Plugin error from DADA2 denoise-paired

Hello. I’m hoping for some help with an error during denoising with DADA2.

I’m running the following:

qiime dada2 denoise-paired
–i-demultiplexed-seqs demux.qza
–p-trim-left-f 5
–p-trim-left-r 5
–p-trunc-len-f 150
–p-trunc-len-r 150
–o-table table.qza
–o-representative-sequences rep-seqs.qza
–o-denoising-stats denoising-stats.qza

And I get this error:

Plugin error from dada2:
[Errno 2] No such file or directory: ‘run_dada_paired.R’

I’m running qiime2-p3.6.5 via Terminal installed on a university cluster, and have been able to successfully run all the Atacama Soils tutorial steps successfully up til this point.

What version of QIIME 2 are you running?

Can you please activate your QIIME 2 environment and run the following commands:

qiime info
conda list

Thanks!

Yes, of course. Thanks!

qiime info produces

System versions
Python version: 3.5.5
QIIME 2 release: 2018.6
QIIME 2 version: 2018.6.0
q2cli version: 2018.6.0

Installed plugins
alignment: 2018.6.0
composition: 2018.6.0
cutadapt: 2018.6.0
dada2: 2018.6.0
deblur: 2018.6.0
demux: 2018.6.0
diversity: 2018.6.0
emperor: 2018.6.0
feature-classifier: 2018.6.0
feature-table: 2018.6.0
gneiss: 2018.6.0
longitudinal: 2018.6.0
metadata: 2018.6.0
phylogeny: 2018.6.0
quality-control: 2018.6.1
quality-filter: 2018.6.0
sample-classifier: 2018.6.0
taxa: 2018.6.0
types: 2018.6.0
vsearch: 2018.6.0

Application config directory
/data/olins/.config/q2cli

Getting help
To get help with QIIME 2, visit https://qiime2.org

conda list produces

packages in environment at /gsfs0/public/qiime/miniconda3:

