Error when running DADA2

Hi, I got the following error when trying to perform quality control with DADA2:

Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: run_dada_paired.R /var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/forward /var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/reverse /var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/output.tsv.biom /var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/track.tsv /var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/filt_f /var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/filt_r 260 190 19 42 2.0 2 consensus 1.0 1 1000000
cannot find system Renviron
Error: package or namespace load failed for ‘utils’:
.onLoad a ?chou? dans loadNamespace() pour ‘utils’, d?tails :
appel : options(op.utils[toset])
erreur : valeur incorrecte pour ‘editor’
Error: package or namespace load failed for ‘stats’:
.onLoad a ?chou? dans loadNamespace() pour ‘utils’, d?tails :
appel : options(op.utils[toset])
erreur : valeur incorrecte pour ‘editor’
Pendant le d?marrage - Warnmeldungen:
1: package ‘utils’ in options(“defaultPackages”) was not found
2: package ‘stats’ in options(“defaultPackages”) was not found
3: Setting LC_COLLATE failed, using “C”
4: Setting LC_TIME failed, using “C”
5: Setting LC_MESSAGES failed, using “C”
6: Setting LC_MONETARY failed, using “C”
R version 3.4.1 (2017-06-30)
Le chargement a n?cessit? le package : Rcpp
Error: package or namespace load failed for ‘Rcpp’:
.onLoad a ?chou? dans loadNamespace() pour ‘utils’, d?tails :
appel : options(op.utils[toset])
erreur : valeur incorrecte pour ‘editor’
Erreur : le package ‘Rcpp’ ne peut ?tre charg?
Ex?cution arr?t?e
Traceback (most recent call last):
File “/Users/whalenlab/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 229, in denoise_paired
run_commands([cmd])
File “/Users/whalenlab/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/Users/whalenlab/anaconda3/envs/qiime2-2018.6/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/forward’, ‘/var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/reverse’, ‘/var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/output.tsv.biom’, ‘/var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/track.tsv’, ‘/var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/filt_f’, ‘/var/folders/tp/_zmk_47n2ylcjw6zb_g_vq2m0000gp/T/tmpvsv2vsmh/filt_r’, ‘260’, ‘190’, ‘19’, ‘42’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘1’, ‘1000000’]’ returned non-zero exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/Users/whalenlab/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in denoise_paired
File “/Users/whalenlab/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 232, in bound_callable
output_types, provenance)
File “/Users/whalenlab/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 367, in callable_executor
output_views = self._callable(**view_args)
File “/Users/whalenlab/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 244, in denoise_paired
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more

The command I used was

qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end3-demux.qza --p-trim-left-f 19 --p-trim-left-r 42 --p-trunc-len-f 260 --p-trunc-len-r 190 --p-n-threads 1 --p-max-ee 2 --verbose --o-representative-sequences rep-seqs-dada3.qza --o-table table-dada3.qza --output-dir dada-two

I deleted the startup files of R in my computer a week ago and I did try to put back things from the trash. Is my error somehow related to the deleted R startup files?

Thank you so much.

*Update: I reinstalled R but this same error message appears.

**Update: I uninstalled RStudio and that does not seem to change things. I was able to perform the quality control on a different set of sequences two weeks ago. The only difference between now and then I can think of is that I attempted to install RStudio last week and tried to solve the problem that RStudio could not start by deleting the R startup files.

Hey there @ygao2!

Can you provide the output of the following command (after activating your QIIME 2 environment):

conda list

Also:

echo $R_LIBS_USER

Thanks! :qiime2: :t_rex:

Hi, here’s the output I got:

