### Author:  [@jairideout](https://forum.qiime2.org/u/jairideout)
#### Post date: [October 6, 2017, 11:44pm UTC](https://forum.qiime2.org/t/dada2-error-return-code-5/1422/4 "2017-10-06T23:44:22Z")
Hi @ErikaGanda! Haven't seen this error before -- it may be related to intermittent issues with upstream conda packages that were obtained when you installed QIIME 2 2017.9. Let's try reinstalling QIIME 2 2017.9, with the hope that the upstream packages have been fixed in the meantime 🙂
Run the following commands to remove your existing 2017.9 environment, clean conda's cache, and update conda itself:
```shell
conda env remove -n qiime2-2017.9
conda clean -y --all
conda update conda
```
If you're on macOS, run this to install 2017.9:
```shell
conda create -n qiime2-2017.9 --file https://data.qiime2.org/distro/core/qiime2-2017.9-conda-osx-64.txt
```
Otherwise if you're on Linux, run this:
```shell
conda create -n qiime2-2017.9 --file https://data.qiime2.org/distro/core/qiime2-2017.9-conda-linux-64.txt
```
After you have a new 2017.9 environment set up, can you try running through the [Moving Pictures tutorial](https://docs.qiime2.org/2017.9/tutorials/moving-pictures/) dataset, at least through the DADA2 denoising steps (i.e. [this section](https://docs.qiime2.org/2017.9/tutorials/moving-pictures/#option-1-dada2))? That'll let us know if the install is working properly.
> [@ErikaGanda](#):
>
> (If you think completely getting rid of Rstudio would do the trick, I can do that, run my paired end DADA2, then install Rstudio again. Just want to make a informed guess)
Don't worry about uninstalling RStudio yet, we'll try that as a last resort. Thanks!
---
### Author:  [@ErikaGanda](https://forum.qiime2.org/u/ErikaGanda)
#### Post date: [October 8, 2017, 1:00am UTC](https://forum.qiime2.org/t/dada2-error-return-code-5/1422/6 "2017-10-08T01:00:16Z")
Thank you for your help @jairideout!
Unfortunately I reinstalled qiime2 twice using the code you gave me and while running trough the Moving Pictures tutorial I got the following:
```shell
Saved Visualization to: demux.qzv
(qiime2-2017.9) Erikas-MacBook-Pro:qiime2-moving-pictures-tutorial ErikaGanda$
(qiime2-2017.9) Erikas-MacBook-Pro:qiime2-moving-pictures-tutorial ErikaGanda$ qiime dada2 denoise-single \
> --i-demultiplexed-seqs demux.qza \
> --p-trim-left 0 \
> --p-trunc-len 120 \
> --o-representative-sequences rep-seqs-dada2.qza \
> --o-table table-dada2.qza
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code -5),
please inspect stdout and stderr to learn more.
Debug info has been saved to /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/qiime2-q2cli-err-feycfrpl.log
Erikas-MacBook-Pro:T ErikaGanda$ cat qiime2-q2cli-err-feycfrpl.log
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_single.R /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/qiime2-archive-tbj0gx_1/a268ffce-fb5a-482f-84fa-428f7697a2c2/data /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmp78v3urqt/output.tsv.biom /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmp78v3urqt 120 0 2.0 2 consensus 1.0 1 1000000
dyld: Library not loaded: @rpath/libncurses.5.dylib
Referenced from: /Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/libreadline.6.2.dylib
Reason: image not found
Traceback (most recent call last):
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 126, in denoise_single
run_commands([cmd])
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands
subprocess.run(cmd, check=True)
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_single.R', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/qiime2-archive-tbj0gx_1/a268ffce-fb5a-482f-84fa-428f7697a2c2/data', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmp78v3urqt/output.tsv.biom', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmp78v3urqt', '120', '0', '2.0', '2', 'consensus', '1.0', '1', '1000000']' returned non-zero exit status -5
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/python3.5/site-packages/q2cli/commands.py", line 218, in __call__
results = action(**arguments)
File "", line 2, in denoise_single
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/python3.5/site-packages/qiime2/sdk/action.py", line 201, in callable_wrapper
output_types, provenance)
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/python3.5/site-packages/qiime2/sdk/action.py", line 334, in _callable_executor_
output_views = callable(**view_args)
File "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 137, in denoise_single
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code -5), please inspect stdout and stderr to learn more.
```
Thoughts?
