Hello everyone,
I am running QIIME2 2018.11 on Conda with MacOs Mojave
I get an error message when running dada2. My command is:
qiime dada2 denoise-paired
--i-demultiplexed-seqs paired_end_demux.qza
--p-trim-left-f 17
--p-trunc-len-f 248
--p-trim-left-r 20
--p-trunc-len-r 248
--p-chimera-method consensus
--p-min-fold-parent-over-abundance 1
--p-n-threads 0
--o-representative-sequences rep_seqs_dada2.qza
--o-table table_dada2.qza
--output-dir Qiime2_bioinfo
--verbose >Sequence_read_abundance_filtering.txt
The warning/error message I get is:
During startup - Warning messages:
1: Setting LC_COLLATE failed, using "C"
2: Setting LC_TIME failed, using "C"
3: Setting LC_MESSAGES failed, using "C"
4: Setting LC_MONETARY failed, using "C"
Loading required package: Rcpp
Self-consistency loop terminated before convergence.
I am aware that this topic was already posted here:
But since the discussion was closed without any solution, I hope its ok to post it again...
I run all commands that were suggested in the previous discussion:
conda list
packages in environment at /Users/barbaraweisbrod/miniconda3/envs/qiime2-2018.11:
Name Version Build Channel
_r-mutex 1.0.0 anacondar_1
appnope 0.1.0 py35_0 conda-forge
arb-bio-tools 6.0.6 4 bioconda
asn1crypto 0.24.0 py35_3 conda-forge
backcall 0.1.0 py_0 conda-forge
bibtexparser 1.0.1 py_1 conda-forge
bioconductor-biobase 2.38.0 r341h219a75b_1 bioconda
bioconductor-biocgenerics 0.24.0 r341_1 bioconda
bioconductor-biocparallel 1.12.0 r341h219a75b_1 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 2.1.7 py35h7eb728f_0 conda-forge
blas 1.0 openblas conda-forge
blast 2.6.0 boost1.64_2 bioconda
bleach 3.0.2 py_1 conda-forge
bokeh 0.13.0 py35_0 conda-forge
boost 1.67.0 py35h3e44d54_0 conda-forge
boost-cpp 1.67.0 h3a22d5f_0 conda-forge
bz2file 0.98 py_0 conda-forge
bzip2 1.0.6 1 conda-forge
ca-certificates 2018.10.15 ha4d7672_0 conda-forge
cachecontrol 0.12.5 py_0 conda-forge
cairo 1.14.12 he6fea26_5 conda-forge
certifi 2018.8.24 py35_1001 conda-forge
cffi 1.11.5 py35h5e8e0c9_1 conda-forge
chardet 3.0.4 py35_3 conda-forge
click 7.0 py_0 conda-forge
cryptography 2.3.1 py35hdffb7b8_0 conda-forge
cryptography-vectors 2.3.1 py35_0 conda-forge
curl 7.62.0 h74213dd_0 conda-forge
cutadapt 1.18 py35_0 bioconda
cycler 0.10.0 py_1 conda-forge
cython 0.28.5 py35hfc679d8_0 conda-forge
deblur 1.1.0 py35_0 bioconda
decorator 4.3.0 py_0 conda-forge
emperor 1.0.0beta18 py35_1 conda-forge
entrypoints 0.2.3 py35_2 conda-forge
fastcluster 1.1.25 py35hf8a1672_0 conda-forge
fasttree 2.1.10 0 bioconda
