Error when running dada2: Setting LC_CTYPE failed, using "C"

dada2
(Barbs) #1

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!

1 Like

(Matthew Ryan Dillon) #2

Hi @Barbs! I might’ve missed it somewhere in this post, but is there actually a problem? Or are you just looking for an explanation of why those warnings are there? Thanks!

1 Like

(Barbs) #3

Hi there,

sorry for not pointing it out clearly. The problem is that the command does not finish. This step has always been taken the longest time with other datasets but with this dataset it stopped after 1 day with “Self-consistency loop terminated before convergence” without any output.

Apparently this message can sometimes be ignored: https://benjjneb.github.io/dada2/faq.html#what-if-the-self-consistency-loop-terminated-before-cowhy it occured now. Can I also ignore the warning messages regarding LC_? I did not have this warning message with other datasets!
Sorry if I am being imprecise. I just prefere having a rough idea what the warning message means before I ignore it.

Thanks a lot for your time and help. I really appreciate the patience with beginners questions in the forum!!!

0 Likes

(Matthew Ryan Dillon) #4

No problem! :ok_hand:

I don’t think those warnings have anything to do with the data — they appear to be warnings originating from your computation environment. As you proposed above:

It does appear to be some kind of locale-related warning, but it doesn’t appear to actually be a problem.

If the job hasn’t terminated (exited; failed), then I suggest letting it do its thing…

Check out this section of the DADA2 docs for some rough estimates of computation time needed:

https://benjjneb.github.io/dada2/bigdata.html#how-long-does-it-take

:heart: :qiime2: :heart:


Keep us posted!

1 Like

(Barbs) #5

Hello there!

Sorry for posting again!
Unfortunately I could not solve my problem yet. As you suggested I just let it run for longer (4 days by now). After two days I got another "Self-consistency loop terminated before convergence” but now termination message. I checked the activity monitor and bash activity has 0% CPU.

–verbose gives me:

R version 3.4.1 (2017-06-30)
DADA2 R package version: 1.6.0

  1. Filtering …

  2. Learning Error Rates
    2a) Forward Reads
    Initializing error rates to maximum possible estimate.
    Sample 1 - 8100 reads in 5097 unique sequences.
    Sample 2 - 107037 reads in 49937 unique sequences.
    Sample 3 - 192456 reads in 80241 unique sequences.
    Sample 4 - 113188 reads in 53283 unique sequences.
    Sample 5 - 56392 reads in 25720 unique sequences.
    Sample 6 - 156000 reads in 71085 unique sequences.
    Sample 7 - 37093 reads in 19997 unique sequences.
    Sample 8 - 122810 reads in 53959 unique sequences.
    Sample 9 - 17502 reads in 11236 unique sequences.
    Sample 10 - 96700 reads in 39458 unique sequences.
    Sample 11 - 181241 reads in 69816 unique sequences.
    selfConsist step 2
    selfConsist step 3
    selfConsist step 4
    selfConsist step 5
    selfConsist step 6
    selfConsist step 7
    selfConsist step 8
    selfConsist step 9
    selfConsist step 10
    2b) Reverse Reads
    Initializing error rates to maximum possible estimate.
    Sample 1 - 8100 reads in 4978 unique sequences.
    Sample 2 - 107037 reads in 51318 unique sequences.
    Sample 3 - 192456 reads in 82762 unique sequences.
    Sample 4 - 113188 reads in 52148 unique sequences.
    Sample 5 - 56392 reads in 31363 unique sequences.
    Sample 6 - 156000 reads in 69672 unique sequences.
    Sample 7 - 37093 reads in 19362 unique sequences.
    Sample 8 - 122810 reads in 51299 unique sequences.
    Sample 9 - 17502 reads in 11898 unique sequences.
    Sample 10 - 96700 reads in 38276 unique sequences.
    Sample 11 - 181241 reads in 67563 unique sequences.
    selfConsist step 2
    selfConsist step 3
    selfConsist step 4
    selfConsist step 5
    selfConsist step 6
    selfConsist step 7
    selfConsist step 8
    selfConsist step 9
    selfConsist step 10

  3. Denoise remaining samples …

So as far as I understand there is a problem after sample 10 (I got 83 in total)

Any further suggestions? Thanks a lot!!!

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(Nicholas Bokulich) assigned thermokarst #6
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(Matthew Ryan Dillon) #7

I don’t see a termination message anywhere in the log you have attached — did you miss it in your copy-paste?

I’m not sure I follow — the log is showing that the first 11 samples are used as part of the error rate initialization. Then, it says “Denoise remaining samples …”, which means DADA2 is still running on your remaining samples.

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(Matthew Ryan Dillon) unassigned thermokarst #8
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(Barbs) #9

Hey!

Sorry for the late reply but finally I can close this discussion.
I re-run the command on a much faster computer (took me a while to organise one for free) and everything worked out fine. I guess the main problem was that the job was not moved appropriate to the background. At some point it was always cancelled, giving me error messages after days I didnt understand. So now I moved the command to the background and used <disown. Everything worked out fine!
So in the end it was me being to impatient and my computer being to slow. Sorry for the confusion my post did cause! Thanks!

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(system) closed #10

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.

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