E
---
### Author:  [@jairideout](https://forum.qiime2.org/u/jairideout)
#### Post date: [October 9, 2017, 10:42pm UTC](https://forum.qiime2.org/t/dada2-error-return-code-5/1422/8 "2017-10-09T22:42:47Z")
Thanks for trying that out @ErikaGanda, it's too bad it didn't work! I'm not sure what's going on and need to gather some more details. After activating your `qiime2-2017.9` environment, can you please send me the output from running these commands? Thanks for bearing with me as we debug this.
```shell
uname -a
conda info -a
conda list --show-channel-urls
cat ~/.Rprofile
```
---
### Author:  [@hshcao](https://forum.qiime2.org/u/hshcao)
#### Post date: [October 9, 2017, 10:43pm UTC](https://forum.qiime2.org/t/dada2-error-return-code-5/1422/9 "2017-10-09T22:43:33Z")
I ran into this problem before. it's the R version incompatibility in my problem. I uninstalled R 3.4.1 and installed R 3.3.1 and worked.
happy exploring and fixing it.
HC
---
### Author:  [@jairideout](https://forum.qiime2.org/u/jairideout)
#### Post date: [October 9, 2017, 10:51pm UTC](https://forum.qiime2.org/t/dada2-error-return-code-5/1422/10 "2017-10-09T22:51:58Z")
Thanks for the info @hshcao! @ErikaGanda can you run these commands and send me the output?
```shell
source deactivate
conda list --show-channel-urls
which R
R --version
```
---
### Author:  [@ErikaGanda](https://forum.qiime2.org/u/ErikaGanda)
#### Post date: [October 10, 2017, 1:08am UTC](https://forum.qiime2.org/t/dada2-error-return-code-5/1422/12 "2017-10-10T01:08:35Z")
Thanks @hshcao and @jairideout!
I will try reinstalling R. But it looks like I have version 3.3.1
The output for the code you asked me to run is below:
```shell
Last login: Mon Oct 9 21:02:01 on ttys000
Erikas-MacBook-Pro:~ ErikaGanda$ source deactivate
Erikas-MacBook-Pro:~ ErikaGanda$ conda list --show-channel-urls
# packages in environment at /Users/ErikaGanda/miniconda3:
#
appnope 0.1.0 py35_0 defaults
bioconductor-biobase 2.34.0 r3.3.1_0 bioconda
bioconductor-biocgenerics 0.20.0 r3.3.1_0 bioconda
bioconductor-biocparallel 1.6.6 r3.3.1_0 bioconda
bioconductor-biostrings 2.42.1 r3.3.1_0 bioconda
bioconductor-dada2 1.4.0 r3.3.1_0 bioconda
bioconductor-genomeinfodb 1.10.3 r3.3.1_0 bioconda
bioconductor-genomicalignments 1.8.4 r3.3.1_0 bioconda
bioconductor-genomicranges 1.26.4 r3.3.1_0 bioconda
bioconductor-iranges 2.8.2 r3.3.1_0 bioconda
bioconductor-rsamtools 1.24.0 r3.3.1_0 bioconda
bioconductor-s4vectors 0.12.2 r3.3.1_0 bioconda
bioconductor-shortread 1.32.0 r3.3.1_0 bioconda
bioconductor-summarizedexperiment 1.2.3 r3.3.1_0 bioconda
bioconductor-xvector 0.14.1 r3.3.1_0 bioconda
bioconductor-zlibbioc 1.20.0 r3.3.1_0 bioconda
biom-format 2.1.5 py35_3 qiime2
bkcharts 0.2 py35_0 defaults
blast 2.6.0 boost1.60_0 bioconda
bleach 1.5.0 py35_0 defaults
bokeh 0.12.6 py35_0 defaults
cachecontrol 0.11.7 py35_0 defaults
cffi 1.9.1 py35_0 defaults
click 6.7 py35_0 defaults
conda 4.3.28 py35h51045a2_0 defaults
conda-env 2.6.0 0 defaults