fontconfig 2.13.1 hce039c3_0 conda-forge
fragment-insertion 4.3.5 py35_0 biocore
freetype 2.9.1 h6debe1e_4 conda-forge
future 0.16.0 py35_2 conda-forge
gettext 0.19.8.1 h1f1d5ed_1 conda-forge
glib 2.55.0 h464dc38_2 conda-forge
gneiss 0.4.4 py_0 bioconda
graphite2 1.3.12 h7d4d677_1 conda-forge
gsl 2.1 2 conda-forge
h5py 2.7.0 np112py35_0 conda-forge
harfbuzz 1.9.0 h08d66d9_0 conda-forge
hdf5 1.8.17 11 conda-forge
hdmedians 0.13 py35h7eb728f_1 conda-forge
icu 58.2 hfc679d8_0 conda-forge
idna 2.7 py35_2 conda-forge
ijson 2.3 py35_0 qiime2
intel-openmp 2019.0 118
ipykernel 5.1.0 pyh24bf2e0_0 conda-forge
ipython 7.0.1 py35h24bf2e0_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.4.2 py_0 conda-forge
iqtree 1.6.8 he941832_0 bioconda
java-jdk 8.0.92 1 bioconda
jedi 0.12.1 py35_0 conda-forge
jinja2 2.10 py_1 conda-forge
jpeg 9c h470a237_1 conda-forge
jsonschema 2.6.0 py35_2 conda-forge
jupyter_client 5.2.3 py_1 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
kiwisolver 1.0.1 py35h2d50403_2 conda-forge
krb5 1.16.2 hbb41f41_0 conda-forge
libarbdb 6.0.6 4 bioconda
libcurl 7.62.0 hbdb9355_0 conda-forge
libcxx 7.0.0 h2d50403_2 conda-forge
libedit 3.1.20170329 0 conda-forge
libffi 3.2.1 hfc679d8_5 conda-forge
libgcc 4.8.5 hdbeacc1_10 conda-forge
libgfortran 3.0.1 h93005f0_2
libiconv 1.15 h470a237_3 conda-forge
libopenblas 0.2.20 hdc02c5d_7
libpng 1.6.34 ha92aebf_2 conda-forge
libsodium 1.0.16 h470a237_1 conda-forge
libssh2 1.8.0 h5b517e9_3 conda-forge
libtiff 4.0.9 he6b73bb_2 conda-forge
libxml2 2.9.8 h422b904_5 conda-forge
llvm-meta 7.0.0 0 conda-forge
lockfile 0.12.2 py_1 conda-forge
mafft 7.310 1 bioconda
markupsafe 1.0 py35h470a237_1 conda-forge
matplotlib 2.2.3 py35h0e0179f_0 conda-forge
mistune 0.8.3 py35h470a237_2 conda-forge
mkl 2019.0 118
msgpack-python 0.5.6 py35h2d50403_3 conda-forge
natsort 5.4.0 py_0 conda-forge
nbconvert 5.3.1 py_1 conda-forge
nbformat 4.4.0 py_1 conda-forge
ncurses 5.9 10 conda-forge
nose 1.3.7 py35_2 conda-forge
notebook 5.7.0 py35_0 conda-forge
numpy 1.12.1 py35_nomkl_0
openblas 0.3.5 ha44fe06_0 conda-forge
openjdk 8.0.152 h393ad39_1
openmp 7.0.0 h2d50403_0 conda-forge
openssl 1.0.2p h470a237_2 conda-forge
packaging 18.0 py_0 conda-forge
pandas 0.22.0 py35_1 conda-forge
pandoc 2.3.1 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
pango 1.40.14 he752989_2 conda-forge
parso 0.3.1 py_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pcre 8.39 0 conda-forge
pexpect 4.6.0 py35_0 conda-forge
pickleshare 0.7.5 py35_0 conda-forge
pigz 2.3.4 0 conda-forge
pip 18.0 py35_1001 conda-forge