#packages in environment at /Users/whalenlab/anaconda3/envs/qiime2-2018.6:
##Name Version Build Channel
appnope 0.1.0 py35_0 conda-forge
asn1crypto 0.24.0 py35_0 conda-forge
backcall 0.1.0 py_0 conda-forge
bibtexparser 1.0.1 py35_0 conda-forge
bioconductor-biobase 2.38.0 r3.4.1_0 bioconda
bioconductor-biocgenerics 0.24.0 r3.4.1_0 bioconda
bioconductor-biocparallel 1.12.0 r3.4.1_0 bioconda
bioconductor-biostrings 2.46.0 r3.4.1_0 bioconda
bioconductor-dada2 1.6.0 r3.4.1_0 bioconda
bioconductor-delayedarray 0.4.1 r3.4.1_0 bioconda
bioconductor-genomeinfodb 1.14.0 r3.4.1_0 bioconda
bioconductor-genomeinfodbdata 1.0.0 r3.4.1_1 bioconda
bioconductor-genomicalignments 1.14.1 r3.4.1_0 bioconda
bioconductor-genomicranges 1.30.3 r3.4.1_0 bioconda
bioconductor-iranges 2.12.0 r3.4.1_0 bioconda
bioconductor-rsamtools 1.30.0 r3.4.1_0 bioconda
bioconductor-s4vectors 0.16.0 r3.4.1_0 bioconda
bioconductor-shortread 1.36.0 r3.4.1_0 bioconda
bioconductor-summarizedexperiment 1.8.0 r3.4.1_0 bioconda
bioconductor-xvector 0.18.0 r3.4.1_0 bioconda
bioconductor-zlibbioc 1.24.0 r3.4.1_0 bioconda
biom-format 2.1.6 py35_8 qiime2
blas 1.1 openblas conda-forge
blast 2.6.0 boost1.64_2 bioconda
bleach 2.1.3 py_0 conda-forge
bokeh 0.12.16 py35_0 conda-forge
ca-certificates 2018.4.16 0 conda-forge
cachecontrol 0.12.4 py_0 conda-forge
cairo 1.14.10 0 conda-forge
certifi 2018.4.16 py35_0 conda-forge
cffi 1.11.5 py35_0 conda-forge
chardet 3.0.4 py35_0 conda-forge
clangdev 6.0.0 default_0 conda-forge
click 6.7 py_1 conda-forge
cryptography 2.2.1 py35_0 conda-forge
curl 7.60.0 h93b3f91_0 conda-forge
cutadapt 1.16 py35_1 bioconda
cycler 0.10.0 py35_0 conda-forge
cython 0.28.3 py35hfc679d8_0 conda-forge
deblur 1.0.4 py35_2 bioconda
decorator 4.3.0 py_0 conda-forge
emperor 1.0.0beta16 py35_1 conda-forge
entrypoints 0.2.3 py35_1 conda-forge
fastcluster 1.1.25 py35_0 conda-forge
fasttree 2.1.10 0 bioconda
fontconfig 2.12.6 0 conda-forge
freetype 2.8.1 0 conda-forge
future 0.16.0 py35_0 conda-forge
gettext 0.19.8.1 0 conda-forge
glib 2.55.0 0 conda-forge
gneiss 0.4.4 py36h3f02924_1 biocore
graphite2 1.3.11 h7d4d677_0 conda-forge
gsl 2.1 2 conda-forge
h5py 2.7.0 np112py35_0 conda-forge
harfbuzz 1.7.6 0 conda-forge
hdf5 1.8.17 11 conda-forge
html5lib 1.0.1 py_0 conda-forge
icu 58.2 hfc679d8_0 conda-forge
idna 2.6 py35_1 conda-forge
ijson 2.3 py35_0 qiime2
intel-openmp 2018.0.3 0
ipykernel 4.8.2 py35_0 conda-forge
ipython 6.4.0 py35_0 conda-forge
ipython_genutils 0.2.0 py35_0 conda-forge
ipywidgets 7.2.1 py35_1 conda-forge
jedi 0.12.0 py35_0 conda-forge
jinja2 2.10 py35_0 conda-forge
jpeg 9b 2 conda-forge
jsonschema 2.6.0 py35_1 conda-forge
jupyter_client 5.2.3 py35_0 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
kiwisolver 1.0.1 py35_1 conda-forge
krb5 1.14.6 0 conda-forge
libcxx 6.0.0 0 conda-forge