cryptography 1.7.1 py35_0 defaults
curl 7.54.1 0 defaults
cycler 0.10.0 py35_0 defaults
deblur 1.0.2 py35_0 biocore
decorator 4.0.11 py35_0 defaults
emperor 1.0.0beta8 py35_2 conda-forge
entrypoints 0.2.3 py35_0 defaults
fasttree 2.1.9 2 bioconda
freetype 2.5.5 2 defaults
future 0.16.0 py35_1 defaults
gneiss 0.4.1 py35ha7bfd4e_6 biocore
gsl 2.2.1 0 defaults
h5py 2.7.0 np113py35_0 defaults
hdf5 1.8.17 2 defaults
html5lib 0.999 py35_0 defaults
icu 54.1 0 defaults
idna 2.2 py35_0 defaults
ijson 2.3 py35_0 qiime2
ipykernel 4.6.1 py35_0 defaults
ipython 6.1.0 py35_0 defaults
ipython_genutils 0.2.0 py35_0 defaults
ipywidgets 6.0.0 py35_0 defaults
jbig 2.1 0 defaults
jedi 0.10.2 py35_2 defaults
jinja2 2.9.6 py35_0 defaults
jpeg 9b 0 defaults
jsonschema 2.6.0 py35_0 defaults
jupyter_client 5.1.0 py35_0 defaults
jupyter_core 4.3.0 py35_0 defaults
krb5 1.13.2 0 defaults
libgcc 4.8.5 1 defaults
libiconv 1.14 0 defaults
libpng 1.6.27 0 defaults
libssh2 1.8.0 0 defaults
libtiff 4.0.6 3 defaults
libxml2 2.9.4 0 defaults
lockfile 0.12.2 py35_0 defaults
mafft 7.221 0 bioconda
markupsafe 0.23 py35_2 defaults
matplotlib 2.0.2 np113py35_0 defaults
mistune 0.7.4 py35_0 defaults
mkl 2017.0.3 0 defaults
natsort 5.0.3 py35_0 defaults
nbconvert 5.2.1 py35_0 defaults
nbformat 4.3.0 py35_0 defaults
ncurses 5.9 10 defaults
nose 1.3.7 py35_1 defaults
notebook 5.0.0 py35_0 defaults
numpy 1.13.1 py35_0 defaults
openssl 1.0.2l 0 defaults
pandas 0.20.2 np113py35_0 defaults
pandocfilters 1.4.1 py35_0 defaults
path.py 10.3.1 py35_0 defaults
patsy 0.4.1 py35_0 defaults
pcre 8.39 1 defaults
pexpect 4.2.1 py35_0 defaults
pickleshare 0.7.4 py35_0 defaults
pip 9.0.1 py35_1 defaults
pip 9.0.1
prompt_toolkit 1.0.14 py35_0 defaults
psutil 5.2.2 py35_0 defaults
ptyprocess 0.5.1 py35_0 defaults
pyasn1 0.1.9 py35_0 defaults
pycosat 0.6.1 py35_1 defaults
pycparser 2.17 py35_0 defaults
pycrypto 2.6.1 py35_4 defaults
pygments 2.2.0 py35_0 defaults
pyopenssl 16.2.0 py35_0 defaults
pyparsing 2.1.4 py35_0 defaults
pyqt 5.6.0 py35_2 defaults
python 3.5.3 1 defaults
python-dateutil 2.6.0 py35_0 defaults
pytz 2017.2 py35_0 defaults
pyyaml 3.12 py35_0 defaults
pyzmq 16.0.2 py35_0 defaults
q2-alignment 2017.7.0 py35_0 qiime2/label/r2017.7
q2-composition 2017.6.0 py35_0 qiime2/label/r2017.6
q2-dada2 2017.7.0 py35_0 qiime2/label/r2017.7
q2-deblur 2017.7.0 py35_0 qiime2/label/r2017.7
q2-demux 2017.7.0 py35_0 qiime2/label/r2017.7
q2-diversity 2017.7.0 py35_0 qiime2/label/r2017.7
q2-emperor 2017.7.0 py35_0 qiime2/label/r2017.7
q2-feature-classifier 2017.7.0 py35_0 qiime2/label/r2017.7
q2-feature-table 2017.7.0 py35_0 qiime2/label/r2017.7
q2-gneiss 2017.7.0 py35_0 qiime2/label/r2017.7
q2-metadata 2017.7.0 py35_0 qiime2/label/r2017.7
q2-phylogeny 2017.7.0 py35_0 qiime2/label/r2017.7
q2-quality-filter 2017.7.0 py35_0 qiime2/label/r2017.7
q2-taxa 2017.7.0 py35_0 qiime2/label/r2017.7
q2-types 2017.7.0 py35_0 qiime2/label/r2017.7
q2cli 2017.7.0 py35_0 qiime2/label/r2017.7