pixman 0.34.0 h470a237_3 conda-forge
prometheus_client 0.4.2 py_0 conda-forge
prompt_toolkit 2.0.7 py_0 conda-forge
psutil 5.4.7 py35h470a237_1 conda-forge
ptyprocess 0.6.0 py35_1000 conda-forge
pycparser 2.19 py_0 conda-forge
pygments 2.2.0 py_1 conda-forge
pyopenssl 18.0.0 py35_0 conda-forge
pyparsing 2.3.0 py_0 conda-forge
pysocks 1.6.8 py35_2 conda-forge
python 3.5.5 1 conda-forge
python-dateutil 2.7.5 py_0 conda-forge
pytz 2018.7 py_0 conda-forge
pyyaml 3.13 py35h470a237_1 conda-forge
pyzmq 17.1.2 py35hae99301_0 conda-forge
q2-alignment 2018.11.0 py35_0 qiime2/label/r2018.11
q2-composition 2018.11.0 py35_0 qiime2/label/r2018.11
q2-cutadapt 2018.11.0 py35_0 qiime2/label/r2018.11
q2-dada2 2018.11.0 py35_0 qiime2/label/r2018.11
q2-deblur 2018.11.0 py35_0 qiime2/label/r2018.11
q2-demux 2018.11.0 py35_0 qiime2/label/r2018.11
q2-diversity 2018.11.0 py35_0 qiime2/label/r2018.11
q2-emperor 2018.11.0 py35_0 qiime2/label/r2018.11
q2-feature-classifier 2018.11.0 py35_0 qiime2/label/r2018.11
q2-feature-table 2018.11.0 py35_0 qiime2/label/r2018.11
q2-fragment-insertion 2018.11.0 py35_0 qiime2/label/r2018.11
q2-gneiss 2018.11.0 py35_0 qiime2/label/r2018.11
q2-longitudinal 2018.11.0 py35_0 qiime2/label/r2018.11
q2-metadata 2018.11.0 py35_0 qiime2/label/r2018.11
q2-phylogeny 2018.11.0 py35_0 qiime2/label/r2018.11
q2-quality-control 2018.11.0 py35_0 qiime2/label/r2018.11
q2-quality-filter 2018.11.0 py35_0 qiime2/label/r2018.11
q2-sample-classifier 2018.11.0 py35_0 qiime2/label/r2018.11
q2-taxa 2018.11.0 py35_0 qiime2/label/r2018.11
q2-types 2018.11.0 py35_0 qiime2/label/r2018.11
q2-vsearch 2018.11.0 py35_0 qiime2/label/r2018.11
q2cli 2018.11.0 py35_0 qiime2/label/r2018.11
q2templates 2018.11.0 py35_0 qiime2/label/r2018.11
qiime2 2018.11.0 py35_0 qiime2/label/r2018.11
r-assertthat 0.2.0 r341h6115d3f_1 conda-forge
r-base 3.4.1 4 conda-forge
r-bh 1.66.0_1 r341_1001 conda-forge
r-bitops 1.0_6 r341hc070d10_2 conda-forge
r-cli 1.0.0 r341h6115d3f_1 conda-forge
r-colorspace 1.3_2 r341hc070d10_2 conda-forge
r-crayon 1.3.4 r341h6115d3f_1 conda-forge
r-data.table 1.11.4 r341hc070d10_2 conda-forge
r-digest 0.6.18 r341hc070d10_0 conda-forge
r-fansi 0.3.0 r341hc070d10_0 conda-forge
r-formatr 1.5 r341h6115d3f_1 conda-forge
r-futile.logger 1.4.3 r341h6115d3f_1 conda-forge
r-futile.options 1.0.1 r341h6115d3f_0 conda-forge
r-ggplot2 3.1.0 r341h6115d3f_0 conda-forge
r-glue 1.3.0 r341h470a237_2 conda-forge
r-gtable 0.2.0 r341h6115d3f_1 conda-forge
r-hwriter 1.3.2 r341h6115d3f_1 conda-forge
r-labeling 0.3 r341h6115d3f_1 conda-forge
r-lambda.r 1.2.3 r341h6115d3f_0 conda-forge