libffi 3.2.1 3 conda-forge
libgcc 4.8.5 hdbeacc1_10
libgfortran 3.0.1 h93005f0_2
libiconv 1.15 h470a237_1 conda-forge
libpng 1.6.34 0 conda-forge
libsodium 1.0.16 0 conda-forge
libssh2 1.8.0 h5b517e9_2 conda-forge
libtiff 4.0.9 he6b73bb_0 conda-forge
libxml2 2.9.8 0 conda-forge
llvm-meta 6.0.0 0 conda-forge
llvmdev 6.0.0 default_3 conda-forge
lockfile 0.12.2 py35_0 conda-forge
mafft 7.310 1 bioconda
markupsafe 1.0 py35_0 conda-forge
matplotlib 2.2.2 py35_1 conda-forge
mistune 0.8.3 py35_1 conda-forge
mkl 2018.0.3 1
msgpack-python 0.5.6 py35h2d50403_2 conda-forge
natsort 5.3.2 py_0 conda-forge
nbconvert 5.3.1 py_1 conda-forge
nbformat 4.4.0 py35_0 conda-forge
ncurses 5.9 10 conda-forge
nose 1.3.7 py35_2 conda-forge
notebook 5.5.0 py35_0 conda-forge
numpy 1.12.1 py35_blas_openblas_200 [blas_openblas] conda-forge
openblas 0.2.19 2 conda-forge
openjdk 8.0.121 zulu8.20.0.5_0 conda-forge
openssl 1.0.2o 0 conda-forge
packaging 17.1 py_0 conda-forge
pandas 0.23.1 py35_0 conda-forge
pandoc 2.2.1 hde52d81_0 conda-forge
pandocfilters 1.4.2 py35_0 conda-forge
pango 1.40.14 0 conda-forge
parso 0.2.1 py_0 conda-forge
patsy 0.5.0 py35_0 conda-forge
pcre 8.39 0 conda-forge
pexpect 4.6.0 py35_0 conda-forge
pickleshare 0.7.4 py35_0 conda-forge
pigz 2.3.4 0 conda-forge
pip 9.0.3 py35_0 conda-forge
pip 10.0.1
pixman 0.34.0 2 conda-forge
prompt_toolkit 1.0.15 py35_0 conda-forge
psutil 5.4.6 py35_0 conda-forge
ptyprocess 0.5.2 py35_0 conda-forge
pycparser 2.18 py35_0 conda-forge
pygments 2.2.0 py35_0 conda-forge
pyopenssl 18.0.0 py35_0 conda-forge
pyparsing 2.2.0 py35_0 conda-forge
pysocks 1.6.8 py35_1 conda-forge
python 3.5.5 1 conda-forge
python-dateutil 2.7.3 py_0 conda-forge
pytz 2018.4 py_0 conda-forge
pyyaml 3.12 py35_1 conda-forge
pyzmq 17.0.0 py35_4 conda-forge
q2-alignment 2018.6.0 py35_0 qiime2/label/r2018.6
q2-composition 2018.6.0 py35_0 qiime2/label/r2018.6
q2-cutadapt 2018.6.0 py35_0 qiime2/label/r2018.6
q2-dada2 2018.6.0 py35_0 qiime2/label/r2018.6
q2-deblur 2018.6.0 py35_0 qiime2/label/r2018.6
q2-demux 2018.6.0 py35_0 qiime2/label/r2018.6
q2-diversity 2018.6.0 py35_0 qiime2/label/r2018.6
q2-emperor 2018.6.0 py35_0 qiime2/label/r2018.6
q2-feature-classifier 2018.6.0 py35_0 qiime2/label/r2018.6
q2-feature-table 2018.6.0 py35_0 qiime2/label/r2018.6
q2-gneiss 2018.6.0 py35_0 qiime2/label/r2018.6
q2-longitudinal 2018.6.0 py35_0 qiime2/label/r2018.6
q2-metadata 2018.6.0 py35_0 qiime2/label/r2018.6
q2-phylogeny 2018.6.0 py35_0 qiime2/label/r2018.6
q2-quality-control 2018.6.0 py35_0 qiime2/label/r2018.6
q2-quality-filter 2018.6.0 py35_0 qiime2/label/r2018.6
q2-sample-classifier 2018.6.0 py35_0 qiime2/label/r2018.6
q2-taxa 2018.6.0 py35_0 qiime2/label/r2018.6
q2-types 2018.6.0 py35_0 qiime2/label/r2018.6
q2-vsearch 2018.6.0 py35_0 qiime2/label/r2018.6