q2templates 2017.7.0 py35_0 qiime2/label/r2017.7
qiime2 2017.7.0 py35_0 qiime2/label/r2017.7
qt 5.6.2 2 defaults
r 3.3.1 r3.3.1_0 defaults
r-base 3.3.1 0 defaults
r-bh 1.60.0_2 r3.3.1_0 defaults
r-bitops 1.0_6 r3.3.1_2 defaults
r-boot 1.3_18 r3.3.1_0 defaults
r-chron 2.3_47 r3.3.1_0 defaults
r-class 7.3_14 r3.3.1_0 defaults
r-cluster 2.0.4 r3.3.1_0 defaults
r-codetools 0.2_14 r3.3.1_0 defaults
r-colorspace 1.2_6 r3.3.1_0 defaults
r-data.table 1.9.6 r3.3.1_0 defaults
r-dichromat 2.0_0 r3.3.1_2 defaults
r-digest 0.6.9 r3.3.1_0 defaults
r-foreign 0.8_66 r3.3.1_0 defaults
r-futile.logger 1.4.1 r3.3.1_0 bioconda
r-futile.options 1.0.0 r3.3.1_0 bioconda
r-ggplot2 2.1.0 r3.3.1_0 defaults
r-gtable 0.2.0 r3.3.1_0 defaults
r-hwriter 1.3.2 r3.3.1_0 bioconda
r-kernsmooth 2.23_15 r3.3.1_0 defaults
r-labeling 0.3 r3.3.1_2 defaults
r-lambda.r 1.1.7 r3.3.1_0 bioconda
r-lattice 0.20_33 r3.3.1_0 defaults
r-latticeextra 0.6_28 r3.3.1_0 defaults
r-magrittr 1.5 r3.3.1_2 defaults
r-mass 7.3_45 r3.3.1_0 defaults
r-matrix 1.2_6 r3.3.1_0 defaults
r-mgcv 1.8_12 r3.3.1_0 defaults
r-munsell 0.4.3 r3.3.1_0 defaults
r-nlme 3.1_128 r3.3.1_0 defaults
r-nnet 7.3_12 r3.3.1_0 defaults
r-plyr 1.8.4 r3.3.1_0 defaults
r-rcolorbrewer 1.1_2 r3.3.1_3 defaults
r-rcpp 0.12.5 r3.3.1_0 defaults
r-rcppparallel 4.3.20 r3.3.1_1 bioconda
r-rcurl 1.95_4.8 r3.3.1_0 defaults
r-recommended 3.3.1 r3.3.1_0 defaults
r-reshape2 1.4.1 1a defaults
r-rpart 4.1_10 r3.3.1_0 defaults
r-scales 0.4.0 r3.3.1_0 defaults
r-snow 0.4_1 r3.3.1_0 bioconda
r-spatial 7.3_11 r3.3.1_0 defaults
r-stringi 1.1.1 r3.3.1_0 defaults
r-stringr 1.0.0 r3.3.1_0 defaults
r-survival 2.39_4 r3.3.1_0 defaults
readline 6.2 2 defaults
requests 2.14.2 py35_0 defaults
ruamel_yaml 0.11.14 py35_0 defaults
scikit-bio 0.5.1 np113py35_0 defaults
scikit-learn 0.18.2 np113py35_0 defaults
scipy 0.19.1 np113py35_0 defaults
seaborn 0.7.1 py35_0 defaults
setuptools 27.2.0 py35_0 defaults
simplegeneric 0.8.1 py35_1 defaults
sip 4.18 py35_0 defaults
six 1.10.0 py35_0 defaults
sortmerna 2.0 1 bioconda
sqlite 3.13.0 0 defaults
statsmodels 0.8.0 np113py35_0 defaults
terminado 0.6 py35_0 defaults
testpath 0.3.1 py35_0 defaults
tk 8.5.18 0 defaults
tornado 4.5.1 py35_0 defaults
traitlets 4.3.2 py35_0 defaults
tzlocal 1.3 py35_0 qiime2
vsearch 2.0.3 1 bioconda
wcwidth 0.1.7 py35_0 defaults
wheel 0.29.0 py35_0 defaults
widgetsnbextension 2.0.0 py35_0 defaults
xz 5.2.2 1 defaults
yaml 0.1.6 0 defaults
zlib 1.2.8 3 defaults
Erikas-MacBook-Pro:~ ErikaGanda$ which R
/Users/ErikaGanda/miniconda3/bin/R
Erikas-MacBook-Pro:~ ErikaGanda$ R --version
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin11.0.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
http://www.gnu.org/licenses/.
```
---
### Author:  [@ErikaGanda](https://forum.qiime2.org/u/ErikaGanda)
#### Post date: [October 10, 2017, 1:19am UTC](https://forum.qiime2.org/t/dada2-error-return-code-5/1422/13 "2017-10-10T01:19:33Z")
Sorry @jairideout I skipped your first reply.
