Qiime2-2018.2, dada2 denoising, error (return code 1)

Hi, there.
I installed qiime2 via miniconda, and successfully reached to demux.qza.

During dada2-denoising, I met the error and log as belows.
Please examine and any comment would be very helpful to me.
Thank you very much.


(qiime2-2018.2) [[email protected] paired_end]$ qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --p-trunc-len-f 120 --p-trunc-len-r 120 --o-representative-sequences rep-dada2.qza --o-table table-dada2.qza --verbose

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 /tmp/tmpqoltoplx/forward /tmp/tmpqoltoplx/reverse /tmp/tmpqoltoplx/output.tsv.biom /tmp/tmpqoltoplx/filt_f /tmp/tmpqoltoplx/filt_r 120 120 0 0 2.0 2 consensus 1.0 1 1000000

R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
Error: package or namespace load failed for ‘dada2’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/home/lsw/anaconda2/envs/qiime2-2018.2/lib/R/library/RCurl/libs/RCurl.so’:
/home/lsw/anaconda2/envs/qiime2-2018.2/lib/R/library/RCurl/libs/…/…/…/…/libcurl.so.4: undefined symbol: libssh2_scp_recv2
Execution halted
Plugin error from dada2:

An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.


Hi @lsw,

This is a new one for us. Could you provide the output to the following:

conda --version

and inside your environment:

conda list

Usually we see these issues when your system R starts interacting with your conda R, but that doesn’t seem to be the case here. So I am wondering if a package is corrupt. You might try updating conda (conda update conda), cleaning your package-cache conda clean --all, and re-installing the environment (remove first with conda env remove -n qiime2-2018.2).

Thank you, ebolyen,
please see below. hope this is what you want.

[[email protected] Genotech_ChaSH] conda --version conda 4.4.11 [[email protected] Genotech_ChaSH] conda list

packages in environment at /home/lsw/anaconda2:

Name Version Build Channel

_nb_ext_conf 0.2.0 py27_0
alabaster 0.7.8 py27_0
anaconda custom py27_0
anaconda-client 1.4.0 py27_0
anaconda-navigator 1.2.1 py27_0
argcomplete 1.0.0 py27_1
astropy 1.2.1 np111py27_0
babel 2.3.3 py27_0
backports 1.0 py27_0
backports.functools-lru-cache 1.5
backports_abc 0.4 py27_0
beautifulsoup4 4.4.1 py27_0
biom-format 2.1.6
bitarray 0.8.1 py27_0
blaze 0.10.1 py27_0
bokeh 0.12.0 py27_0
boto 2.40.0 py27_0
bottleneck 1.1.0 np111py27_0
burrito 0.9.1
burrito-fillings 0.1.1
ca-certificates 2017.08.26 h1d4fec5_0
cairo 1.12.18 6
cdecimal 2.3 py27_2
certifi 2018.1.18 py27_0
cffi 1.6.0 py27_0
chest 0.2.3 py27_0
click 6.6 py27_0
cloudpickle 0.2.1 py27_0
clyent 1.2.2 py27_0
cogent 1.5.3
colorama 0.3.7 py27_0
conda 4.4.11 py27_0
conda-build 1.21.3 py27_0
conda-env 2.6.0 h36134e3_1
configobj 5.0.6 py27_0
configparser 3.5.0b2 py27_1
contextlib2 0.5.3 py27_0
cryptography 1.4 py27_0
curl 7.49.0 0
cycler 0.10.0 py27_0
cython 0.24 py27_0
cytoolz 0.9.0.1 py27h14c3975_0
dask 0.10.0 py27_0
datashape 0.5.2 py27_0
decorator 4.0.10 py27_0
dill 0.2.5 py27_0
docutils 0.12 py27_2
dynd-python 0.7.2 py27_0
emperor 0.9.60
entrypoints 0.2.2 py27_0
enum34 1.1.6 py27_0
et_xmlfile 1.0.1 py27_0
fastcache 1.0.2 py27_1
flask 0.11.1 py27_0
flask-cors 2.1.2 py27_0
fontconfig 2.11.1 6
freetype 2.5.5 1
funcsigs 1.0.2 py27_0
functools32 3.2.3.2 py27_0
future 0.16.0
futures 3.0.5 py27_0
gdata 2.0.18
get_terminal_size 1.0.0 py27_0
gevent 1.1.1 py27_0
greenlet 0.4.10 py27_0
grin 1.2.1 py27_3
h5py 2.6.0 np111py27_1
hdf5 1.8.16 0
heapdict 1.0.0 py27_1
idna 2.1 py27_0
imagesize 0.7.1 py27_0
ipaddress 1.0.16 py27_0
ipykernel 4.3.1 py27_0
ipython 4.2.0 py27_0
ipython_genutils 0.1.0 py27_0
ipywidgets 4.1.1 py27_0
itsdangerous 0.24 py27_0
jbig 2.1 0
jdcal 1.2 py27_1
jedi 0.9.0 py27_1
jinja2 2.8 py27_1
jpeg 8d 1
jsonschema 2.5.1 py27_0
jupyter 1.0.0 py27_3
jupyter_client 4.3.0 py27_0
jupyter_console 4.1.1 py27_0
jupyter_core 4.1.0 py27_0
libdynd 0.7.2 0
libffi 3.2.1 0
libgcc-ng 7.2.0 hdf63c60_3
libgfortran 3.0.0 1
libpng 1.6.22 0
libsodium 1.0.10 0
libtiff 4.0.6 2
libxml2 2.9.2 0
libxslt 1.1.28 0
llvmlite 0.11.0 py27_0
locket 0.2.0 py27_1
lxml 3.6.0 py27_0
markupsafe 0.23 py27_2
matplotlib 1.5.1 np111py27_0
mistune 0.7.2 py27_0
mkl 11.3.3 0
mkl-service 1.1.2 py27_2
mock 2.0.0
mpmath 0.19 py27_1
multipledispatch 0.4.8 py27_0
natsort 3.5.6
nb_anacondacloud 1.1.0 py27_0
nb_conda 1.1.0 py27_0
nb_conda_kernels 1.0.3 py27_0
nbconvert 4.2.0 py27_0
nbformat 4.0.1 py27_0
nbpresent 3.0.2 py27_0
networkx 1.11 py27_0
nltk 3.2.1 py27_0
nose 1.3.7 py27_1
notebook 4.2.1 py27_0
numba 0.26.0 np111py27_0
numexpr 2.6.0 np111py27_0
numpy 1.11.1 py27_0
numpy 1.14.2
odo 0.5.0 py27_1
openpyxl 2.3.2 py27_0
openssl 1.0.2n hb7f436b_0
pandas 0.18.1 np111py27_0
partd 0.3.4 py27_0
patchelf 0.9 0
path.py 8.2.1 py27_0
pathlib2 2.1.0 py27_0
patsy 0.4.1 py27_0
pbr 3.1.1
pep8 1.7.0 py27_0
pexpect 4.0.1 py27_0
pickleshare 0.7.2 py27_0
pillow 3.2.0 py27_1
pip 9.0.2
pip 8.1.2 py27_0
pixman 0.32.6 0
ply 3.8 py27_0
psutil 4.3.0 py27_0
ptyprocess 0.5.1 py27_0
py 1.4.31 py27_0
pyasn1 0.1.9 py27_0
pycairo 1.10.0 py27_0
pycosat 0.6.3 py27ha4109ae_0
pycparser 2.14 py27_1
pycrypto 2.6.1 py27_4
pycurl 7.43.0 py27_0
pyflakes 1.2.3 py27_0
pygments 2.1.3 py27_0
pynast 1.2.2
pyopenssl 16.2.0 py27_0
pyparsing 2.1.4 py27_0
pyparsing 2.2.0
pyqi 0.3.2
pyqt 4.11.4 py27_3
pytables 3.2.2 np111py27_4
pytest 2.9.2 py27_0
python 2.7.12 1
python-dateutil 2.7.0
python-dateutil 2.5.3 py27_0
pytz 2018.3
pytz 2016.4 py27_0
pyyaml 3.11 py27_4
pyzmq 15.2.0 py27_1
qcli 0.1.1
qiime 1.9.1
qiime-default-reference 0.1.3
qt 4.8.7 3
qtconsole 4.2.1 py27_0
qtpy 1.0.2 py27_0
readline 6.2 2
redis 3.2.0 0
redis-py 2.10.5 py27_0
requests 2.14.2 py27_0
rope 0.9.4 py27_1
ruamel_yaml 0.11.14 py27_1
scikit-bio 0.2.3
scikit-image 0.12.3 np111py27_1
scikit-learn 0.17.1 np111py27_2
scipy 0.17.1 np111py27_1
scipy 1.0.0
setuptools 38.5.1 py27_0
simplegeneric 0.8.1 py27_1
singledispatch 3.4.0.3 py27_0
sip 4.16.9 py27_0
six 1.10.0 py27_0
six 1.11.0
snowballstemmer 1.2.1 py27_0
sockjs-tornado 1.0.3 py27_0
sphinx 1.4.1 py27_0
sphinx_rtd_theme 0.1.9 py27_0
spyder 2.3.9 py27_0
sqlalchemy 1.0.13 py27_0
sqlite 3.13.0 0
ssl_match_hostname 3.4.0.2 py27_1
statsmodels 0.6.1 np111py27_1
subprocess32 3.2.7
sympy 1.0 py27_0
terminado 0.6 py27_0
tk 8.5.18 0
toolz 0.8.0 py27_0
tornado 4.3 py27_1
traitlets 4.2.1 py27_0
unicodecsv 0.14.1 py27_0
werkzeug 0.11.10 py27_0
wget 1.19.1 he4ec0ba_0
wheel 0.29.0 py27_0
xlrd 1.0.0 py27_0
xlsxwriter 0.9.2 py27_0
xlwt 1.1.2 py27_0
xz 5.2.2 0
yaml 0.1.6 0
zeromq 4.1.4 0
zlib 1.2.11 ha838bed_2

Hi @lsw,

It looks like your conda is up to date. Your conda-list is showing your root environment, which does seem to have a lot of things in it, but ultimately shouldn’t impact your QIIME 2 installation.

Let’s have you run the following to see if that helps:

conda env remove -n qiime2-2018.2
conda clean -y --all

Then follow the installation instructions again.

Also, just to cover our bases, could you provide the output from:

uname --all

(it will tell me what version if the Linux kernel you are running)

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