q2cli 2018.6.0 py35_0 qiime2/label/r2018.6
q2templates 2018.6.0 py35_0 qiime2/label/r2018.6
qiime2 2018.6.0 py35_0 qiime2/label/r2018.6
r-assertthat 0.2.0 r3.4.1_0 conda-forge
r-base 3.4.1 4 conda-forge
r-bh 1.66.0_1 r3.4.1_0 conda-forge
r-bitops 1.0_6 r3.4.1_0 conda-forge
r-cli 1.0.0 r3.4.1_0 conda-forge
r-colorspace 1.3_2 r3.4.1_0 conda-forge
r-crayon 1.3.4 r3.4.1_0 conda-forge
r-data.table 1.11.4 r341hc070d10_0 conda-forge
r-dichromat 2.0_0 r3.4.1_0 conda-forge
r-digest 0.6.15 r3.4.1_0 conda-forge
r-futile.logger 1.4.3 r3.4.1_0 conda-forge
r-futile.options 1.0.0 r3.4.1_0 conda-forge
r-ggplot2 2.2.1 r3.4.1_0 conda-forge
r-glue 1.2.0 r3.4.1_0 conda-forge
r-gtable 0.2.0 r3.4.1_0 conda-forge
r-hwriter 1.3.2 r3.4.1_0 conda-forge
r-labeling 0.3 r3.4.1_0 conda-forge
r-lambda.r 1.2 r3.4.1_0 conda-forge
r-lattice 0.20_34 r3.4.1_0 conda-forge
r-latticeextra 0.6_28 r3.4.1_0 conda-forge
r-lazyeval 0.2.1 r3.4.1_0 conda-forge
r-magrittr 1.5 r3.4.1_0 conda-forge
r-mass 7.3_48 r3.4.1_0 conda-forge
r-matrix 1.2_14 r3.4.1_0 conda-forge
r-matrixstats 0.53.1 r341_0 conda-forge
r-munsell 0.5.0 r341_0 conda-forge
r-pillar 1.2.1 r3.4.1_0 conda-forge
r-plyr 1.8.4 r3.4.1_0 conda-forge
r-r6 2.2.2 r3.4.1_0 conda-forge
r-rcolorbrewer 1.1_2 r3.4.1_0 conda-forge
r-rcpp 0.12.15 r3.4.1_0 conda-forge
r-rcppparallel 4.4.0 r3.4.1_0 conda-forge
r-rcurl 1.95_4.8 r3.4.1_0 conda-forge
r-reshape2 1.4.3 r3.4.1_0 conda-forge
r-rlang 0.2.1 r341_0 conda-forge
r-scales 0.5.0 r3.4.1_0 conda-forge
r-snow 0.4_2 r3.4.1_0 conda-forge
r-stringi 1.1.7 r3.4.1_1 conda-forge
r-stringr 1.3.0 r3.4.1_0 conda-forge
r-tibble 1.4.2 r3.4.1_0 conda-forge
r-utf8 1.1.3 r3.4.1_0 conda-forge
r-viridislite 0.3.0 r3.4.1_0 conda-forge
raxml 8.2.10 h470a237_1 bioconda
readline 7.0 0 conda-forge
requests 2.19.1 py35_0 conda-forge
scikit-bio 0.5.1 py35_0 qiime2
scikit-learn 0.19.1 py35_blas_openblas_200 [blas_openblas] conda-forge
scipy 0.19.1 py35_blas_openblas_202 [blas_openblas] conda-forge
seaborn 0.8.1 py35_0 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 39.2.0 py35_0 conda-forge
simplegeneric 0.8.1 py35_0 conda-forge
six 1.11.0 py35_1 conda-forge
sortmerna 2.0 2 bioconda
sqlite 3.20.1 2 conda-forge
statsmodels 0.9.0 py35_0 conda-forge
terminado 0.8.1 py35_0 conda-forge
testpath 0.3.1 py35_0 conda-forge
tk 8.6.7 0 conda-forge
tornado 5.0.2 py35_0 conda-forge
traitlets 4.3.2 py35_0 conda-forge
tzlocal 1.3 py35_0 qiime2
unifrac 0.9.2 py35h1806a49_1 biocore
urllib3 1.22 py35_0 conda-forge
vsearch 2.7.0 1 bioconda
wcwidth 0.1.7 py35_0 conda-forge
webencodings 0.5.1 py35_0 conda-forge
wget 1.19.5 hf30b1f0_0
wheel 0.31.0 py35_0 conda-forge
widgetsnbextension 3.2.1 py35_0 conda-forge
xopen 0.3.2 py35_0 bioconda
xz 5.2.3 0 conda-forge
yaml 0.1.7 0 conda-forge
zeromq 4.2.5 1 conda-forge
zlib 1.2.11 h470a237_3 conda-forge

