Qiime2 Python API unifrac dist matrix error: FileNotFoundError: [Errno 2] No such file or directory: 'ssu'

Hi all,

I am trying to generate an unweighted unifrac with the qiime2 python API and get the following output and error:

from qiime2 import Artifact
from qiime2.plugins import diversity_lib

tab1N=('/home/sdegregori/TOL/GMTOLsubsample/GMTOLsong_tablef_V4_N1_pythontest.qza')
phyf=('/home/sdegregori/TOL/GMTOLsubsample/GMTOLsong_rooted_treef.qza')
table1N = Artifact.load(tab1N)
phylogenyf = Artifact.load(phyf)

distance_matrix_result = diversity_lib.methods.unweighted_unifrac(table=table1N,phylogeny=phylogenyf)
distance_matrix = distance_matrix_result.distance_matrix
distance_matrix.save('/home/sdegregori/TOL/GMTOLsubsample/adonis/UW1N.qza')
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command:

ssu -i /tmp/qiime2/sdegregori/data/cf615d32-1809-41f8-a49f-6524020e030d/data/feature-table.biom -t /tmp/qiime2/sdegregori/data/47068e69-1522-4054-9c8f-49ae9c8a0d3d/data/tree.nwk -m unweighted -o /tmp/q2-LSMatFormat-5ivdpzio

FileNotFoundError                         Traceback (most recent call last)
Cell In[47], line 1
----> 1 distance_matrix_result = diversity_lib.methods.unweighted_unifrac(table=table1N,phylogeny=phylogenyf)
      2 distance_matrix = distance_matrix_result.distance_matrix
      3 distance_matrix.save('/home/sdegregori/TOL/GMTOLsubsample/adonis/UW1N.qza')

File <decorator-gen-190>:2, in unweighted_unifrac(table, phylogeny, threads, bypass_tips)

File ~/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py:234, in Action._bind.<locals>.bound_callable(*args, **kwargs)
    230         warn(self._build_deprecation_message(),
    231              FutureWarning)
    233 # Execute
--> 234 outputs = self._callable_executor_(scope, callable_args,
    235                                    output_types, provenance)
    237 if len(outputs) != len(self.signature.outputs):
    238     raise ValueError(
    239         "Number of callable outputs must match number of "
    240         "outputs defined in signature: %d != %d" %
    241         (len(outputs), len(self.signature.outputs)))

File ~/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py:381, in Method._callable_executor_(self, scope, view_args, output_types, provenance)
    380 def _callable_executor_(self, scope, view_args, output_types, provenance):
--> 381     output_views = self._callable(**view_args)
    382     output_views = tuplize(output_views)
    384     # TODO this won't work if the user has annotated their "view API" to
    385     # return a `typing.Tuple` with some number of components. Python will
    386     # return a tuple when there are multiple return values, and this length
   (...)
    389     # due to how Python handles multiple returns, and can be worked around
    390     # by using something like `typing.List` instead.

File <decorator-gen-103>:2, in unweighted_unifrac(table, phylogeny, threads, bypass_tips)

File ~/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py:69, in _disallow_empty_tables(wrapped_function, *args, **kwargs)
     66     if tab_obj.is_empty():
     67         raise ValueError("The provided table is empty")
---> 69 return wrapped_function(*args, **kwargs)

File <decorator-gen-102>:2, in unweighted_unifrac(table, phylogeny, threads, bypass_tips)

File ~/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py:112, in _validate_requested_cpus(wrapped_function, *args, **kwargs)
    107 if cpus_requested > cpus_available:
    108     raise ValueError(f"The value passed to '{param_name}' cannot exceed "
    109                      f"the number of processors ({cpus_available}) "
    110                      "available to the system.")
--> 112 return wrapped_function(*bound_arguments.args, **bound_arguments.kwargs)

File ~/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_diversity_lib/beta.py:221, in unweighted_unifrac(table, phylogeny, threads, bypass_tips)
    218 if bypass_tips:
    219     cmd += ['-f']
--> 221 _omp_cmd_wrapper(threads, cmd)
    223 return result

File ~/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py:128, in _omp_cmd_wrapper(threads, cmd, verbose)
    126 env = environ.copy()
    127 env.update({'OMP_NUM_THREADS': str(threads)})
--> 128 return _run_external_cmd(cmd, verbose=verbose, env=env)

File ~/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_diversity_lib/_util.py:122, in _run_external_cmd(cmd, verbose, env)
    117     print("Running external command line application. This may print"
    118           " messages to stdout and/or stderr.\nThe command being run is"
    119           " below. This command cannot be manually re-run as it will"
    120           " depend on temporary files that no longer exist.\n\nCommand:\n")
    121     print(" ".join(cmd), end='\n\n')
--> 122 return subprocess.run(cmd, check=True, env=env)

File ~/miniconda3/envs/qiime2-2023.2/lib/python3.8/subprocess.py:493, in run(input, capture_output, timeout, check, *popenargs, **kwargs)
    490     kwargs['stdout'] = PIPE
    491     kwargs['stderr'] = PIPE
--> 493 with Popen(*popenargs, **kwargs) as process:
    494     try:
    495         stdout, stderr = process.communicate(input, timeout=timeout)

