DADA2 error, or maybe environment error..

Hi, everyone. I'm new to qiime2.

I used qiime2 at one server, and I started DADA2 denoising step in the other server.
But, I am keep encountering same error. I thought it was something only related to DADA2, but as I searched in forum and tried all things I could do, It seems like the error is not confined to dada2, but whole environment.

First, I tried
(qiime2-2021.4) ~$ time qiime dada2 denoise-paired
--i-demultiplexed-seqs merged_demux_seqs.qza
--p-trim-left-f 20
--p-trunc-len-f 290
--p-trim-left-r 0
--p-trunc-len-r 225
--p-max-ee-f 2
--p-max-ee-r 2
--p-chimera-method consensus
--o-table table_denoise.qza
--o-representative-sequences denoise-rep-seq.qza
--o-denoising-stats denoise-stats.qza

Traceback (most recent call last):
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/bin/qiime", line 11, in
sys.exit(qiime())
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1137, in call
return self.main(*args, **kwargs)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1061, in main
with self.make_context(prog_name, args, **extra) as ctx:
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 923, in make_context
self.parse_args(ctx, args)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/click/command.py", line 43, in parse_args
return super().parse_args(ctx, args)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1624, in parse_args
rest = super().parse_args(ctx, args)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1375, in parse_args
parser = self.make_parser(ctx)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/click/command.py", line 33, in make_parser
param.add_to_parser(parser, ctx)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 2658, in add_to_parser
parser.add_option(
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/click/parser.py", line 126, in add_option
option = Q2Option(opts, dest, action=action, nargs=nargs,
TypeError: init() got multiple values for argument 'obj'

And even if I type qiime --help, same error comes up

So I even re-installed qiime for 4 times with new conda env, but didn't work...:frowning:

What should I do..?
Thank you!

Hello @hjpyun,

I think you are right, especially because of this:

Perhaps the conda environment is messed up. Can you activate the qiime2-2021.4 environment, run this command

conda list

and post the result? We can take a look to make sure the environment is correct.

Colin

P.S. Also, are you running this on a Ubuntu server, or CentOS, or some other operating system?

Hi, everyone. I have some problems with qiime2 dada2 denoise-paired

The thing is that the same error is coming up.
I tried changing parameters (trunc, trim length) but same error is coming up.

qiime dada2 denoise-paired \

--i-demultiplexed-seqs merged_demux_seqs.qza
--p-trim-left-f 20
--p-trunc-len-f 290
--p-trim-left-r 0
--p-trunc-len-r 225
--p-max-ee-f 2
--p-max-ee-r 2
--p-chimera-method consensus
--o-table table_denoise.qza
--o-representative-sequences denoise-rep-seq.qza
--o-denoising-stats denoise-stats.qza


Traceback (most recent call last):
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/bin/qiime", line 11, in
sys.exit(qiime())
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1137, in call
return self.main(*args, **kwargs)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1061, in main
with self.make_context(prog_name, args, **extra) as ctx:
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 923, in make_context
self.parse_args(ctx, args)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/click/command.py", line 43, in parse_args
return super().parse_args(ctx, args)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1624, in parse_args
rest = super().parse_args(ctx, args)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1375, in parse_args
parser = self.make_parser(ctx)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/click/command.py", line 33, in make_parser
param.add_to_parser(parser, ctx)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 2658, in add_to_parser
parser.add_option(
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/click/parser.py", line 126, in add_option
option = Q2Option(opts, dest, action=action, nargs=nargs,
TypeError: init() got multiple values for argument 'obj'

The thing is that I saw one of the forum topic that has same error (but related to rescript) so I followed (just in case), but exactly same error came out.

qiime dev refresh-cache

Traceback (most recent call last):
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/bin/qiime", line 11, in
sys.exit(qiime())
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1137, in call
return self.main(*args, **kwargs)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1061, in main
with self.make_context(prog_name, args, **extra) as ctx:
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 923, in make_context
self.parse_args(ctx, args)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/click/command.py", line 43, in parse_args
return super().parse_args(ctx, args)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1624, in parse_args
rest = super().parse_args(ctx, args)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1375, in parse_args
parser = self.make_parser(ctx)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/click/command.py", line 33, in make_parser
param.add_to_parser(parser, ctx)
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 2658, in add_to_parser
parser.add_option(
File "/data1/hjpyun/.conda/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/click/parser.py", line 126, in add_option
option = Q2Option(opts, dest, action=action, nargs=nargs,
TypeError: init() got multiple values for argument 'obj'

So, I thought the error was related to my qiime env so I removed and re-installed it for 4 times, but nothing has changed :frowning:

I really hope that the seniors who know this problem in the forum can help me,Thank you very much.