Name Version Build Channel

_r-mutex 1.0.0 anacondar_1
asn1crypto 0.24.0 py35_3 conda-forge
backcall 0.1.0 py_0 conda-forge
bioconductor-biobase 2.34.0 r3.3.2_0 bioconda
bioconductor-biocgenerics 0.22.0 r3.3.2_0 bioconda
bioconductor-biocparallel 1.6.6 r3.3.2_1 bioconda
bioconductor-biostrings 2.42.1 r3.3.2_0 bioconda
bioconductor-dada2 1.4.0 r3.3.2_0 bioconda
bioconductor-genomeinfodb 1.10.3 r3.3.2_0 bioconda
bioconductor-genomicalignments 1.10.0 r3.3.2_0 bioconda
bioconductor-genomicranges 1.26.4 r3.3.2_0 bioconda
bioconductor-iranges 2.8.2 r3.3.2_0 bioconda
bioconductor-rsamtools 1.26.1 r3.3.2_0 bioconda
bioconductor-s4vectors 0.12.2 r3.3.2_0 bioconda
bioconductor-shortread 1.32.0 r3.3.2_0 bioconda
bioconductor-summarizedexperiment 1.4.0 r3.3.2_2 bioconda
bioconductor-xvector 0.14.1 r3.3.2_0 bioconda
bioconductor-zlibbioc 1.20.0 r3.3.2_1 bioconda
blas 1.0 mkl
bzip2 1.0.6 h14c3975_1002 conda-forge
ca-certificates 2018.11.29 ha4d7672_0 conda-forge
cairo 1.14.8 0
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
conda 4.5.11 py35_0 conda-forge
conda-env 2.6.0 h36134e3_1
cryptography 2.3.1 py35hdffb7b8_0 conda-forge
cryptography-vectors 2.3.1 py35_0 conda-forge
curl 7.62.0 h646f8bb_1000 conda-forge
cycler 0.10.0 py_1 conda-forge
dbus 1.13.0 h4e0c4b3_1000 conda-forge
decorator 4.3.2 py_0 conda-forge
expat 2.2.5 hfc679d8_2 conda-forge
fontconfig 2.12.1 3
freetype 2.5.5 2
future 0.16.0 py35_2 conda-forge
glib 2.50.2 1
gsl 2.1 2 conda-forge
gst-plugins-base 1.8.0 0 conda-forge
gstreamer 1.8.0 1 conda-forge
h5py 2.8.0
harfbuzz 0.9.39 2
hdf5 1.10.2 hc401514_3 conda-forge
icu 54.1 0
idna 2.7 py35_2 conda-forge
ijson 2.3 py_1 conda-forge
intel-openmp 2019.1 144
ipython 7.0.1 py35h24bf2e0_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
jbig 2.1 h14c3975_2001 conda-forge
jedi 0.12.1 py35_0 conda-forge
jpeg 8d 2
krb5 1.16.1 hbb41f41_0 conda-forge
libcurl 7.62.0 h01ee5af_1000 conda-forge
libedit 3.1.20170329 h6b74fdf_2
libffi 3.2.1 hd88cf55_4
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-ng 7.3.0 hdf63c60_0 conda-forge
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.2.0 hdf63c60_3 conda-forge
libiconv 1.14 4 conda-forge
libpng 1.6.36 h84994c4_1000 conda-forge
libssh2 1.8.0 h1ad7b7a_1003 conda-forge
libstdcxx-ng 7.2.0 hdf63c60_3
libtiff 4.0.6 2
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.4 0
mkl 2018.0.3 1
natsort 6.0.0 py_0 conda-forge
ncurses 6.1 hf484d3e_0
openssl 1.0.2r h14c3975_0 conda-forge
pango 1.40.3 1
parso 0.3.4 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
pip 18.0 py35_1001 conda-forge
pixman 0.34.0 h14c3975_1003 conda-forge
prompt_toolkit 2.0.9 py_0 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
ptyprocess 0.6.0 py35_1000 conda-forge
pycosat 0.6.3 py35h14c3975_1001 conda-forge
pycparser 2.19 py_0 conda-forge
pygments 2.3.1 py_0 conda-forge
pyopenssl 18.0.0 py35_0 conda-forge
pyparsing 2.3.1 py_0 conda-forge
pyqt 5.6.0 py35h8210e8a_7 conda-forge
pysocks 1.6.8 py35_2 conda-forge
python 3.5.5 hc3d631a_4
python-dateutil 2.8.0 py_0 conda-forge
pytz 2018.9 py_0 conda-forge
pyyaml 3.13 py35h470a237_1 conda-forge
qt 5.6.2 2
r-assertthat 0.2.0 r3.3.2_0 conda-forge
r-base 3.3.2 0
r-bh 1.66.0_1 r3.3.2_0 conda-forge
r-bitops 1.0_6 r3.3.2_0 conda-forge
r-cli 1.0.0 r3.3.2_0 conda-forge
r-colorspace 1.3_2 r3.3.2_0 conda-forge
r-crayon 1.3.4 r3.3.2_0 conda-forge
r-data.table 1.10.4 r3.3.2_0 conda-forge
r-dichromat 2.0_0 r3.3.2_0 conda-forge
r-digest 0.6.15 r3.3.2_0 conda-forge
r-futile.logger 1.4.3 r3.3.2_0 conda-forge
r-futile.options 1.0.0 r3.3.2_0 conda-forge
r-ggplot2 2.2.1 r3.3.2_0 conda-forge
r-glue 1.2.0 r3.3.2_0 conda-forge
r-gtable 0.2.0 r3.3.2_0 conda-forge
r-hwriter 1.3.2 r3.3.2_0 conda-forge
r-labeling 0.3 r3.3.2_0 conda-forge
r-lambda.r 1.2 r3.3.2_0 conda-forge
r-lattice 0.20_34 r3.3.2_0 conda-forge
r-latticeextra 0.6_28 r3.3.2_0 conda-forge
r-lazyeval 0.2.1 r3.3.2_0 conda-forge
r-magrittr 1.5 r3.3.2_0 conda-forge
r-mass 7.3_48 r3.3.2_0 conda-forge
r-matrix 1.2_14 r3.3.2_0 conda-forge
r-munsell 0.4.3 r3.3.2_0 conda-forge
r-pillar 1.2.1 r3.3.2_0 conda-forge
r-plyr 1.8.4 r3.3.2_0 conda-forge
r-r6 2.2.2 r3.3.2_0 conda-forge
r-rcolorbrewer 1.1_2 r3.3.2_0 conda-forge
r-rcpp 0.12.16 r3.3.2_0 conda-forge
r-rcppparallel 4.4.0 r3.3.2_0 conda-forge
r-rcurl 1.95_4.8 r3.3.2_0 conda-forge
r-reshape2 1.4.3 r3.3.2_0 conda-forge
r-rlang 0.2.0 r3.3.2_0 conda-forge
r-scales 0.5.0 r3.3.2_0 conda-forge
r-snow 0.4_2 r3.3.2_0 conda-forge
r-stringi 1.1.7 r3.3.2_0 conda-forge
r-stringr 1.3.0 r3.3.2_0 conda-forge
r-tibble 1.4.2 r3.3.2_0 conda-forge
r-utf8 1.1.3 r3.3.2_0 conda-forge
r-viridislite 0.3.0 r3.3.2_0 conda-forge
readline 7.0 ha6073c6_4
requests 2.19.1 py35_1 conda-forge
ruamel_yaml 0.15.71 py35h470a237_0 conda-forge
setuptools 40.4.3 py35_0 conda-forge
simplegeneric 0.8.1 py_1 conda-forge
sip 4.18.1 py35hfc679d8_0 conda-forge
six 1.11.0 py35_1 conda-forge
sqlite 3.23.1 he433501_0
tk 8.6.7 hc745277_3
traitlets 4.3.2 py35_0 conda-forge
tzlocal 1.5.1 py_0 conda-forge
urllib3 1.23 py35_1 conda-forge
wcwidth 0.1.7 py_1 conda-forge
wget 1.19.5 h1ad7b7a_0
wheel 0.32.0 py35_1000 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.2 h14c3975_1007 conda-forge
xz 5.2.4 h14c3975_4
yaml 0.1.7 had09818_2
zlib 1.2.11 ha838bed_2

Did you run both of those commands in the same conda environment? The conda info command seems to indicate that you ran the command in your base environment…

1 Like

15 off-topic replies have been split into a new topic: Environment and installation issues

Please keep replies on-topic in the future.

I just noticed that the user accounts in this thread swapped — I thought I was talking to the same person the whole time. In the future @qiuwa, it is usually best to start a new topic, rather than hijack someone else’s thread! I split your thread out into a new topic, @qiuwa

Just to clarify, @quiwa and I are working together on this. They are the research computing person, and I’m the biologist. I asked for help answering some of your questions, and then have been monitoring as it seems the issue was related to the installation.

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Yes. The same conda enviorment. I installed it and made module to export the path. I install qiime for her group to use. We had the same error. Should I do any variables setting? Thanks, Wei

Thanks @Heather_Olins & @qiuwa! In the future it is helpful to let us know these kinds of details! :house_with_garden:

Will do. My apologies for the confusion, and thanks very much for all your help with this!

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