and

/Users/whalenlab/anaconda3/envs/qiime2-2018.6/lib/R/library/

Thank you so much!

Hi @ygao2,

This is definitely strange. It looks a little bit like the locale is perhaps causing issues (it’s also plenty likely this is unrelated).

But just in case, what do the following commands have:

locale

and

locale -a

Are you talking about something like .Rprofile? Or something else?

In principle it shouldn’t matter since we’ve tried to fix the conda environment isolation with R, but its always possible there’s something else leaking we didn’t know about.


Something else I might try would be to remove your environment and try re-installing.

You can remove a conda environment with:

conda env remove -n <name of env here>

Then probably follow up with a conda clean:

conda clean --all

and then try reinstalling like normal.

If there were any packages corrupted during first install, that should fix it.

Hi,

Here are the results I got:

LANG=
LC_COLLATE=“C”
LC_CTYPE=“UTF-8”
LC_MESSAGES=“C”
LC_MONETARY=“C”
LC_NUMERIC=“C”
LC_TIME=“C”
LC_ALL=

and

af_ZA
af_ZA.ISO8859-1
af_ZA.ISO8859-15
af_ZA.UTF-8
am_ET
am_ET.UTF-8
be_BY
be_BY.CP1131
be_BY.CP1251
be_BY.ISO8859-5
be_BY.UTF-8
bg_BG
bg_BG.CP1251
bg_BG.UTF-8
ca_ES
ca_ES.ISO8859-1
ca_ES.ISO8859-15
ca_ES.UTF-8
cs_CZ
cs_CZ.ISO8859-2
cs_CZ.UTF-8
da_DK
da_DK.ISO8859-1
da_DK.ISO8859-15
da_DK.UTF-8
de_AT
de_AT.ISO8859-1
de_AT.ISO8859-15
de_AT.UTF-8
de_CH
de_CH.ISO8859-1
de_CH.ISO8859-15
de_CH.UTF-8
de_DE
de_DE.ISO8859-1
de_DE.ISO8859-15
de_DE.UTF-8
el_GR
el_GR.ISO8859-7
el_GR.UTF-8
en_AU
en_AU.ISO8859-1
en_AU.ISO8859-15
en_AU.US-ASCII
en_AU.UTF-8
en_CA
en_CA.ISO8859-1
en_CA.ISO8859-15
en_CA.US-ASCII
en_CA.UTF-8
en_GB
en_GB.ISO8859-1
en_GB.ISO8859-15
en_GB.US-ASCII
en_GB.UTF-8
en_IE
en_IE.UTF-8
en_NZ
en_NZ.ISO8859-1
en_NZ.ISO8859-15
en_NZ.US-ASCII
en_NZ.UTF-8
en_US
en_US.ISO8859-1
en_US.ISO8859-15
en_US.US-ASCII
en_US.UTF-8
es_ES
es_ES.ISO8859-1
es_ES.ISO8859-15
es_ES.UTF-8
et_EE
et_EE.ISO8859-15
et_EE.UTF-8
eu_ES
eu_ES.ISO8859-1
eu_ES.ISO8859-15
eu_ES.UTF-8
fi_FI
fi_FI.ISO8859-1
fi_FI.ISO8859-15
fi_FI.UTF-8
fr_BE
fr_BE.ISO8859-1
fr_BE.ISO8859-15
fr_BE.UTF-8
fr_CA
fr_CA.ISO8859-1
fr_CA.ISO8859-15
fr_CA.UTF-8
fr_CH
fr_CH.ISO8859-1
fr_CH.ISO8859-15
fr_CH.UTF-8
fr_FR
fr_FR.ISO8859-1
fr_FR.ISO8859-15
fr_FR.UTF-8
he_IL
he_IL.UTF-8