Here you go:
```shell
Last login: Mon Oct 9 21:03:26 on ttys000
Erikas-MacBook-Pro:~ ErikaGanda$ source activate qiime2-2017.9
(qiime2-2017.9) Erikas-MacBook-Pro:~ ErikaGanda$ uname -a
Darwin Erikas-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0: Sun Jun 4 21:40:08 PDT 2017; root:xnu-2782.70.3~1/RELEASE_X86_64 x86_64
(qiime2-2017.9) Erikas-MacBook-Pro:~ ErikaGanda$ conda info -a
Current conda install:
platform : osx-64
conda version : 4.3.28
conda is private : False
conda-env version : 4.3.28
conda-build version : not installed
python version : 3.5.3.final.0
requests version : 2.14.2
root environment : /Users/ErikaGanda/miniconda3 (writable)
default environment : /Users/ErikaGanda/miniconda3/envs/qiime2-2017.9
envs directories : /Users/ErikaGanda/miniconda3/envs
/Users/ErikaGanda/.conda/envs
package cache : /Users/ErikaGanda/miniconda3/pkgs
/Users/ErikaGanda/.conda/pkgs
channel URLs : https://repo.continuum.io/pkgs/main/osx-64
https://repo.continuum.io/pkgs/main/noarch
https://repo.continuum.io/pkgs/free/osx-64
https://repo.continuum.io/pkgs/free/noarch
https://repo.continuum.io/pkgs/r/osx-64
https://repo.continuum.io/pkgs/r/noarch
https://repo.continuum.io/pkgs/pro/osx-64
https://repo.continuum.io/pkgs/pro/noarch
config file : None
netrc file : None
offline mode : False
user-agent : conda/4.3.28 requests/2.14.2 CPython/3.5.3 Darwin/14.5.0 OSX/10.10.5
UID:GID : 501:20
# conda environments:
#
myenv /Users/ErikaGanda/miniconda3/envs/myenv
office-microbes /Users/ErikaGanda/miniconda3/envs/office-microbes
py3k /Users/ErikaGanda/miniconda3/envs/py3k
qiime2 /Users/ErikaGanda/miniconda3/envs/qiime2
qiime2-2017.2 /Users/ErikaGanda/miniconda3/envs/qiime2-2017.2
qiime2-2017.6 /Users/ErikaGanda/miniconda3/envs/qiime2-2017.6
qiime2-2017.7 /Users/ErikaGanda/miniconda3/envs/qiime2-2017.7
qiime2-2017.9 * /Users/ErikaGanda/miniconda3/envs/qiime2-2017.9
root /Users/ErikaGanda/miniconda3
sys.version: 3.5.3 |Continuum Analytics, Inc.| (defau...
sys.prefix: /Users/ErikaGanda/miniconda3
sys.executable: /Users/ErikaGanda/miniconda3/bin/python
conda location: /Users/ErikaGanda/miniconda3/lib/python3.5/site-packages/conda
conda-build: None
conda-env: /Users/ErikaGanda/miniconda3/bin/conda-env
user site dirs:
CIO_TEST:
CONDA_DEFAULT_ENV: qiime2-2017.9
CONDA_ENVS_PATH:
DYLD_LIBRARY_PATH:
PATH: /Users/ErikaGanda/miniconda3/envs/qiime2-2017.9/bin:/Users/ErikaGanda/miniconda3/bin:/Users/ErikaGanda/miniconda3/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Library/TeX/texbin
PYTHONHOME:
PYTHONPATH:
WARNING: could not import _license.show_info
# try:
# $ conda install -n root _license
(qiime2-2017.9) Erikas-MacBook-Pro:~ ErikaGanda$ conda list --show-channel-urls
# packages in environment at /Users/ErikaGanda/miniconda3/envs/qiime2-2017.9:
#
appnope 0.1.0 py35_0 conda-forge
asn1crypto 0.22.0 py35_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
biom-format 2.1.5 py35_3 qiime2
blast 2.6.0 boost1.64_2 bioconda
bleach 2.0.0 py35_0 conda-forge
bokeh 0.12.9 py35_0 conda-forge
ca-certificates 2017.7.27.1 0 conda-forge
cachecontrol 0.12.3 py35_0 defaults
cairo 1.14.6 4 conda-forge
certifi 2017.7.27.1 py35_0 conda-forge
cffi 1.10.0 py35_0 conda-forge
chardet 3.0.4 py35_0 conda-forge