File ~/miniconda3/envs/qiime2-2023.2/lib/python3.8/subprocess.py:858, in Popen.__init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors, text)
    854         if self.text_mode:
    855             self.stderr = io.TextIOWrapper(self.stderr,
    856                     encoding=encoding, errors=errors)
--> 858     self._execute_child(args, executable, preexec_fn, close_fds,
    859                         pass_fds, cwd, env,
    860                         startupinfo, creationflags, shell,
    861                         p2cread, p2cwrite,
    862                         c2pread, c2pwrite,
    863                         errread, errwrite,
    864                         restore_signals, start_new_session)
    865 except:
    866     # Cleanup if the child failed starting.
    867     for f in filter(None, (self.stdin, self.stdout, self.stderr)):

File ~/miniconda3/envs/qiime2-2023.2/lib/python3.8/subprocess.py:1704, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, start_new_session)
   1702     if errno_num != 0:
   1703         err_msg = os.strerror(errno_num)
-> 1704     raise child_exception_type(errno_num, err_msg, err_filename)
   1705 raise child_exception_type(err_msg)

FileNotFoundError: [Errno 2] No such file or directory: 'ssu'

Is this something to do with my temp folder?
When I run the first chunks to just load the artifact files the code works fine so I know the files are there and the paths are correct. FYI I am doing this in jupyterhub on a university HPC.
Any ideas would be appreciateed!

Hello @Sam_Degregori. At first glance, it looks like you're running things in a correctly configured QIIME 2 conda environment successfully since you were able to run those imports. Can you run the following in your Jupyter Notebook and post the results here:

import subprocess

subprocess.run(['which', 'ssu'])

Hi @Oddant1,

Thanks.

Here is the output:

import subprocess
subprocess.run(['which', 'ssu'])
which: no ssu in (/sbin:/bin:/usr/sbin:/usr/bin)

CompletedProcess(args=['which', 'ssu'], returncode=1)

Seems like its not there?
Cheers,
Sam

Is it possible for you to run things on the command line on this cluster, or can you only do jupyter? If you can do command line, then can you please run the command which ssu from the command line with your QIIME 2 conda environment active?

Additionally, can you please upload the contents of your .bashrc file?

1 Like

So i get this for which ssu in the terminal:

/usr/bin/which: no ssu in (/home/sdegregori/miniconda3/bin:/home/sdegregori/miniconda3/condabin:/usr/lib64/qt-3.3/bin:/home/sdegregori/perl5/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/slurm-20.11.7/bin:/opt/slurm-20.11.7/sbin:/opt/slurm-20.11.7/bin:/opt/slurm-20.11.7/sbin)

And then this for my bashrc file:

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/sdegregori/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/sdegregori/miniconda3/etc/profile.d/conda.sh" ]; then
        . "/home/sdegregori/miniconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/sdegregori/miniconda3/bin:$PATH"
    fi
fi
unset __conda_setup

Does that give more info?

Ok that is strange. I was expecting your conda bin to not be on your path, but clearly it is. Can you please, while inside of your conda environment, run qiime info and conda list and post the results here. The conda list output might be rather long, but that's ok.

So qiime info spits out:

System versions
Python version: 3.8.15
QIIME 2 release: 2023.2
QIIME 2 version: 2023.2.0
q2cli version: 2023.2.0

Installed plugins
alignment: 2023.2.0
composition: 2023.2.0
cutadapt: 2023.2.0
dada2: 2023.2.0
deblur: 2023.2.0
demux: 2023.2.0
diversity: 2023.2.0
diversity-lib: 2023.2.0
emperor: 2023.2.0
feature-classifier: 2023.2.0
feature-table: 2023.2.0
fragment-insertion: 2023.2.0
gneiss: 2023.2.0
longitudinal: 2023.2.0
metadata: 2023.2.0
phylogeny: 2023.2.0
quality-control: 2023.2.0
quality-filter: 2023.2.0
sample-classifier: 2023.2.0
taxa: 2023.2.0
types: 2023.2.0
vsearch: 2023.2.0
woltka: 0.1.5

Application config directory
/home/sdegregori/miniconda3/envs/qiime2-2023.2/var/q2cli

Getting help
To get help with QIIME 2, visit https://qiime2.org

And then conda list spits out:

(qiime2-2023.2) [sdegregori@b2-004]~/TOL/Merged% conda list
# packages in environment at /home/sdegregori/miniconda3/envs/qiime2-2023.2:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
alsa-lib                  1.2.8                h166bdaf_0    conda-forge
altair                    4.2.2              pyhd8ed1ab_0    conda-forge
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
argcomplete               2.0.0              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py38h0a891b7_3    conda-forge
astor                     0.8.1              pyh9f0ad1d_0    conda-forge
asttokens                 2.2.1              pyhd8ed1ab_0    conda-forge
atpublic                  3.0.1              pyhd8ed1ab_0    conda-forge
attr                      2.5.1                h166bdaf_1    conda-forge
attrs                     22.2.0             pyh71513ae_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.2             pyha770c72_0    conda-forge
bibtexparser              1.4.0              pyhd8ed1ab_0    conda-forge
binutils_impl_linux-64    2.40                 hf600244_0    conda-forge
bioconductor-ancombc      2.0.1             r42hdfd78af_0    bioconda
bioconductor-beachmat     2.14.0            r42hc247a5b_0    bioconda
bioconductor-biobase      2.58.0            r42hc0cfd56_0    bioconda
bioconductor-biocbaseutils 1.0.0             r42hdfd78af_0    bioconda
bioconductor-biocgenerics 0.44.0            r42hdfd78af_0    bioconda
bioconductor-biocneighbors 1.16.0            r42hc247a5b_0    bioconda
bioconductor-biocparallel 1.32.5            r42hc247a5b_0    bioconda
bioconductor-biocsingular 1.14.0            r42hc247a5b_0    bioconda
bioconductor-biomformat   1.26.0            r42hdfd78af_0    bioconda
bioconductor-biostrings   2.66.0            r42hc0cfd56_0    bioconda
bioconductor-dada2        1.26.0            r42hc247a5b_0    bioconda
bioconductor-data-packages 20230202             hdfd78af_0    bioconda
bioconductor-decipher     2.26.0            r42hc0cfd56_0    bioconda
bioconductor-decontam     1.18.0            r42hdfd78af_0    bioconda
bioconductor-delayedarray 0.24.0            r42hc0cfd56_0    bioconda
bioconductor-delayedmatrixstats 1.20.0            r42hdfd78af_0    bioconda
bioconductor-dirichletmultinomial 1.40.0            r42hda872b5_0    bioconda
bioconductor-genomeinfodb 1.34.8            r42hdfd78af_0    bioconda
bioconductor-genomeinfodbdata 1.2.9             r42hdfd78af_0    bioconda
bioconductor-genomicalignments 1.34.0            r42hc0cfd56_0    bioconda
bioconductor-genomicranges 1.50.0            r42hc0cfd56_0    bioconda
bioconductor-iranges      2.32.0            r42hc0cfd56_0    bioconda
bioconductor-matrixgenerics 1.10.0            r42hdfd78af_0    bioconda
bioconductor-mia          1.6.0             r42hdfd78af_0    bioconda
bioconductor-multiassayexperiment 1.24.0            r42hdfd78af_0    bioconda
bioconductor-multtest     2.54.0            r42hc0cfd56_0    bioconda
bioconductor-phyloseq     1.42.0            r42hdfd78af_0    bioconda
bioconductor-rhdf5        2.42.0            r42hbe1951d_1    bioconda
bioconductor-rhdf5filters 1.10.0            r42hc247a5b_0    bioconda
bioconductor-rhdf5lib     1.20.0            r42hc0cfd56_0    bioconda
bioconductor-rhtslib      2.0.0             r42hc0cfd56_0    bioconda
bioconductor-rsamtools    2.14.0            r42hc247a5b_0    bioconda
bioconductor-s4vectors    0.36.0            r42hc0cfd56_0    bioconda
bioconductor-scaledmatrix 1.6.0             r42hdfd78af_0    bioconda
bioconductor-scater       1.26.0            r42hdfd78af_0    bioconda
bioconductor-scuttle      1.8.0             r42hc247a5b_0    bioconda
bioconductor-shortread    1.56.0            r42hc247a5b_0    bioconda
bioconductor-singlecellexperiment 1.20.0            r42hdfd78af_0    bioconda
bioconductor-sparsematrixstats 1.10.0            r42hc247a5b_0    bioconda
bioconductor-summarizedexperiment 1.28.0            r42hdfd78af_0    bioconda
bioconductor-treeio       1.22.0            r42hdfd78af_0    bioconda
bioconductor-treesummarizedexperiment 2.6.0             r42hdfd78af_0    bioconda
bioconductor-xvector      0.38.0            r42hc0cfd56_0    bioconda
bioconductor-zlibbioc     1.44.0            r42hc0cfd56_0    bioconda
biom-format               2.1.12           py38h26c90d9_2    conda-forge
blast                     2.13.0               hf3cf87c_0    bioconda
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
bokeh                     3.0.3              pyhd8ed1ab_0    conda-forge
bowtie2                   2.5.1            py38h77f66f0_0    bioconda
brotli                    1.0.9                h166bdaf_8    conda-forge
brotli-bin                1.0.9                h166bdaf_8    conda-forge
brotlipy                  0.7.0           py38h0a891b7_1005    conda-forge
bwidget                   1.9.14               ha770c72_1    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2023.5.7             hbcca054_0    conda-forge
cachecontrol              0.12.11            pyhd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.16.0            ha61ee94_1014    conda-forge
certifi                   2023.5.7           pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py38h4a40e3a_3    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
click                     8.1.3           unix_pyhd8ed1ab_2    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.7            py38hfbd4bf9_0    conda-forge
cryptography              39.0.0           py38h1724139_0    conda-forge
curl                      7.87.0               h6312ad2_0    conda-forge
cutadapt                  4.2              py38hbff2b2d_0    bioconda
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cython                    0.29.33          py38h8dc9893_0    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
deblur                    1.1.1              pyhdfd78af_0    bioconda