hi_IN.ISCII-DEV
hr_HR
hr_HR.ISO8859-2
hr_HR.UTF-8
hu_HU
hu_HU.ISO8859-2
hu_HU.UTF-8
hy_AM
hy_AM.ARMSCII-8
hy_AM.UTF-8
is_IS
is_IS.ISO8859-1
is_IS.ISO8859-15
is_IS.UTF-8
it_CH
it_CH.ISO8859-1
it_CH.ISO8859-15
it_CH.UTF-8
it_IT
it_IT.ISO8859-1
it_IT.ISO8859-15
it_IT.UTF-8
ja_JP
ja_JP.eucJP
ja_JP.SJIS
ja_JP.UTF-8
kk_KZ
kk_KZ.PT154
kk_KZ.UTF-8
ko_KR
ko_KR.CP949
ko_KR.eucKR
ko_KR.UTF-8
lt_LT
lt_LT.ISO8859-13
lt_LT.ISO8859-4
lt_LT.UTF-8
nl_BE
nl_BE.ISO8859-1
nl_BE.ISO8859-15
nl_BE.UTF-8
nl_NL
nl_NL.ISO8859-1
nl_NL.ISO8859-15
nl_NL.UTF-8
no_NO
no_NO.ISO8859-1
no_NO.ISO8859-15
no_NO.UTF-8
pl_PL
pl_PL.ISO8859-2
pl_PL.UTF-8
pt_BR
pt_BR.ISO8859-1
pt_BR.UTF-8
pt_PT
pt_PT.ISO8859-1
pt_PT.ISO8859-15
pt_PT.UTF-8
ro_RO
ro_RO.ISO8859-2
ro_RO.UTF-8
ru_RU
ru_RU.CP1251
ru_RU.CP866
ru_RU.ISO8859-5
ru_RU.KOI8-R
ru_RU.UTF-8
sk_SK
sk_SK.ISO8859-2
sk_SK.UTF-8
sl_SI
sl_SI.ISO8859-2
sl_SI.UTF-8
sr_YU
sr_YU.ISO8859-2
sr_YU.ISO8859-5
sr_YU.UTF-8
sv_SE
sv_SE.ISO8859-1
sv_SE.ISO8859-15
sv_SE.UTF-8
tr_TR
tr_TR.ISO8859-9
tr_TR.UTF-8
uk_UA
uk_UA.ISO8859-5
uk_UA.KOI8-U
uk_UA.UTF-8
zh_CN
zh_CN.eucCN
zh_CN.GB18030
zh_CN.GB2312
zh_CN.GBK
zh_CN.UTF-8
zh_HK
zh_HK.Big5HKSCS
zh_HK.UTF-8
zh_TW
zh_TW.Big5
zh_TW.UTF-8
C

Yes, those are mostly what I removed and I did try to recover everything from the trash.

Thank you so much.

I was able to run in the same environment with a different set of data (that was also after the release of Qiime2 2018.6). One difference between the two trials I can think of is that I played around with R and RStudio between running the two data sets (there could totally be some other differences).

Hi @ygao2!

Ok, let’s try making this work without touching the .Rprofile you shouldn’t need that anymore with 2018.6.

Try setting this environment variable:

export LC_ALL= en_US.UTF-8

(This is what I would set for example, if there’s a better locale, feel free to use that one instead, just make sure it ends in .UTF-8).

This strategy doesn’t exactly line up with:

But we can try it and see.

To maybe figure out why RStudio may (or may not) have changed things, try running the following in your QIIME 2 environment:

R -e ".libPaths()"

That should tell us where it’s loading libraries from (hopefully only the conda environment).

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