click 6.7 py35_0 conda-forge
cryptography 2.0.3 py35_0 conda-forge
curl 7.54.1 0 conda-forge
cycler 0.10.0 py35_0 conda-forge
cython 0.27 py35_0 conda-forge
deblur 1.0.2 py35_0 biocore
decorator 4.1.2 py35_0 conda-forge
emperor 1.0.0beta11 py35_2 conda-forge
entrypoints 0.2.3 py35_1 conda-forge
fastcluster 1.1.23 np113py35_0 conda-forge
fasttree 2.1.9 2 bioconda
fontconfig 2.12.1 4 conda-forge
freetype 2.7 1 conda-forge
future 0.16.0 py35_0 conda-forge
gettext 0.19.8.1 0 conda-forge
glib 2.51.4 0 conda-forge
gneiss 0.4.1 py35ha7bfd4e_6 biocore
graphite2 1.3.9 0 conda-forge
gsl 2.1 2 conda-forge
h5py 2.7.0 np113py35_0 defaults
harfbuzz 1.4.3 0 conda-forge
hdf5 1.8.17 11 conda-forge
html5lib 0.999999999 py35_0 conda-forge
icu 58.1 1 conda-forge
idna 2.6 py_0 conda-forge
ijson 2.3 py35_0 qiime2
intel-openmp 2018.0.0 hdd0ccc9_7 defaults
ipykernel 4.6.1 py35_0 conda-forge
ipython 6.2.0 py35_0 conda-forge
ipython_genutils 0.2.0 py35_0 conda-forge
ipywidgets 7.0.1 py_2 conda-forge
jedi 0.10.2 py35_0 conda-forge
jinja2 2.9.6 py35_0 conda-forge
jpeg 9b 1 conda-forge
jsonschema 2.6.0 py35_0 conda-forge
jupyter_client 5.1.0 py35_0 conda-forge
jupyter_core 4.3.0 py35_0 conda-forge
krb5 1.14.2 0 conda-forge
libcxx 4.0.1 h579ed51_0 defaults
libcxxabi 4.0.1 hebd6815_0 defaults
libffi 3.2.1 3 conda-forge
libgcc 4.8.5 hdbeacc1_10 defaults
libgfortran 3.0.1 h93005f0_2 defaults
libiconv 1.14 4 conda-forge
libpng 1.6.28 1 conda-forge
libsodium 1.0.10 0 conda-forge
libssh2 1.8.0 1 conda-forge
libtiff 4.0.7 0 conda-forge
libxml2 2.9.5 0 conda-forge
lockfile 0.12.2 py35_0 conda-forge
mafft 7.221 0 bioconda
markupsafe 1.0 py35_0 conda-forge
matplotlib 2.0.2 py35_2 conda-forge
mistune 0.7.4 py35_0 conda-forge
mkl 2018.0.0 hc285769_4 defaults
msgpack-python 0.4.8 py35_0 conda-forge
natsort 5.0.2 py35_0 conda-forge
nbconvert 5.3.1 py_1 conda-forge
nbformat 4.4.0 py35_0 conda-forge
ncurses 5.9 10 conda-forge
nose 1.3.7 py35_2 conda-forge
notebook 5.1.0 py35_0 conda-forge
numpy 1.13.1 py35he58e7f4_2 defaults
openssl 1.0.2l 0 conda-forge
pandas 0.20.3 py35_1 conda-forge
pandoc 1.19.2 0 conda-forge
pandocfilters 1.4.1 py35_0 conda-forge
pango 1.40.4 0 conda-forge
patsy 0.4.1 py35_0 conda-forge
pcre 8.39 0 conda-forge
pexpect 4.2.1 py35_0 conda-forge
pickleshare 0.7.4 py35_0 conda-forge
pip 9.0.1 py35_0 conda-forge
pixman 0.34.0 0 conda-forge
prompt_toolkit 1.0.15 py35_0 conda-forge
psutil 5.2.2 py35_0 conda-forge
ptyprocess 0.5.2 py35_0 conda-forge
pycparser 2.18 py35_0 conda-forge
pygments 2.2.0 py35_0 conda-forge
pyopenssl 17.2.0 py35_0 conda-forge
pyparsing 2.2.0 py35_0 conda-forge
pysocks 1.6.7 py35_0 conda-forge
python 3.5.4 0 conda-forge
python-dateutil 2.6.1 py35_0 conda-forge
pytz 2017.2 py35_0 conda-forge
pyyaml 3.12 py35_1 conda-forge
pyzmq 16.0.2 py35_2 conda-forge
q2-alignment 2017.9.0 py35_0 qiime2/label/r2017.9
q2-composition 2017.9.0 py35_0 qiime2/label/r2017.9
q2-dada2 2017.9.0 py35_0 qiime2/label/r2017.9
q2-deblur 2017.9.0 py35_0 qiime2/label/r2017.9
q2-demux 2017.9.0 py35_0 qiime2/label/r2017.9
q2-diversity 2017.9.0 py35_0 qiime2/label/r2017.9
q2-emperor 2017.9.0 py35_0 qiime2/label/r2017.9
q2-feature-classifier 2017.9.0 py35_0 qiime2/label/r2017.9
q2-feature-table 2017.9.0 py35_0 qiime2/label/r2017.9
