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

User Support
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) [lsw@lsw 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.

3

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).

5

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

[lsw@lsw Genotech_ChaSH] conda --version conda 4.4.11 [lsw@lsw 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

7

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)

9

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