debugpy                   1.6.6            py38h8dc9893_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
dill                      0.3.6              pyhd8ed1ab_1    conda-forge
dnaio                     0.10.0           py38hbff2b2d_0    bioconda
dokdo                     1.0.0                    pypi_0    pypi
emperor                   1.0.3            py38h578d9bd_0    conda-forge
entrez-direct             16.2                 he881be0_1    bioconda
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.1.0              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
fastcluster               1.2.6            py38h8f669ce_2    conda-forge
fasttree                  2.1.11               hec16e2b_1    bioconda
fftw                      3.3.10          nompi_hc118613_107    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
flufl.lock                7.1                pyhd8ed1ab_0    conda-forge
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                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.38.0           py38h0a891b7_1    conda-forge
formulaic                 0.5.2              pyhd8ed1ab_0    conda-forge
freetype                  2.12.1               hca18f0e_1    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
future                    0.18.3             pyhd8ed1ab_0    conda-forge
gcc_impl_linux-64         12.2.0              hcc96c02_19    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gfortran_impl_linux-64    12.2.0              h55be85b_19    conda-forge
giflib                    5.2.1                h0b41bf4_3    conda-forge
glib                      2.74.1               h6239696_1    conda-forge
glib-tools                2.74.1               h6239696_1    conda-forge
glpk                      5.0                  h445213a_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gneiss                    0.4.6                      py_0    bioconda
graphite2                 1.3.13            h58526e2_1001    conda-forge
graphlib-backport         1.0.3              pyhd8ed1ab_0    conda-forge
gsl                       2.7                  he838d99_0    conda-forge
gst-plugins-base          1.21.3               h4243ec0_1    conda-forge
gstreamer                 1.21.3               h25f0c4b_1    conda-forge
gstreamer-orc             0.4.33               h166bdaf_0    conda-forge
gxx_impl_linux-64         12.2.0              hcc96c02_19    conda-forge
h5py                      2.10.0          nompi_py38h9915d05_106    conda-forge
harfbuzz                  6.0.0                h8e241bc_0    conda-forge
hdf5                      1.10.6          nompi_h6a2412b_1114    conda-forge
hdmedians                 0.14.2           py38h26c90d9_3    conda-forge
hmmer                     3.1b2                         3    bioconda
htslib                    1.16                 h6bc39ce_0    bioconda
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
ijson                     3.2.0.post0        pyhd8ed1ab_0    conda-forge
importlib-metadata        4.8.3            py38h578d9bd_0    conda-forge
importlib_metadata        4.8.3                hd8ed1ab_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
interface_meta            1.3.0              pyhd8ed1ab_0    conda-forge
iow                       1.0.5            py38h8ded8fe_1    bioconda
ipykernel                 6.21.2             pyh210e3f2_0    conda-forge
ipython                   8.10.0             pyh41d4057_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.0.4              pyhd8ed1ab_0    conda-forge
iqtree                    2.2.0.3              hb97b32f_1    bioconda
isa-l                     2.30.0               ha770c72_4    conda-forge
jack                      1.9.22               h11f4161_0    conda-forge
jedi                      0.18.2             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.2.0              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h0b41bf4_3    conda-forge
jq                        1.6               h36c2ea0_1000    conda-forge
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter_client            8.0.3              pyhd8ed1ab_0    conda-forge
jupyter_core              5.2.0            py38h578d9bd_0    conda-forge
jupyter_events            0.6.3              pyhd8ed1ab_0    conda-forge
jupyter_server            2.3.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.5              pyhd8ed1ab_0    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_15    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4            py38h43d8883_1    conda-forge
krb5                      1.20.1               hf9c8cef_0    conda-forge
lame                      3.100             h166bdaf_1003    conda-forge
lcms2                     2.14                 h6ed2654_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_8    conda-forge
libbrotlidec              1.0.9                h166bdaf_8    conda-forge
libbrotlienc              1.0.9                h166bdaf_8    conda-forge
libcap                    2.66                 ha37c62d_0    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libclang                  15.0.7          default_had23c3d_1    conda-forge
libclang13                15.0.7          default_h3e3d535_1    conda-forge
libcups                   2.3.3                h36d4200_3    conda-forge
libcurl                   7.87.0               h6312ad2_0    conda-forge
libdb                     6.2.32               h9c3ff4c_0    conda-forge
libdeflate                1.13                 h166bdaf_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.10               h9b69904_4    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libflac                   1.4.2                h27087fc_0    conda-forge