q2-gneiss 2017.9.0 py35_0 qiime2/label/r2017.9
q2-longitudinal 2017.9.0 py35_0 qiime2/label/r2017.9
q2-metadata 2017.9.0 py35_0 qiime2/label/r2017.9
q2-phylogeny 2017.9.0 py35_0 qiime2/label/r2017.9
q2-quality-filter 2017.9.0 py35_0 qiime2/label/r2017.9
q2-sample-classifier 2017.9.0 py35_0 qiime2/label/r2017.9
q2-taxa 2017.9.0 py35_0 qiime2/label/r2017.9
q2-types 2017.9.0 py35_0 qiime2/label/r2017.9
q2-vsearch 2017.9.0 py35_0 qiime2/label/r2017.9
q2cli 2017.9.0 py35_0 qiime2/label/r2017.9
q2templates 2017.9.0 py35_0 qiime2/label/r2017.9
qiime2 2017.9.0 py35_0 qiime2/label/r2017.9
r-base 3.3.2 5 conda-forge
r-bh 1.62.0_1 r3.3.2_0 conda-forge
r-bitops 1.0_6 r3.3.2_0 conda-forge
r-colorspace 1.3_2 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 0.6.12 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-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 1.1.9 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 0.2.0 r3.3.2_0 conda-forge
r-magrittr 1.5 r3.3.2_0 conda-forge
r-mass 7.3_45 r3.3.2_0 conda-forge
r-matrix 1.2_7.1 r3.3.2_0 conda-forge
r-munsell 0.4.3 r3.3.2_0 conda-forge
r-plyr 1.8.4 r3.3.2_0 conda-forge
r-rcolorbrewer 1.1_2 r3.3.2_0 conda-forge
r-rcpp 0.12.10 r3.3.2_0 conda-forge
r-rcppparallel 4.3.20 r3.3.2_0 conda-forge
r-rcurl 1.95_4.8 r3.3.2_0 conda-forge
r-reshape2 1.4.2 r3.3.2_0 conda-forge
r-rlang 0.1.2 r3.3.2_0 conda-forge
r-scales 0.4.1 r3.3.2_0 conda-forge
r-snow 0.4_2 r3.3.2_0 conda-forge
r-stringi 1.1.2 r3.3.2_0 conda-forge
r-stringr 1.2.0 r3.3.2_0 conda-forge
r-tibble 1.3.3 r3.3.2_0 conda-forge
readline 6.2 0 conda-forge
requests 2.18.4 py35_1 conda-forge
scikit-bio 0.5.1 np113py35_0 defaults
scikit-learn 0.19.0 py35hd036984_2 defaults
scipy 0.19.1 py35hf362045_3 defaults
seaborn 0.8.1 py35_0 conda-forge
setuptools 36.3.0 py35_0 conda-forge
simplegeneric 0.8.1 py35_0 conda-forge
six 1.11.0 py35_1 conda-forge
sortmerna 2.0 1 bioconda
sqlite 3.13.0 1 conda-forge
statsmodels 0.8.0 py35_0 conda-forge
terminado 0.6 py35_0 conda-forge
testpath 0.3.1 py35_0 conda-forge
tk 8.5.19 2 conda-forge
tornado 4.5.2 py35_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 1.22 py35_0 conda-forge
vsearch 2.0.3 1 bioconda
wcwidth 0.1.7 py35_0 conda-forge
webencodings 0.5 py35_0 conda-forge
wheel 0.30.0 py_1 conda-forge
widgetsnbextension 3.0.3 py35_2 conda-forge
xz 5.2.3 0 conda-forge
yaml 0.1.6 0 conda-forge
zeromq 4.2.1 1 conda-forge
zlib 1.2.8 3 conda-forge
(qiime2-2017.9) Erikas-MacBook-Pro:~ ErikaGanda$ cat ~/.Rprofile
cat: /Users/ErikaGanda/.Rprofile: No such file or directory
(qiime2-2017.9) Erikas-MacBook-Pro:~ ErikaGanda$
```
---
### Author:  [@jairideout](https://forum.qiime2.org/u/jairideout)
#### Post date: [October 10, 2017, 8:54pm UTC](https://forum.qiime2.org/t/dada2-error-return-code-5/1422/15 "2017-10-10T20:54:22Z")
Thanks for the output from those commands @ErikaGanda! It looks like your root conda environment (i.e. the default environment you're using when an environment isn't activated) has an old qiime2 install (2017.7). This may be causing issues with your `qiime2-2017.9` environment because there are some mismatched R/readline/ncurses packages in the root environment that I wouldn't expect to function properly.
