I have installed the newer qiime2 2017.2 based on the manual. Howerver, when I run the qiime dada2 denoise-single command, an error was throwed:
Command: run_dada_single.R /tmp/qiime2-archive-2898ww0a/26bd94e3-c63e-4208-a60c-6a7e4b42dd7c/data /tmp/tmpdwnq7bkj/output.tsv.biom /tmp/tmpdwnq7bkj 100 0 2.0 2 1 1000000
R version 3.3.2 (2016-10-31)
Error in library(dada2) : there is no package called ‘dada2’
Execution halted
The dada2 library couldn't be find in R 3.3.2, but I have installed the q2-dada2 module. And I also run the command qiime dev refresh-cache, it's useless for me. Do I need open the R and install the dada2 library from biocLite?
Any help would be appreciated. Thank you!
My conda env list was as follows:
biom-format 2.1.5 py35_3 qiime2
bokeh 0.12.4 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
bzip2 1.0.6 3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
cachecontrol 0.11.7 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
cairo 1.14.8 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
click 6.7 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
curl 7.52.1 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
cycler 0.10.0 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
dbus 1.10.10 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
decorator 4.0.11 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
emperor 1.0.0beta5 py35_2 conda-forge
entrypoints 0.2.2 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
expat 2.1.0 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
fasttree 2.1.8 0 biocore
fontconfig 2.12.1 3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
freetype 2.5.5 2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
future 0.16.0 py35_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
glib 2.50.2 1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
gsl 2.2.1 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
gst-plugins-base 1.8.0 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
gstreamer 1.8.0 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
h5py 2.6.0 np111py35_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
harfbuzz 0.9.39 2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
hdf5 1.8.17 1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
icu 54.1 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ijson 2.3 py35_0 qiime2
ipykernel 4.5.2 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ipython 5.1.0 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ipython_genutils 0.1.0 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ipywidgets 5.2.2 py35_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jbig 2.1 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jinja2 2.9.4 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jpeg 9b 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jsonschema 2.5.1 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jupyter_client 4.4.0 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jupyter_core 4.2.1 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libffi 3.2.1 1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libgcc 5.2.0 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libgfortran 3.0.0 1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libiconv 1.14 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libpng 1.6.27 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libsodium 1.0.10 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libtiff 4.0.6 3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libxcb 1.12 1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libxml2 2.9.4 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
lockfile 0.12.2 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
mafft 7.305 0 bioconda
markupsafe 0.23 py35_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
matplotlib 2.0.0 np111py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
mistune 0.7.3 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
mkl 2017.0.1 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
natsort 5.0.1 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
nbconvert 4.2.0 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
nbformat 4.2.0 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ncurses 5.9 10 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
nose 1.3.7 py35_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
notebook 4.3.1 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
numpy 1.11.3 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
openssl 1.0.2k 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pandas 0.19.2 np111py35_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pango 1.40.3 1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
path.py 10.0 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
patsy 0.4.1 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pcre 8.39 1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pexpect 4.2.1 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pickleshare 0.7.4 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pip 9.0.1 py35_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pixman 0.34.0 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
prompt_toolkit 1.0.9 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
psutil 5.1.2 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ptyprocess 0.5.1 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pygments 2.1.3 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pyparsing 2.1.4 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pyqt 5.6.0 py35_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
python 3.5.2 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
python-dateutil 2.6.0 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pytz 2016.10 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pyyaml 3.12 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pyzmq 16.0.2 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
q2-alignment 2017.2.0 py35_0 qiime2
q2-composition 2017.2.0 py35_0 qiime2
q2-dada2 2017.2.0 py35r3.3.2_0 qiime2
q2-demux 2017.2.0 py35_0 qiime2
q2-diversity 2017.2.0 py35_0 qiime2
q2-emperor 2017.2.0 py35_0 qiime2
q2-feature-classifier 2017.2.0 py35_0 qiime2
q2-feature-table 2017.2.0 py35_0 qiime2
q2-phylogeny 2017.2.0 py35_0 qiime2
q2-taxa 2017.2.0 py35_0 qiime2
q2-types 2017.2.0 py35_0 qiime2
q2cli 2017.2.0 py35_0 qiime2
q2templates 2017.2.0 py35_0 qiime2
qiime2 2017.2.0 py35_0 qiime2
qt 5.6.2 3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
r 3.3.2 r3.3.2_0 r
r-base 3.3.2 1 r
r-boot 1.3_18 r3.3.2_0 r
r-class 7.3_14 r3.3.2_0 r
r-cluster 2.0.5 r3.3.2_0 r
r-codetools 0.2_15 r3.3.2_0 r
r-foreign 0.8_67 r3.3.2_0 r
r-kernsmooth 2.23_15 r3.3.2_0 r
r-lattice 0.20_34 r3.3.2_0 r
r-mass 7.3_45 r3.3.2_0 r
r-matrix 1.2_7.1 r3.3.2_0 r
r-mgcv 1.8_16 r3.3.2_0 r
r-nlme 3.1_128 r3.3.2_0 r
r-nnet 7.3_12 r3.3.2_0 r
r-recommended 3.3.2 r3.3.2_0 r
r-rpart 4.1_10 r3.3.2_0 r
r-spatial 7.3_11 r3.3.2_0 r
r-survival 2.40_1 r3.3.2_0 r
readline 6.2 2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
requests 2.12.4 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
scikit-bio 0.5.1 np111py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
scikit-learn 0.18.1 np111py35_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
scipy 0.18.1 np111py35_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
seaborn 0.7.1 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
setuptools 27.2.0 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
simplegeneric 0.8.1 py35_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sip 4.18 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
six 1.10.0 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sqlite 3.13.0 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
statsmodels 0.6.1 np111py35_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
terminado 0.6 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
tk 8.5.18 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
tornado 4.4.2 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
traitlets 4.3.1 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
tzlocal 1.3 py35_0 qiime2
wcwidth 0.1.7 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
wheel 0.29.0 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
widgetsnbextension 1.2.6 py35_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
xz 5.2.2 1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
yaml 0.1.6 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
zeromq 4.1.5 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
zlib 1.2.8 3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free