I've merged in your duplicate post into this thread.

No need to post twice. We read all the post on the forums! :woman_technologist: :man_technologist:

2 Likes

Thank you for reply :slightly_smiling_face:

1) conda list

(qiime2-2021.4) [email protected]:~$ conda list

packages in environment at /data1/hjpyun/.conda/envs/qiime2-2021.4:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_llvm conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
_sysroot_linux-64_curr_repodata_hack 3 h5bd9786_12 conda-forge
alsa-lib 1.2.3 h516909a_0 conda-forge
argon2-cffi 20.1.0 py38h497a2fe_2 conda-forge
async_generator 1.10 py_0 conda-forge
attrs 21.2.0 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
bibtexparser 1.1.0 py_0 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_1 conda-forge
binutils_linux-64 2.36 hf3e587d_33 conda-forge
bioconductor-biobase 2.50.0 r40hd029910_1 bioconda
bioconductor-biocgenerics 0.36.0 r40hdfd78af_1 bioconda
bioconductor-biocparallel 1.24.1 r40h399db7b_0 bioconda
bioconductor-biostrings 2.58.0 r40hd029910_1 bioconda
bioconductor-dada2 1.18.0 r40h399db7b_1 bioconda
bioconductor-delayedarray 0.16.3 r40hd029910_0 bioconda
bioconductor-genomeinfodb 1.26.4 r40hdfd78af_0 bioconda
bioconductor-genomeinfodbdata 1.2.4 r40hdfd78af_2 bioconda
bioconductor-genomicalignments 1.26.0 r40hd029910_1 bioconda
bioconductor-genomicranges 1.42.0 r40hd029910_1 bioconda
bioconductor-iranges 2.24.1 r40hd029910_0 bioconda
bioconductor-matrixgenerics 1.2.1 r40hdfd78af_0 bioconda
bioconductor-rhtslib 1.22.0 r40hd029910_1 bioconda
bioconductor-rsamtools 2.6.0 r40h399db7b_1 bioconda
bioconductor-s4vectors 0.28.1 r40hd029910_0 bioconda
bioconductor-shortread 1.48.0 r40h399db7b_1 bioconda
bioconductor-summarizedexperiment 1.20.0 r40hdfd78af_1 bioconda
bioconductor-xvector 0.30.0 r40hd029910_1 bioconda
bioconductor-zlibbioc 1.36.0 r40hd029910_1 bioconda
biom-format 2.1.10 py38h0b5ebd8_0 conda-forge
blas 2.106 openblas conda-forge
blast 2.12.0 pl5262h3289130_0 bioconda
bleach 3.3.1 pyhd8ed1ab_0 conda-forge
bokeh 2.3.3 py38h578d9bd_0 conda-forge
bowtie2 2.4.2 py38hc2f83ea_2 bioconda
brotlipy 0.7.0 py38h497a2fe_1001 conda-forge
bwidget 1.9.14 ha770c72_0 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.17.1 h7f98852_1 conda-forge
ca-certificates 2021.5.30 ha878542_0 conda-forge
cachecontrol 0.12.6 py_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.16.0 h6cf1ce9_1008 conda-forge
certifi 2021.5.30 py38h578d9bd_0 conda-forge
cffi 1.14.6 py38ha65f79e_0 conda-forge
chardet 4.0.0 py38h578d9bd_1 conda-forge
charset-normalizer 2.0.0 pyhd8ed1ab_0 conda-forge
click 8.0.1 py38h578d9bd_0 conda-forge
cryptography 3.4.7 py38ha5dfef3_0 conda-forge
curl 7.77.0 hea6ffbf_0 conda-forge
cutadapt 3.4 py38h4a8c8d9_1 bioconda
cycler 0.10.0 py_2 conda-forge
cython 0.29.24 py38h709712a_0 conda-forge
dbus 1.13.6 h48d8840_2 conda-forge
deblur 1.1.0 py_2 bioconda
debugpy 1.4.1 py38h709712a_0 conda-forge
decorator 4.4.2 py_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dendropy 4.5.2 pyh3252c3a_0 bioconda
dnaio 0.5.1 py38h4a8c8d9_0 bioconda
emperor 1.0.3 py38h578d9bd_0 conda-forge
entrez-direct 13.9 pl5262he881be0_2 bioconda
