
CONDA_SHLVL=1
__LMOD_STACK_CXX=Zysr
PERL5LIB=/software/centos7/usr/share/autoconf:/software/centos7/usr/share/automake-1.13:/software/centos7/usr/lib64/perl5/vendor_perl:/software/centos7/usr/share/perl5/vendor_perl:/software/centos7/usr/lib64/perl5:/software/centos7/usr/share/perl5
LIBRARY_PATH=/software/apps/compilers/gcc/5.5.0/lib64:/software/apps/compilers/gcc/5.5.0/lib:/software/centos7/lib64:/software/centos7/lib:/software/centos7/usr/lib64:/software/centos7/usr/lib:/software/apps/slurm/current/lib/slurm:/software/apps/slurm/current/lib
LMOD_PACKAGE_PATH=/software/lmod/site
CONDA_PROMPT_MODIFIER=(base)
LMOD_PKG=/software/lmod/lmod
LMOD_VERSION=7.8.1
SSH_TTY=/dev/pts/192
LC_ALL=en_US.utf8
__LMOD_STACK_FC=Z2ZvcnRyYW4=
__LMOD_REF_COUNT_LOADEDMODULES=centos7/current:1;MARCC/summer-2018:1;gcc/5.5.0:1;openmpi/3.1:1;slurm/.current:1
__LMOD_STACK_CC=Z2Nj
[email protected]
LMOD_sys=Linux
LD_LIBRARY_PATH=/software/apps/mpi/openmpi/3.1/gcc/5.5/lib:/software/apps/compilers/gcc/5.5.0/lib64:/software/apps/compilers/gcc/5.5.0/lib:/usr/lib:/usr/lib64:/software/centos7/lib64:/software/centos7/lib:/software/centos7/usr/lib64:/software/centos7/usr/lib:/software/apps/slurm/current/lib/slurm:/software/apps/slurm/current/lib::
CONDA_EXE=/home-1/[email protected]/miniconda3/bin/conda
MARCC_COMPILER_MINOR=5
VALGRIND_LIB=/software/centos7/lib64/valgrind
__LMOD_STACK_F77=Z2ZvcnRyYW4=
_ModuleTable004_=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
CPATH=/software/apps/compilers/gcc/5.5.0/include:/software/apps/compilers/gcc/5.5.0/lib/gcc/x86_64-redhat-linux/5.5.0/include:/software/apps/compilers/gcc/5.5.0/lib/gcc/x86_64-redhat-linux/5.5.0/include-fixed:/software/apps/compilers/gcc/5.5.0/lib/gcc/x86_64-redhat-linux/5.5.0/plugin/include:/software/apps/compilers/gcc/5.5.0/lib/gcc/x86_64-redhat-linux/5.5.0/install-tools/include:/software/centos7/usr/local/include/:/software/centos7/usr/include/
__LMOD_REF_COUNT__LMFILES_=/software/lmod/modulefiles/compiler_and_base/centos7/current.lua:1;/software/lmod/modulefiles/compiler_and_base/MARCC/summer-2018.lua:1;/software/lmod/modulefiles/compiler_and_base/gcc/5.5.0.lua:1;/software/lmod/modulefiles/mpi_compiler/gcc/5.5/openmpi/3.1.lua:1;/software/lmod/modulefiles/apps/slurm/.current.lua:1
_CE_CONDA=
MPI_CXXFLAGS=-I/software/apps/mpi/openmpi/3.1/gcc/5.5/include
MPI_CFLAGS=-I/software/apps/mpi/openmpi/3.1/gcc/5.5/include
LMOD_FAMILY_MPI_VERSION=3.1
FONTCONFIG_PATH=/software/centos7/etc/fonts/
_ModuleTable001_=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
MAIL=/var/spool/mail/[email protected]