libgcc-devel_linux-64     12.2.0              h3b97bd3_19    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgcrypt                 1.10.1               h166bdaf_0    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libglib                   2.74.1               h606061b_1    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libgpg-error              1.46                 h620e276_0    conda-forge
libhwloc                  2.9.0                hd6dc26d_0    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libidn2                   2.3.4                h166bdaf_0    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
liblapacke                3.9.0           16_linux64_openblas    conda-forge
libllvm11                 11.1.0               he0ac6c6_5    conda-forge
libllvm15                 15.0.7               hadd5161_1    conda-forge
libnghttp2                1.51.0               hdcd2b5c_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libpq                     15.1                 h2baec63_3    conda-forge
libsanitizer              12.2.0              h46fd767_19    conda-forge
libsndfile                1.2.0                hb75c966_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.40.0               h753d276_1    conda-forge
libssh2                   1.10.0               haa6b8db_3    conda-forge
libstdcxx-devel_linux-64  12.2.0              h3b97bd3_19    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libsystemd0               252                  h2a991cd_0    conda-forge
libtiff                   4.4.0                h0e0dad5_3    conda-forge
libtool                   2.4.7                h27087fc_0    conda-forge
libudev1                  253                  h0b41bf4_0    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp-base              1.2.4                h166bdaf_0    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxkbcommon              1.5.0                h79f4944_1    conda-forge
libxml2                   2.10.3               hca2bb57_4    conda-forge
libxslt                   1.1.37               h873f0b0_0    conda-forge
libzlib                   1.2.13               h166bdaf_4    conda-forge
llvmlite                  0.39.1           py38h38d86a4_1    conda-forge
lockfile                  0.12.2                     py_1    conda-forge
lxml                      4.9.2            py38h215a2d7_0    conda-forge
lz4                       4.3.2            py38hd012fdc_0    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
mafft                     7.515                hec16e2b_0    bioconda
make                      4.3                  hd18ef5c_1    conda-forge
markupsafe                2.1.2            py38h1de0b5d_0    conda-forge
matplotlib                3.6.0            py38h578d9bd_0    conda-forge
matplotlib-base           3.6.0            py38hb021067_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mistune                   2.0.5              pyhd8ed1ab_0    conda-forge
mpfr                      4.1.0                h9202a9a_1    conda-forge
mpg123                    1.31.2               hcb278e6_0    conda-forge
msgpack-python            1.0.4            py38h43d8883_1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mysql-common              8.0.32               h14678bc_0    conda-forge
mysql-libs                8.0.32               h54cf53e_0    conda-forge
natsort                   8.3.0              pyhd8ed1ab_0    conda-forge
nbclassic                 0.5.2              pyhd8ed1ab_0    conda-forge
nbclient                  0.7.2              pyhd8ed1ab_0    conda-forge
nbconvert                 7.2.9              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.2.9              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.2.9              pyhd8ed1ab_0    conda-forge
nbformat                  5.7.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h27087fc_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
networkx                  3.0                pyhd8ed1ab_0    conda-forge
nlopt                     2.7.1            py38hca016a5_3    conda-forge
nose                      1.3.7                   py_1006    conda-forge
notebook                  6.5.2              pyha770c72_1    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
nspr                      4.35                 h27087fc_0    conda-forge
nss                       3.88                 he45b914_0    conda-forge
numba                     0.56.4           py38hefa3cd7_1    conda-forge
numpy                     1.23.5           py38h7042d01_0    conda-forge
oniguruma                 6.9.8                h166bdaf_0    conda-forge
openjdk                   17.0.3               h58dac75_5    conda-forge
openjpeg                  2.5.0                h7d73246_1    conda-forge
openssl                   1.1.1u               hd590300_0    conda-forge
packaging                 23.0               pyhd8ed1ab_0    conda-forge
pandas                    1.5.3            py38hdc8b05c_1    conda-forge
pandoc                    2.19.2               h32600fe_2    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.50.13              hd33c08f_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
patsy                     0.5.3              pyhd8ed1ab_0    conda-forge
pbzip2                    1.1.13                        0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
perl                      5.32.1          2_h7f98852_perl5    conda-forge
perl-archive-tar          2.40            pl5321hdfd78af_0    bioconda
perl-carp                 1.50            pl5321hd8ed1ab_0    conda-forge
perl-common-sense         3.75            pl5321hd8ed1ab_0    conda-forge
perl-compress-raw-bzip2   2.201           pl5321h166bdaf_0    conda-forge
perl-compress-raw-zlib    2.202           pl5321h166bdaf_0    conda-forge
perl-encode               3.19            pl5321h166bdaf_0    conda-forge
perl-exporter             5.74            pl5321hd8ed1ab_0    conda-forge
perl-exporter-tiny        1.002002        pl5321hd8ed1ab_0    conda-forge
perl-extutils-makemaker   7.66            pl5321hd8ed1ab_0    conda-forge