entrypoints 0.3 pyhd8ed1ab_1003 conda-forge
expat 2.4.1 h9c3ff4c_0 conda-forge
fastcluster 1.1.26 py38hc5bc63f_2 conda-forge
fasttree 2.1.10 0 bioconda
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.13.1 hba837de_1005 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
future 0.18.2 py38h578d9bd_3 conda-forge
gcc_impl_linux-64 9.3.0 hda68d29_13 conda-forge
gcc_linux-64 9.3.0 hf25ea35_33 conda-forge
gettext 0.19.8.1 h0b5b191_1005 conda-forge
gfortran_impl_linux-64 9.3.0 hc4a2995_19 conda-forge
gfortran_linux-64 9.3.0 hdc58fab_33 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
glib 2.68.3 h9c3ff4c_0 conda-forge
glib-tools 2.68.3 h9c3ff4c_0 conda-forge
gneiss 0.4.6 py_0 bioconda
graphite2 1.3.13 h58526e2_1001 conda-forge
gsl 2.6 he838d99_2 conda-forge
gst-plugins-base 1.18.4 hf529b03_2 conda-forge
gstreamer 1.18.4 h76c114f_2 conda-forge
gxx_impl_linux-64 9.3.0 h64c220c_13 conda-forge
gxx_linux-64 9.3.0 h3fbe746_33 conda-forge
h5py 3.3.0 nompi_py38h9915d05_100 conda-forge
harfbuzz 2.8.2 h83ec7ef_0 conda-forge
hdf5 1.10.6 nompi_h6a2412b_1114 conda-forge
hdmedians 0.14.2 py38hb5d20a5_0 conda-forge
hmmer 3.1b2 3 bioconda
htslib 1.13 h9093b5e_0 bioconda
icu 68.1 h58526e2_0 conda-forge
idna 3.1 pyhd3deb0d_0 conda-forge
ijson 3.1.3 pyhd3deb0d_0 conda-forge
importlib-metadata 4.6.1 py38h578d9bd_0 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
ipykernel 6.0.3 py38hd0cf306_0 conda-forge
ipython 7.25.0 py38hd0cf306_1 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.6.3 pyhd3deb0d_0 conda-forge
iqtree 2.1.4_beta hdcc8f71_0 bioconda
isa-l 2.30.0 ha770c72_4 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
jedi 0.18.0 py38h578d9bd_2 conda-forge
jinja2 3.0.1 pyhd8ed1ab_0 conda-forge
joblib 1.0.1 pyhd8ed1ab_0 conda-forge
jpeg 9d h36c2ea0_0 conda-forge
jsonschema 3.2.0 pyhd8ed1ab_3 conda-forge
jupyter_client 6.1.12 pyhd8ed1ab_0 conda-forge
jupyter_core 4.7.1 py38h578d9bd_0 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
jupyterlab_widgets 1.0.0 pyhd8ed1ab_1 conda-forge
kernel-headers_linux-64 3.10.0 h4a8ded7_12 conda-forge
kiwisolver 1.3.1 py38h1fd1430_1 conda-forge
krb5 1.19.1 hcc1bbae_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_1 conda-forge
lerc 2.2.1 h9c3ff4c_0 conda-forge
libblas 3.9.0 6_openblas conda-forge
libcblas 3.9.0 6_openblas conda-forge
libclang 11.1.0 default_ha53f305_1 conda-forge
libcurl 7.77.0 h2574ce0_0 conda-forge
libdeflate 1.7 h7f98852_5 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 hcdb4288_3 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-devel_linux-64 11.1.0 h80e7780_2 conda-forge
libgcc-ng 11.1.0 hc902ee8_2 conda-forge
libgfortran-ng 9.3.0 hff62375_19 conda-forge
libgfortran5 9.3.0 hff62375_19 conda-forge
libglib 2.68.3 h3e27bee_0 conda-forge
libgomp 11.1.0 hc902ee8_2 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 6_openblas conda-forge
liblapacke 3.9.0 6_openblas conda-forge
libllvm11 11.1.0 hf817b99_2 conda-forge
libnghttp2 1.43.0 h812cca2_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.12 pthreads_h4812303_1 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libpq 13.3 hd57d9b9_0 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libssh2 1.9.0 ha56f1ee_6 conda-forge