r-lattice 0.20_35 r341hc070d10_0 conda-forge
r-latticeextra 0.6_28 r341h6115d3f_1 conda-forge
r-lazyeval 0.2.1 r341hc070d10_2 conda-forge
r-magrittr 1.5 r341h6115d3f_1 conda-forge
r-mass 7.3_50 r341hc070d10_2 conda-forge
r-matrix 1.2_14 r341hc070d10_2 conda-forge
r-matrixstats 0.54.0 r341hc070d10_0 conda-forge
r-mgcv 1.8_24 r341hc070d10_2 conda-forge
r-munsell 0.5.0 r341h6115d3f_1 conda-forge
r-nlme 3.1_137 r341h364d78e_0 conda-forge
r-pillar 1.3.0 r341h6115d3f_0 conda-forge
r-plyr 1.8.4 r341h9d2a408_2 conda-forge
r-r6 2.2.2 r341h6115d3f_1 conda-forge
r-rcolorbrewer 1.1_2 r341h6115d3f_1 conda-forge
r-rcpp 0.12.17 r341h9d2a408_2 conda-forge
r-rcppparallel 4.4.1 r341h9d2a408_0 conda-forge
r-rcurl 1.95_4.11 r341hc070d10_3 conda-forge
r-reshape2 1.4.3 r341h9d2a408_2 conda-forge
r-rlang 0.3.0.1 r341h470a237_0 conda-forge
r-scales 1.0.0 r341h9d2a408_1 conda-forge
r-snow 0.4_3 r341h6115d3f_0 conda-forge
r-stringi 1.2.4 r341h9d2a408_1 conda-forge
r-stringr 1.3.1 r341h6115d3f_1 conda-forge
r-tibble 1.4.2 r341hc070d10_2 conda-forge
r-utf8 1.1.4 r341hc070d10_0 conda-forge
r-viridislite 0.3.0 r341h6115d3f_1 conda-forge
r-withr 2.1.2 r341h6115d3f_0 conda-forge
raxml 8.2.12 h470a237_0 bioconda
readline 7.0 0 conda-forge
requests 2.19.1 py35_1 conda-forge
scikit-bio 0.5.4 py35_0 conda-forge
scikit-learn 0.19.1 py35_nomklhf06d1bf_0
scipy 0.19.1 py35_nomklh15481bc_3
seaborn 0.9.0 py_0 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 40.4.3 py35_0 conda-forge
simplegeneric 0.8.1 py_1 conda-forge
sina 1.4.0 h4ef8376_0 bioconda
six 1.11.0 py35_1 conda-forge
sortmerna 2.0 he941832_3 bioconda
sqlite 3.20.1 2 conda-forge
statsmodels 0.9.0 py35_0 conda-forge
tbb 2019.2 h2d50403_0 conda-forge
terminado 0.8.1 py35_1 conda-forge
testpath 0.3.1 py35_1 conda-forge
tk 8.6.8 ha92aebf_0 conda-forge
tornado 5.1.1 py35h470a237_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 1.23 py35_1 conda-forge
vsearch 2.7.0 1 bioconda
wcwidth 0.1.7 py_1 conda-forge
webencodings 0.5.1 py_1 conda-forge
wget 1.19.5 hf30b1f0_0
wheel 0.32.0 py35_1000 conda-forge
widgetsnbextension 3.4.2 py35_0 conda-forge
xopen 0.3.5 py_0 bioconda
xz 5.2.4 h470a237_1 conda-forge
yaml 0.1.7 h470a237_1 conda-forge
zeromq 4.2.5 hfc679d8_6 conda-forge
zlib 1.2.11 h470a237_4 conda-forge
echo $R_LIBS_USER
/Users/barbaraweisbrod/miniconda3/envs/qiime2-2018.11/lib/R/library/
locale
LANG=
LC_COLLATE="C"
LC_CTYPE="UTF-8"
LC_MESSAGES="C"
LC_MONETARY="C"
LC_NUMERIC="C"
LC_TIME="C"
LC_ALL="UTF-8"
locale -a
en_NZ
nl_NL.UTF-8
pt_BR.UTF-8
fr_CH.ISO8859-15
eu_ES.ISO8859-15