perl-io-compress          2.201           pl5321h87f3376_0    bioconda
perl-io-zlib              1.14            pl5321hdfd78af_0    bioconda
perl-json                 4.10            pl5321hdfd78af_0    bioconda
perl-json-xs              2.34            pl5321h9f5acd7_5    bioconda
perl-list-moreutils       0.430           pl5321hdfd78af_0    bioconda
perl-list-moreutils-xs    0.430           pl5321hec16e2b_1    bioconda
perl-parent               0.241           pl5321hd8ed1ab_0    conda-forge
perl-pathtools            3.75            pl5321h166bdaf_0    conda-forge
perl-scalar-list-utils    1.63            pl5321h166bdaf_0    conda-forge
perl-storable             3.15            pl5321h166bdaf_0    conda-forge
perl-types-serialiser     1.01            pl5321hdfd78af_0    bioconda
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pigz                      2.6                  h27826a3_0    conda-forge
pillow                    9.2.0            py38h9eb91d8_3    conda-forge
pip                       23.0.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
platformdirs              3.0.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0              pyhd8ed1ab_5    conda-forge
ply                       3.11                       py_1    conda-forge
prometheus_client         0.16.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.36             pyha770c72_0    conda-forge
psutil                    5.9.4            py38h0a891b7_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pulseaudio                16.1                 h4ab2085_1    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.14.0             pyhd8ed1ab_0    conda-forge
pynndescent               0.5.8              pyh1a96a4e_0    conda-forge
pyopenssl                 23.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.7           py38ha0d8c90_3    conda-forge
pyqt5-sip                 12.11.0          py38h8dc9893_3    conda-forge
pyrsistent                0.19.3           py38h1de0b5d_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytest                    7.2.1              pyhd8ed1ab_0    conda-forge
python                    3.8.15          h257c98d_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.16.3             pyhd8ed1ab_0    conda-forge
python-isal               1.1.0            py38h0a891b7_1    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.8                      3_cp38    conda-forge
pytz                      2022.7.1           pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py38h0a891b7_5    conda-forge
pyzmq                     25.0.0           py38he24dcef_0    conda-forge
q2-alignment              2023.2.0                 py38_0    qiime2/label/r2023.2
q2-composition            2023.2.0                 py38_0    qiime2/label/r2023.2
q2-cutadapt               2023.2.0                 py38_0    qiime2/label/r2023.2
q2-dada2                  2023.2.0                 py38_0    qiime2/label/r2023.2
q2-deblur                 2023.2.0                 py38_0    qiime2/label/r2023.2
q2-demux                  2023.2.0                 py38_0    qiime2/label/r2023.2
q2-diversity              2023.2.0                 py38_0    qiime2/label/r2023.2
q2-diversity-lib          2023.2.0                 py38_0    qiime2/label/r2023.2
q2-emperor                2023.2.0                 py38_0    qiime2/label/r2023.2
q2-feature-classifier     2023.2.0                 py38_0    qiime2/label/r2023.2
q2-feature-table          2023.2.0                 py38_0    qiime2/label/r2023.2
q2-fragment-insertion     2023.2.0                 py38_0    qiime2/label/r2023.2
q2-gneiss                 2023.2.0                 py38_0    qiime2/label/r2023.2
q2-longitudinal           2023.2.0                 py38_0    qiime2/label/r2023.2
q2-metadata               2023.2.0                 py38_0    qiime2/label/r2023.2
q2-mystery-stew           2023.2.0                 py38_0    qiime2/label/r2023.2
q2-phylogeny              2023.2.0                 py38_0    qiime2/label/r2023.2
q2-quality-control        2023.2.0                 py38_0    qiime2/label/r2023.2
q2-quality-filter         2023.2.0                 py38_0    qiime2/label/r2023.2
q2-sample-classifier      2023.2.0                 py38_0    qiime2/label/r2023.2
q2-taxa                   2023.2.0                 py38_0    qiime2/label/r2023.2
q2-types                  2023.2.0                 py38_0    qiime2/label/r2023.2
q2-vsearch                2023.2.0                 py38_0    qiime2/label/r2023.2
q2cli                     2023.2.0                 py38_0    qiime2/label/r2023.2
q2galaxy                  2023.2.0                 py38_0    qiime2/label/r2023.2
q2templates               2023.2.0                 py38_0    qiime2/label/r2023.2
qiime2                    2023.2.0                 py38_0    qiime2/label/r2023.2
qt-main                   5.15.6               h18908ee_6    conda-forge
r-acepack                 1.4.1           r42h8da6f51_1007    conda-forge
r-ade4                    1.7_22            r42he1ae0d6_0    conda-forge
r-ape                     5.7_1             r42h358215d_0    conda-forge
r-askpass                 1.1               r42h06615bd_3    conda-forge
r-assertthat              0.2.1             r42hc72bb7e_3    conda-forge
r-backports               1.4.1             r42h06615bd_1    conda-forge
r-base                    4.2.2                h6b4767f_2    conda-forge
r-base64enc               0.1_3           r42h06615bd_1005    conda-forge
r-beeswarm                0.4.0             r42h06615bd_2    conda-forge
r-bh                      1.81.0_1          r42hc72bb7e_0    conda-forge
r-bibtex                  0.5.1             r42hc72bb7e_0    conda-forge
r-bit                     4.0.5             r42h06615bd_0    conda-forge
r-bit64                   4.0.5             r42h06615bd_1    conda-forge
r-bitops                  1.0_7             r42h06615bd_1    conda-forge