libstdcxx-devel_linux-64 11.1.0 h80e7780_2 conda-forge
libstdcxx-ng 11.1.0 h56837e0_2 conda-forge
libtiff 4.3.0 hf544144_1 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libuv 1.41.1 h7f98852_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.2.0 h7f98852_2 conda-forge
libxcb 1.13 h7f98852_1003 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.12 h72842e0_0 conda-forge
libxslt 1.1.33 h15afd5d_2 conda-forge
llvm-openmp 12.0.1 h4bd325d_0 conda-forge
lockfile 0.12.2 py_1 conda-forge
lxml 4.6.3 py38hf1fe3a4_0 conda-forge
lz4 3.1.3 py38hebdc3cf_0 conda-forge
lz4-c 1.9.3 h9c3ff4c_0 conda-forge
mafft 7.487 h779adbc_0 bioconda
make 4.3 hd18ef5c_1 conda-forge
markupsafe 2.0.1 py38h497a2fe_0 conda-forge
matplotlib 3.4.2 py38h578d9bd_0 conda-forge
matplotlib-base 3.4.2 py38hcc49a3a_0 conda-forge
matplotlib-inline 0.1.2 pyhd8ed1ab_2 conda-forge
mistune 0.8.4 py38h497a2fe_1004 conda-forge
more-itertools 8.8.0 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.2 py38h1fd1430_1 conda-forge
mysql-common 8.0.25 ha770c72_2 conda-forge
mysql-libs 8.0.25 hfa10184_2 conda-forge
natsort 7.1.1 pyhd8ed1ab_0 conda-forge
nbclient 0.5.3 pyhd8ed1ab_0 conda-forge
nbconvert 6.1.0 py38h578d9bd_0 conda-forge
nbformat 5.1.3 pyhd8ed1ab_0 conda-forge
ncurses 6.2 h58526e2_4 conda-forge
nest-asyncio 1.5.1 pyhd8ed1ab_0 conda-forge
networkx 2.6.1 pyhd8ed1ab_1 conda-forge
nodejs 15.14.0 h92b4a50_0 conda-forge
nose 1.3.7 py_1006 conda-forge
notebook 6.4.0 pyha770c72_0 conda-forge
nspr 4.30 h9c3ff4c_0 conda-forge
nss 3.67 hb5efdd6_0 conda-forge
numpy 1.21.1 py38h9894fe3_0 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openblas 0.3.12 pthreads_h04b7a96_1 conda-forge
openjdk 11.0.9.1 h5cc2fde_1 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 1.1.1k h7f98852_0 conda-forge
packaging 21.0 pyhd8ed1ab_0 conda-forge
pandas 1.3.1 py38h1abd341_0 conda-forge
pandoc 2.14.1 h7f98852_0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
pango 1.48.7 hb8ff022_0 conda-forge
parso 0.8.2 pyhd8ed1ab_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.37 h032f7d1_0 conda-forge
perl 5.26.2 h36c2ea0_1008 conda-forge
perl-app-cpanminus 1.7044 pl526_1 bioconda
perl-archive-tar 2.32 pl526_0 bioconda
perl-base 2.23 pl526_1 bioconda
perl-business-isbn 3.004 pl526_0 bioconda
perl-business-isbn-data 20140910.003 pl526_0 bioconda
perl-carp 1.38 pl526_3 bioconda
perl-common-sense 3.74 pl526_2 bioconda
perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda
perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda
perl-constant 1.33 pl526_1 bioconda
perl-data-dumper 2.173 pl526_0 bioconda
perl-digest-hmac 1.03 pl526_3 bioconda
perl-digest-md5 2.55 pl526_0 bioconda
perl-encode 2.88 pl526_1 bioconda
perl-encode-locale 1.05 pl526_6 bioconda
perl-exporter 5.72 pl526_1 bioconda
perl-exporter-tiny 1.002001 pl526_0 bioconda
perl-extutils-makemaker 7.36 pl526_1 bioconda
perl-file-listing 6.04 pl526_1 bioconda
perl-file-path 2.16 pl526_0 bioconda
perl-file-temp 0.2304 pl526_2 bioconda
perl-html-parser 3.72 pl526h6bb024c_5 bioconda
perl-html-tagset 3.20 pl526_3 bioconda
perl-html-tree 5.07 pl526_1 bioconda