en_US.US-ASCII
af_ZA
bg_BG
cs_CZ.UTF-8
fi_FI
zh_CN.UTF-8
eu_ES
sk_SK.ISO8859-2
nl_BE
fr_BE
sk_SK
en_US.UTF-8
en_NZ.ISO8859-1
de_CH
sk_SK.UTF-8
de_DE.UTF-8
am_ET.UTF-8
zh_HK
be_BY.UTF-8
uk_UA
pt_PT.ISO8859-1
en_AU.US-ASCII
kk_KZ.PT154
en_US
nl_BE.ISO8859-15
de_AT.ISO8859-1
hr_HR.ISO8859-2
fr_FR.ISO8859-1
af_ZA.UTF-8
am_ET
fi_FI.ISO8859-1
ro_RO.UTF-8
af_ZA.ISO8859-15
en_NZ.UTF-8
fi_FI.UTF-8
hr_HR.UTF-8
da_DK.UTF-8
ca_ES.ISO8859-1
en_AU.ISO8859-15
ro_RO.ISO8859-2
de_AT.UTF-8
pt_PT.ISO8859-15
sv_SE
fr_CA.ISO8859-1
fr_BE.ISO8859-1
en_US.ISO8859-15
it_CH.ISO8859-1
en_NZ.ISO8859-15
en_AU.UTF-8
de_AT.ISO8859-15
af_ZA.ISO8859-1
hu_HU.UTF-8
et_EE.UTF-8
he_IL.UTF-8
uk_UA.KOI8-U
be_BY
kk_KZ
hu_HU.ISO8859-2
it_CH
pt_BR
ko_KR
it_IT
fr_BE.UTF-8
ru_RU.ISO8859-5
zh_TW
zh_CN.GB2312
no_NO.ISO8859-15
de_DE.ISO8859-15
en_CA
fr_CH.UTF-8
sl_SI.UTF-8
uk_UA.ISO8859-5
pt_PT
hr_HR
cs_CZ
fr_CH
he_IL
zh_CN.GBK
zh_CN.GB18030
fr_CA
pl_PL.UTF-8
ja_JP.SJIS
sr_YU.ISO8859-5
be_BY.CP1251
sr_YU.ISO8859-2
sv_SE.UTF-8
sr_YU.UTF-8
de_CH.UTF-8
sl_SI
pt_PT.UTF-8
ro_RO
en_NZ.US-ASCII
ja_JP
zh_CN
fr_CH.ISO8859-1
ko_KR.eucKR
be_BY.ISO8859-5
nl_NL.ISO8859-15
en_GB.ISO8859-1
en_CA.US-ASCII
is_IS.ISO8859-1
ru_RU.CP866
nl_NL
fr_CA.ISO8859-15
sv_SE.ISO8859-15
hy_AM
en_CA.ISO8859-15
en_US.ISO8859-1
zh_TW.Big5
ca_ES.UTF-8
ru_RU.CP1251
en_GB.UTF-8
en_GB.US-ASCII
ru_RU.UTF-8
eu_ES.UTF-8
es_ES.ISO8859-1
hu_HU
el_GR.ISO8859-7
en_AU
it_CH.UTF-8
en_GB
sl_SI.ISO8859-2
ru_RU.KOI8-R
nl_BE.UTF-8
et_EE
fr_FR.ISO8859-15
cs_CZ.ISO8859-2
lt_LT.UTF-8
pl_PL.ISO8859-2
fr_BE.ISO8859-15
is_IS.UTF-8
tr_TR.ISO8859-9
da_DK.ISO8859-1
lt_LT.ISO8859-4
lt_LT.ISO8859-13
zh_TW.UTF-8
bg_BG.CP1251
el_GR.UTF-8
be_BY.CP1131
da_DK.ISO8859-15
is_IS.ISO8859-15
no_NO.ISO8859-1
nl_NL.ISO8859-1
nl_BE.ISO8859-1
sv_SE.ISO8859-1
pt_BR.ISO8859-1
zh_CN.eucCN
it_IT.UTF-8
en_CA.UTF-8
uk_UA.UTF-8
de_CH.ISO8859-15
de_DE.ISO8859-1
ca_ES
sr_YU
hy_AM.ARMSCII-8
ru_RU
zh_HK.UTF-8
eu_ES.ISO8859-1
is_IS
bg_BG.UTF-8
ja_JP.UTF-8
it_CH.ISO8859-15
fr_FR.UTF-8
ko_KR.UTF-8
et_EE.ISO8859-15
kk_KZ.UTF-8
ca_ES.ISO8859-15
en_IE.UTF-8
es_ES
de_CH.ISO8859-1
en_CA.ISO8859-1
es_ES.ISO8859-15
en_AU.ISO8859-1
el_GR
da_DK
no_NO
it_IT.ISO8859-1
en_IE
zh_HK.Big5HKSCS
hi_IN.ISCII-DEV
ja_JP.eucJP
it_IT.ISO8859-15
pl_PL
ko_KR.CP949
fr_CA.UTF-8
fi_FI.ISO8859-15
en_GB.ISO8859-15
fr_FR
hy_AM.UTF-8
no_NO.UTF-8
es_ES.UTF-8
de_AT
tr_TR.UTF-8
de_DE
lt_LT
tr_TR
C
POSIX
R -e ".libPaths()
[1] "/Users/barbaraweisbrod/miniconda3/envs/qiime2-2018.11/lib/R/library"
I hope its just some locale settings that I don't get.
Thanks a lot for your time and help!