r-blob                    1.2.3             r42hc72bb7e_1    conda-forge
r-boot                    1.3_28.1          r42hc72bb7e_0    conda-forge
r-broom                   1.0.3             r42hc72bb7e_0    conda-forge
r-bslib                   0.4.2             r42hc72bb7e_0    conda-forge
r-cachem                  1.0.7             r42h133d619_0    conda-forge
r-cairo                   1.6_0             r42h06615bd_1    conda-forge
r-callr                   3.7.3             r42hc72bb7e_0    conda-forge
r-cellranger              1.1.0           r42hc72bb7e_1005    conda-forge
r-checkmate               2.1.0             r42h06615bd_1    conda-forge
r-class                   7.3_21            r42h133d619_0    conda-forge
r-cli                     3.6.0             r42h38f115c_0    conda-forge
r-clipr                   0.8.0             r42hc72bb7e_1    conda-forge
r-cluster                 2.1.4             r42h8da6f51_0    conda-forge
r-codetools               0.2_19            r42hc72bb7e_0    conda-forge
r-colorspace              2.1_0             r42h133d619_0    conda-forge
r-cpp11                   0.4.3             r42hc72bb7e_0    conda-forge
r-crayon                  1.5.2             r42hc72bb7e_1    conda-forge
r-curl                    4.3.3             r42h06615bd_1    conda-forge
r-cvxr                    1.0_11            r42h7525677_0    conda-forge
r-data.table              1.14.8            r42h133d619_0    conda-forge
r-dbi                     1.1.3             r42hc72bb7e_1    conda-forge
r-dbplyr                  2.3.1             r42hc72bb7e_0    conda-forge
r-deldir                  1.0_6             r42h8da6f51_1    conda-forge
r-desctools               0.99.48           r42haa30946_0    conda-forge
r-digest                  0.6.31            r42h38f115c_0    conda-forge
r-doparallel              1.0.17            r42hc72bb7e_1    conda-forge
r-dorng                   1.8.6             r42hc72bb7e_0    conda-forge
r-dplyr                   1.1.0             r42h38f115c_0    conda-forge
r-dqrng                   0.3.0             r42h7525677_1    conda-forge
r-dtplyr                  1.3.0             r42hc72bb7e_0    conda-forge
r-e1071                   1.7_13            r42h38f115c_0    conda-forge
r-ecosolver               0.5.4             r42h06615bd_1    conda-forge
r-ellipsis                0.3.2             r42h06615bd_1    conda-forge
r-emmeans                 1.8.4_1           r42hc72bb7e_0    conda-forge
r-energy                  1.7_11            r42h38f115c_0    conda-forge
r-estimability            1.4.1             r42hc72bb7e_1    conda-forge
r-evaluate                0.20              r42hc72bb7e_0    conda-forge
r-exact                   3.2               r42hc72bb7e_1    conda-forge
r-expm                    0.999_7           r42hb20cf53_0    conda-forge
r-fansi                   1.0.4             r42h133d619_0    conda-forge
r-farver                  2.1.1             r42h7525677_1    conda-forge
r-fastmap                 1.1.1             r42h38f115c_0    conda-forge
r-fnn                     1.1.3.1           r42h7525677_1    conda-forge
r-forcats                 1.0.0             r42hc72bb7e_0    conda-forge
r-foreach                 1.5.2             r42hc72bb7e_1    conda-forge
r-foreign                 0.8_84            r42h133d619_0    conda-forge
r-formatr                 1.14              r42hc72bb7e_0    conda-forge
r-formula                 1.2_5             r42hc72bb7e_0    conda-forge
r-frictionless            1.0.2             r42hc72bb7e_0    conda-forge
r-fs                      1.6.1             r42h38f115c_0    conda-forge
r-futile.logger           1.4.3           r42hc72bb7e_1004    conda-forge
r-futile.options          1.0.1           r42hc72bb7e_1003    conda-forge
r-gargle                  1.3.0             r42h785f33e_0    conda-forge
r-gbrd                    0.4_11          r42hc72bb7e_1004    conda-forge
r-generics                0.1.3             r42hc72bb7e_1    conda-forge
r-getopt                  1.20.3            r42ha770c72_3    conda-forge
r-ggbeeswarm              0.7.1             r42hc72bb7e_0    conda-forge
r-ggplot2                 3.4.1             r42hc72bb7e_0    conda-forge
r-ggrastr                 1.0.1             r42hc72bb7e_1    conda-forge
r-ggrepel                 0.9.3             r42h38f115c_0    conda-forge
r-gld                     2.6.6             r42h06615bd_0    conda-forge
r-glue                    1.6.2             r42h06615bd_1    conda-forge
r-gmp                     0.7_1             r42h38f115c_0    conda-forge
r-googledrive             2.0.0             r42hc72bb7e_1    conda-forge
r-googlesheets4           1.0.1             r42h785f33e_1    conda-forge
r-gridextra               2.3             r42hc72bb7e_1004    conda-forge
r-gsl                     2.1_8             r42hd8b83a8_0    conda-forge
r-gtable                  0.3.1             r42hc72bb7e_1    conda-forge
r-haven                   2.5.1             r42h7525677_0    conda-forge
r-highr                   0.10              r42hc72bb7e_0    conda-forge
r-hmisc                   4.8_0             r42hac0b197_0    conda-forge
r-hms                     1.1.2             r42hc72bb7e_1    conda-forge
r-htmltable               2.4.1             r42hc72bb7e_1    conda-forge
r-htmltools               0.5.4             r42h38f115c_0    conda-forge
r-htmlwidgets             1.6.1             r42hc72bb7e_0    conda-forge
r-httr                    1.4.5             r42hc72bb7e_0    conda-forge
r-hwriter                 1.3.2.1           r42hc72bb7e_1    conda-forge
r-ids                     1.0.1             r42hc72bb7e_2    conda-forge
r-igraph                  1.4.1             r42h65ed38e_0    conda-forge
r-interp                  1.1_3             r42h7525677_1    conda-forge
r-irlba                   2.3.5.1           r42h5f7b363_0    conda-forge