PATH=/home-1/[email protected]/miniconda3/envs/qiime2-2020.2/bin:/home-1/[email protected]/miniconda3/bin:/home-1/[email protected]/miniconda3/condabin:/software/apps/mpi/openmpi/3.1/gcc/5.5/bin:/software/apps/compilers/gcc/5.5.0/bin:/software/apps/marcc/bin:/software/centos7/bin:/software/centos7/sbin:/software/apps/slurm/current/sbin:/software/apps/slurm/current/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/home-1/[email protected]/.local/bin:/home-1/[email protected]/bin
CONDA_PREFIX=/home-1/[email protected]/miniconda3
PWD=/home-1/[email protected]
_LMFILES_=/software/lmod/modulefiles/compiler_and_base/centos7/current.lua:/software/lmod/modulefiles/compiler_and_base/MARCC/summer-2018.lua:/software/lmod/modulefiles/compiler_and_base/gcc/5.5.0.lua:/software/lmod/modulefiles/mpi_compiler/gcc/5.5/openmpi/3.1.lua:/software/lmod/modulefiles/apps/slurm/.current.lua
MARCC_COMPILER=gcc
LANG=en_US.UTF-8
MODULEPATH=/software/lmod/modulefiles/mpi_compiler/gcc/5.5:/software/lmod/modulefiles/compiler_and_base:/software/lmod/modulefiles/apps:/software/lmod/modulefiles/holding_apps:/software/lmod/modulefiles/compiled_apps/gcc/5.5:/software/lmod/modulefiles/mpi_compiled_apps/gcc/5.5/openmpi/3.1
LOADEDMODULES=centos7/current:MARCC/summer-2018:gcc/5.5.0:openmpi/3.1:slurm/.current
_ModuleTable_Sz_=5
F77=gfortran
_ModuleTable005_=ZWZpbGVzL2hvbGRpbmdfYXBwcyIsfQ==
LMOD_CMD=/software/lmod/lmod/libexec/lmod
LMOD_AVAIL_STYLE=en_grouped
_CE_M=
CXX=g++
HISTCONTROL=ignoredups
SHLVL=1
HOME=/home-1/[email protected]
__LMOD_REF_COUNT_PERL5LIB=/software/centos7/usr/share/autoconf:1;/software/centos7/usr/share/automake-1.13:1;/software/centos7/usr/lib64/perl5/vendor_perl:1;/software/centos7/usr/share/perl5/vendor_perl:1;/software/centos7/usr/lib64/perl5:1;/software/centos7/usr/share/perl5:1
__LMOD_REF_COUNT_PATH=/software/apps/mpi/openmpi/3.1/gcc/5.5/bin:1;/software/apps/compilers/gcc/5.5.0/bin:1;/software/apps/marcc/bin:1;/software/centos7/bin:1;/software/centos7/sbin:1;/software/apps/slurm/current/sbin:2;/software/apps/slurm/current/bin:2;/usr/local/bin:1;/usr/bin:1;/usr/local/sbin:1;/usr/sbin:1;/opt/ibutils/bin:1
_ModuleTable002_=b2R1bGVmaWxlcy9jb21waWxlcl9hbmRfYmFzZS9jZW50b3M3L2N1cnJlbnQubHVhIixbImZ1bGxOYW1lIl09ImNlbnRvczcvY3VycmVudCIsWyJsb2FkT3JkZXIiXT0xLHByb3BUPXt9LFsic3RhY2tEZXB0aCJdPTEsWyJzdGF0dXMiXT0iYWN0aXZlIixbInVzZXJOYW1lIl09ImNlbnRvczciLH0sZ2NjPXtbImZuIl09Ii9zb2Z0d2FyZS9sbW9kL21vZHVsZWZpbGVzL2NvbXBpbGVyX2FuZF9iYXNlL2djYy81LjUuMC5sdWEiLFsiZnVsbE5hbWUiXT0iZ2NjLzUuNS4wIixbImxvYWRPcmRlciJdPTMscHJvcFQ9e30sWyJzdGFja0RlcHRoIl09MCxbInN0YXR1cyJdPSJhY3RpdmUiLFsidXNlck5hbWUiXT0iZ2NjIix9LG9wZW5tcGk9e1siZm4iXT0iL3NvZnR3YXJlL2xtb2QvbW9k
FC=gfortran
BASH_ENV=/software/lmod/lmod/init/bash
CONDA_PYTHON_EXE=/home-1/[email protected]/miniconda3/bin/python
[email protected]
OMPI_TMPDIR=/tmp
SSH_CONNECTION=172.16.0.9 34964 172.16.5.5 22