Let's explore this a bit:
1. Open a new terminal.
2. Deactivate any active environments (there shouldn't be any, but doesn't hurt to confirm):
```auto
source deactivate
```
3. Reset your root environment to what it was when you first installed conda (this will clear out the old qiime2-2017.7 install and anything else there):
```auto
conda install --revision 1
```
4. Clear conda's cache and update conda:
```auto
conda clean --all -y
conda update conda
```
5. Confirm that qiime2 is no longer installed in the root environment. The following command should say something like "command not found" when you run it:
```auto
qiime
```
6. Delete your `qiime2-2017.9` environment:
```auto
conda env remove -n qiime2-2017.9
```
7. Reinstall `qiime2-2017.9` and activate the environment:
```auto
conda create -n qiime2-2017.9 --file https://data.qiime2.org/distro/core/qiime2-2017.9-conda-osx-64.txt
source activate qiime2-2017.9
```
8. For good measure, let's try out the R Studio workaround, in case you have other versions of R hanging around on your system:
```auto
echo '.libPaths(.libPaths()[2])' > ~/.Rprofile
```
9. Try out the dada2 tutorial commands again, hopefully we'll have better luck!
When you try out the above steps, please send me all of the output produced by running the commands. Hopefully this will fix the issue!
---
### Author:  [@ErikaGanda](https://forum.qiime2.org/u/ErikaGanda)
#### Post date: [October 10, 2017, 9:47pm UTC](https://forum.qiime2.org/t/dada2-error-return-code-5/1422/17 "2017-10-10T21:47:48Z")
YESSSSSS!!! @jairideout
It worked. Thank you so much!
After I ran conda install --revision 1 it looked like miniconda completely disappeared from my computer.
When I ran conda clean --all -y it wouldn't recognize it, it didn't even recognize wget command...
So I manually removed the directory it used to be stored in, and re-installed miniconda.
After doing that I could successfully download and activate qiime2-2017.9. Went back to the moving pictures tutorial and ran qiime dada2 denoise-single
--i-demultiplexed-seqs demux.qza
--p-trim-left 0
--p-trunc-len 120
--o-representative-sequences rep-seqs-dada2.qza
--o-table table-dada2.qza
Saved FeatureTable[Frequency] to: table-dada2.qza
Saved FeatureData[Sequence] to: rep-seqs-dada2.qza
Thank you so much! I really appreciate it, and don't know how I would get to my data without all the help you guys have been giving me in the last couple of years. =)
E
---
### Author:  [@jairideout](https://forum.qiime2.org/u/jairideout)
#### Post date: [October 10, 2017, 10:18pm UTC](https://forum.qiime2.org/t/dada2-error-return-code-5/1422/18 "2017-10-10T22:18:06Z")
> [@ErikaGanda](#):
>
> YESSSSSS!!! @jairideout
>
> It worked. Thank you so much!
Excellent!! 😌
> [@ErikaGanda](#):
>
> After I ran conda install --revision 1 it looked like miniconda completely disappeared from my computer.
>
> When I ran conda clean --all -y it wouldn’t recognize it, it didn’t even recognize wget command…
Oh no, I am so sorry that my instructions destroyed your miniconda install. According to a stackoverflow post, `--revision 1` should have been safe but I guess that's not the case... good to know 🙂
> [@ErikaGanda](#):
>
> So I manually removed the directory it used to be stored in, and re-installed miniconda.
Perfect, I think that was the only way to recover at that point.
A general note: I'd avoid installing things into your root conda environment (it's an easy mistake to make, I do it all the time). I usually try to keep qiime2 and other projects installed into their own environments and keep the root environment pretty minimal.
> [@ErikaGanda](#):
>
> Thank you so much! I really appreciate it, and don’t know how I would get to my data without all the help you guys have been giving me in the last couple of years. =)
Thanks for the feedback, we all really appreciate it! Thank you for being so patient during this debugging process.
Happy QIIMEing! 🌞
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [November 11, 2017, 4:18am UTC](https://forum.qiime2.org/t/dada2-error-return-code-5/1422/19 "2017-11-11T04:18:08Z")
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