perl-http-cookies 6.04 pl526_0 bioconda
perl-http-daemon 6.01 pl526_1 bioconda
perl-http-date 6.02 pl526_3 bioconda
perl-http-message 6.18 pl526_0 bioconda
perl-http-negotiate 6.01 pl526_3 bioconda
perl-io-compress 2.087 pl526he1b5a44_0 bioconda
perl-io-html 1.001 pl526_2 bioconda
perl-io-socket-ssl 2.066 pl526_0 bioconda
perl-io-zlib 1.10 pl526_2 bioconda
perl-json 4.02 pl526_0 bioconda
perl-json-xs 2.34 pl526h6bb024c_3 bioconda
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q2-composition 2021.4.0 py38_0 qiime2/label/r2021.4
q2-cutadapt 2021.4.0 py38_0 qiime2/label/r2021.4
q2-dada2 2021.4.0 py38_0 qiime2/label/r2021.4
q2-deblur 2021.4.0 py38_0 qiime2/label/r2021.4
q2-demux 2021.4.0 py38_0 qiime2/label/r2021.4
q2-diversity 2021.4.0 py38_0 qiime2/label/r2021.4
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q2-emperor 2021.4.0 py38_0 qiime2/label/r2021.4
q2-feature-classifier 2021.4.0 py38_0 qiime2/label/r2021.4
q2-feature-table 2021.4.0 py38_0 qiime2/label/r2021.4
q2-fragment-insertion 2021.4.0 py38_0 qiime2/label/r2021.4
q2-gneiss 2021.4.0 py38_0 qiime2/label/r2021.4
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q2-mystery-stew 2021.4.0 py38_0 qiime2/label/r2021.4
q2-phylogeny 2021.4.0 py38_0 qiime2/label/r2021.4
q2-quality-control 2021.4.0 py38_0 qiime2/label/r2021.4
q2-quality-filter 2021.4.0 py38_0 qiime2/label/r2021.4
q2-sample-classifier 2021.4.0 py38_0 qiime2/label/r2021.4
q2-taxa 2021.4.0 py38_0 qiime2/label/r2021.4
q2-types 2021.4.0 py38_0 qiime2/label/r2021.4
q2-vsearch 2021.4.0 py38_0 qiime2/label/r2021.4
q2cli 2021.4.0 py38_0 qiime2/label/r2021.4
q2galaxy 2021.4.0 py38_0 qiime2/label/r2021.4
q2templates 2021.4.0 py38_0 qiime2/label/r2021.4
qiime2 2021.4.0 py38_0 qiime2/label/r2021.4
qt 5.12.9 hda022c4_4 conda-forge
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r-crayon 1.4.1 r40hc72bb7e_0 conda-forge
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r-futile.options 1.0.1 r40hc72bb7e_1002 conda-forge
r-ggplot2 3.3.5 r40hc72bb7e_0 conda-forge
r-glue 1.4.2 r40hcfec24a_0 conda-forge
r-gtable 0.3.0 r40hc72bb7e_3 conda-forge
r-hwriter 1.3.2 r40hc72bb7e_1003 conda-forge
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r-png 0.1_7 r40hcfec24a_1004 conda-forge
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r-ps 1.6.0 r40hcfec24a_0 conda-forge
r-r6 2.5.0 r40hc72bb7e_0 conda-forge
r-rcolorbrewer 1.1_2 r40h785f33e_1003 conda-forge
r-rcpp 1.0.7 r40h03ef668_0 conda-forge
r-rcppparallel 5.1.4 r40h03ef668_0 conda-forge
r-rcurl 1.98_1.3 r40hcfec24a_0 conda-forge
r-rematch2 2.1.2 r40hc72bb7e_1 conda-forge
r-reshape2 1.4.4 r40h03ef668_1 conda-forge
r-rlang 0.4.11 r40hcfec24a_0 conda-forge
r-rprojroot 2.0.2 r40hc72bb7e_0 conda-forge
r-rstudioapi 0.13 r40hc72bb7e_0 conda-forge
r-scales 1.1.1 r40hc72bb7e_0 conda-forge
r-snow 0.4_3 r40hc72bb7e_1002 conda-forge
r-stringi 1.7.3 r40hcabe038_0 conda-forge
r-stringr 1.4.0 r40hc72bb7e_2 conda-forge
r-testthat 3.0.4 r40h03ef668_0 conda-forge
r-tibble 3.1.3 r40hcfec24a_0 conda-forge
r-utf8 1.2.2 r40hcfec24a_0 conda-forge
r-vctrs 0.3.8 r40hcfec24a_1 conda-forge
r-vegan 2.5_7 r40h52d45c5_0 conda-forge
