DADA2 error (return code -5)

Hi,

I have been getting an error while trying to run DADA2. I went through the similar topics (Exit code -11 and the workaround creating .Rprofile file with .libPaths(.libPaths()[2]) inside)

I do not want to keep bringing new, similar topics, but I had no luck with the solutions mentioned before. Any thoughts?

(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)

Thank you very much.

I am pasting the code, the error, and what I found inside the error log below.

(qiime2-2017.9) dhcp-morris-2127:FISH ErikaGanda$ ls
paired-end-demux.qza	paired-end-demux.qzv	pe-64			pe-64-manifest
(qiime2-2017.9) dhcp-morris-2127:FISH ErikaGanda$ qiime dada2 denoise-paired   --i-demultiplexed-seqs paired-end-demux.qza   --o-table table   --o-representative-sequences rep-seqs   --p-trim-left-f 20   --p-trim-left-r 1   --p-trunc-len-f 265   --p-trunc-len-r 219 


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-1_4i94ut.log

dhcp-morris-2127:T ErikaGanda$ cat qiime2-q2cli-err-1_4i94ut.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_paired.R /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/forward /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/reverse /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/output.tsv.biom /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/filt_f /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/filt_r 265 219 20 1 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 179, in denoise_paired
    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_paired.R', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/forward', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/reverse', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/output.tsv.biom', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/filt_f', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmpyowhhrrw/filt_r', '265', '219', '20', '1', '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 "<decorator-gen-320>", line 2, in denoise_paired
  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 194, in denoise_paired
    " 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.

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 :slight_smile:

Run the following commands to remove your existing 2017.9 environment, clean conda’s cache, and update conda itself:

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:

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:

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 dataset, at least through the DADA2 denoising steps (i.e. this section)? That’ll let us know if the install is working properly.

Don’t worry about uninstalling RStudio yet, we’ll try that as a last resort. Thanks!

1 Like

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:

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 "<decorator-gen-318>", 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

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.

uname -a
conda info -a
conda list --show-channel-urls
cat ~/.Rprofile

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

1 Like

Thanks for the info @hshcao! @ErikaGanda can you run these commands and send me the output?

source deactivate
conda list --show-channel-urls
which R
R --version

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:

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                     <pip>
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/.

Sorry @jairideout I skipped your first reply.

Here you go:

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: <not set>
CONDA_DEFAULT_ENV: qiime2-2017.9
CONDA_ENVS_PATH: <not set>
DYLD_LIBRARY_PATH: <not set>
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: <not set>
PYTHONPATH: <not set>

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$

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):
    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):
    conda install --revision 1
    
  4. Clear conda’s cache and update conda:
    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:
    qiime
    
  6. Delete your qiime2-2017.9 environment:
    conda env remove -n qiime2-2017.9
    
  7. Reinstall qiime2-2017.9 and activate the environment:
    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:
    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!

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

Excellent!! :relieved:

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 :slight_smile:

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.

Thanks for the feedback, we all really appreciate it! Thank you for being so patient during this debugging process.

Happy QIIMEing! :sun_with_face:

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