__LMOD_REF_COUNT_LIBRARY_PATH=/software/apps/compilers/gcc/5.5.0/lib64:1;/software/apps/compilers/gcc/5.5.0/lib:1;/software/centos7/lib64:1;/software/centos7/lib:1;/software/centos7/usr/lib64:1;/software/centos7/usr/lib:1;/software/apps/slurm/current/lib/slurm:1;/software/apps/slurm/current/lib:1
MODULESHOME=/software/lmod/lmod
CONDA_DEFAULT_ENV=base
PKG_CONFIG_PATH=/software/centos7/usr/share/pkgconfig:/software/centos7/usr/lib64/pkgconfig
__LMOD_REF_COUNT_LD_LIBRARY_PATH=/software/apps/mpi/openmpi/3.1/gcc/5.5/lib:1;/software/apps/compilers/gcc/5.5.0/lib64:1;/software/apps/compilers/gcc/5.5.0/lib:1;/usr/lib:1;/usr/lib64:1;/software/centos7/lib64:1;/software/centos7/lib:1;/software/centos7/usr/lib64:1;/software/centos7/usr/lib:1;/software/apps/slurm/current/lib/slurm:2;/software/apps/slurm/current/lib:2
LMOD_SETTARG_FULL_SUPPORT=no
LESSOPEN=||/usr/bin/lesspipe.sh %s
LMOD_FAMILY_COMPILER=gcc
__LMOD_REF_COUNT_PKG_CONFIG_PATH=/software/centos7/usr/share/pkgconfig:1;/software/centos7/usr/lib64/pkgconfig:1
CC=gcc
XDG_RUNTIME_DIR=/run/user/4318
__LMOD_REF_COUNT_MANPATH=/software/apps/mpi/openmpi/3.1/gcc/5.5/share/man:1;/software/apps/compilers/gcc/5.5.0/share/man:1;/software/apps/slurm/current/share/man:1;/software/lmod/lmod/share/man:1
LMOD_DIR=/software/lmod/lmod/libexec
LMOD_FAMILY_MPI=openmpi
BASH_FUNC_module()=() { eval $($LMOD_CMD bash "$@") && eval $(${LMOD_SETTARG_CMD:-:} -s sh)
}
BASH_FUNC_ml()=() { eval $($LMOD_DIR/ml_cmd "$@")
}
_=/software/centos7/bin/env
OLDPWD=/home-1/[email protected]/work/IT_pilotEverything is fine. The $ there means “end of line” and the “^I” means a TAB character. So it’s ok. Let’s see what Thermokarst has on the output you’ve posted.
Cheers
Thanks @cjone228!
See this env var:
This is one of those related ones I was looking for. I suspect that all you need to do is update your LC_ALL to use the same formatting as the value above (your value is formatted differently - the locale databases vary a bit from system to system, and usually are based on an "exact match" of the value):
LC_ALL=en_US.UTF-8
If that doesn't fix it, please run the following and paste all of the results here:
locale
Thanks!
Hi Matt! I changed LC_ALL back to en_US.UTF-8 (this is what it was originally), and tried running my SLURM job again. Unfortunately it failed again, but I’m not surprised. 
When I run locale, I get the following:
(base) [[email protected]@bc-login02 IT_pilot]$ locale
LANG=en_US.UTF-8
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-8Ohhh, I wonder if the locale isn’t consistent within the slurm cluster. You might need to set these env vars inside your submission script. Might also be worth a chat with your sysadmin to see what they think.
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