r-viridislite 0.4.0 r40hc72bb7e_0 conda-forge
r-waldo 0.2.5 r40hc72bb7e_0 conda-forge
r-withr 2.4.2 r40hc72bb7e_0 conda-forge
r-zeallot 0.1.0 r40hc72bb7e_1002 conda-forge
raxml 8.2.12 h779adbc_3 bioconda
readline 8.1 h46c0cb4_0 conda-forge
requests 2.26.0 pyhd8ed1ab_0 conda-forge
rescript 2021.8.0.dev0+6.g81d95ed pypi_0 pypi
samtools 1.13 h8c37831_0 bioconda
scikit-bio 0.5.6 py38h0b5ebd8_4 conda-forge
scikit-learn 0.24.2 py38hdc147b9_0 conda-forge
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seaborn 0.11.1 hd8ed1ab_1 conda-forge
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sed 4.8 he412f7d_0 conda-forge
send2trash 1.7.1 pyhd8ed1ab_0 conda-forge
sepp 4.3.10 py38h3252c3a_2 bioconda
setuptools 49.6.0 py38h578d9bd_3 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sortmerna 2.0 he860b03_4 bioconda
sqlite 3.36.0 h9cd32fc_0 conda-forge
statsmodels 0.12.2 py38h5c078b8_0 conda-forge
sysroot_linux-64 2.17 h4a8ded7_12 conda-forge
tbb 2020.2 h4bd325d_4 conda-forge
terminado 0.10.1 py38h578d9bd_0 conda-forge
testpath 0.5.0 pyhd8ed1ab_0 conda-forge
threadpoolctl 2.2.0 pyh8a188c0_0 conda-forge
tk 8.6.10 h21135ba_1 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tornado 6.1 py38h497a2fe_1 conda-forge
traitlets 5.0.5 py_0 conda-forge
typing_extensions 3.10.0.0 pyha770c72_0 conda-forge
tzlocal 2.1 pyh9f0ad1d_0 conda-forge
unifrac 0.20.2 py38hc37a69a_1 bioconda
urllib3 1.26.6 pyhd8ed1ab_0 conda-forge
vsearch 2.7.0 1 bioconda
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.36.2 pyhd3deb0d_0 conda-forge
widgetsnbextension 3.5.1 py38h578d9bd_4 conda-forge
xmltodict 0.12.0 py_0 conda-forge
xopen 1.1.0 py38h578d9bd_3 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h516909a_0 conda-forge
zeromq 4.3.4 h9c3ff4c_0 conda-forge
zipp 3.5.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
zstd 1.5.0 ha95c52a_0 conda-forge

  1. OS : Ubuntu server

  2. Just in case I made other env qiime2 but here, I have trouble with R version. The thing is that version update, and library path is crashed but I'm afraid to manipulate the setting cause this is shared server of my lab..:frowning:

Thank you again for you reply :slight_smile:

hjpyun

1 Like

Hi @hjpyun!

Jumping in for Colin on this. It seems as though the error you're running into is related to some sort of environment or installation issue. There are a couple of questions that I have that may help us determine the source of the error you're running into.

This is the first thing that stood out to me. Why are you attempting to run QIIME 2 on two separate servers? You should be able to activate your conda environment and run all of your QIIME 2 commands on a single server.

Loading required package: Rcpp
Error: package or namespace load failed for 'Rcpp':
package 'Rcpp' was installed before R 4.0.0: please re-install it
Error: package 'Rcpp' could not be loaded
Execution halted

This appears to be a separate error from what you were running into above. Check out this forum post for a potential solution - this user also runs into a very similar error, related to multiple installations of DADA2.

Cheers,
Liz

1 Like

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