r-isoband                 0.2.7             r42h38f115c_1    conda-forge
r-iterators               1.0.14            r42hc72bb7e_1    conda-forge
r-jpeg                    0.1_10            r42h06615bd_0    conda-forge
r-jquerylib               0.1.4             r42hc72bb7e_1    conda-forge
r-jsonlite                1.8.4             r42h133d619_0    conda-forge
r-knitr                   1.42              r42hc72bb7e_1    conda-forge
r-labeling                0.4.2             r42hc72bb7e_2    conda-forge
r-lambda.r                1.2.4             r42hc72bb7e_2    conda-forge
r-lattice                 0.20_45           r42h06615bd_1    conda-forge
r-latticeextra            0.6_30            r42hc72bb7e_1    conda-forge
r-lazyeval                0.2.2             r42h06615bd_3    conda-forge
r-lifecycle               1.0.3             r42hc72bb7e_1    conda-forge
r-lme4                    1.1_31            r42h7525677_0    conda-forge
r-lmertest                3.1_3             r42hc72bb7e_1    conda-forge
r-lmom                    2.9               r42h8da6f51_1    conda-forge
r-lubridate               1.9.2             r42h133d619_1    conda-forge
r-magrittr                2.0.3             r42h06615bd_1    conda-forge
r-mass                    7.3_58.2          r42h133d619_0    conda-forge
r-matrix                  1.5_3             r42h5f7b363_0    conda-forge
r-matrixstats             0.63.0            r42h06615bd_0    conda-forge
r-memoise                 2.0.1             r42hc72bb7e_1    conda-forge
r-mgcv                    1.8_41            r42h5f7b363_0    conda-forge
r-mime                    0.12              r42h06615bd_1    conda-forge
r-minqa                   1.2.5             r42hb13c81a_0    conda-forge
r-modelr                  0.1.10            r42hc72bb7e_0    conda-forge
r-munsell                 0.5.0           r42hc72bb7e_1005    conda-forge
r-mvtnorm                 1.1_3             r42h8da6f51_1    conda-forge
r-nlme                    3.1_162           r42hac0b197_0    conda-forge
r-nloptr                  2.0.3             r42hb13c81a_1    conda-forge
r-nnet                    7.3_18            r42h06615bd_1    conda-forge
r-numderiv                2016.8_1.1        r42hc72bb7e_4    conda-forge
r-openssl                 2.0.5             r42hb1dc35e_0    conda-forge
r-optparse                1.7.3             r42hc72bb7e_1    conda-forge
r-osqp                    0.6.0.8           r42h38f115c_0    conda-forge
r-permute                 0.9_7             r42hc72bb7e_1    conda-forge
r-pheatmap                1.0.12            r42hc72bb7e_3    conda-forge
r-pillar                  1.8.1             r42hc72bb7e_1    conda-forge
r-pixmap                  0.4_12            r42hc72bb7e_1    conda-forge
r-pkgconfig               2.0.3             r42hc72bb7e_2    conda-forge
r-pkgmaker                0.32.8            r42hc72bb7e_0    conda-forge
r-plogr                   0.2.0           r42hc72bb7e_1004    conda-forge
r-plyr                    1.8.8             r42h7525677_0    conda-forge
r-png                     0.1_8             r42h10cf519_0    conda-forge
r-prettyunits             1.1.1             r42hc72bb7e_2    conda-forge
r-processx                3.8.0             r42h06615bd_0    conda-forge
r-progress                1.2.2             r42hc72bb7e_3    conda-forge
r-proxy                   0.4_27            r42h06615bd_1    conda-forge
r-ps                      1.7.2             r42h06615bd_0    conda-forge
r-purrr                   1.0.1             r42h133d619_0    conda-forge
r-r6                      2.5.1             r42hc72bb7e_1    conda-forge
r-ragg                    1.2.4             r42hc1f6985_0    conda-forge
r-rappdirs                0.3.3             r42h06615bd_1    conda-forge
r-rbibutils               2.2.13            r42h133d619_0    conda-forge
r-rcolorbrewer            1.1_3             r42h785f33e_1    conda-forge
r-rcpp                    1.0.10            r42h38f115c_0    conda-forge
r-rcppannoy               0.0.20            r42h7525677_0    conda-forge
r-rcppeigen               0.3.3.9.3         r42h9f5de39_0    conda-forge
r-rcpphnsw                0.4.1             r42h7525677_1    conda-forge
r-rcppml                  0.3.7             r42h7525677_0    conda-forge
r-rcppparallel            5.1.6             r42h38f115c_0    conda-forge
r-rcppprogress            0.4.2             r42hc72bb7e_2    conda-forge
r-rcurl                   1.98_1.10         r42h133d619_0    conda-forge
r-rdpack                  2.4               r42hc72bb7e_1    conda-forge
r-readr                   2.1.4             r42h38f115c_0    conda-forge
r-readxl                  1.4.2             r42h81ef4d7_0    conda-forge
r-registry                0.5_1             r42hc72bb7e_3    conda-forge
r-rematch                 1.0.1           r42hc72bb7e_1005    conda-forge
r-rematch2                2.1.2             r42hc72bb7e_2    conda-forge
r-reprex                  2.0.2             r42hc72bb7e_1    conda-forge
r-reshape2                1.4.4             r42h7525677_2    conda-forge
r-rlang                   1.0.6             r42h7525677_1    conda-forge
r-rmarkdown               2.20              r42hc72bb7e_0    conda-forge
r-rmpfr                   0.9_1             r42h9d0a025_0    conda-forge
r-rngtools                1.5.2             r42hc72bb7e_1    conda-forge
r-rootsolve               1.8.2.3           r42h8da6f51_1    conda-forge
r-rpart                   4.1.19            r42h06615bd_0    conda-forge
r-rspectra                0.16_1            r42h9f5de39_1    conda-forge
r-rsqlite                 2.2.20            r42h38f115c_0    conda-forge
r-rstudioapi              0.14              r42hc72bb7e_1    conda-forge
r-rsvd                    1.0.5             r42hc72bb7e_1    conda-forge
r-rtsne                   0.16              r42h37cf8d7_1    conda-forge
r-rvest                   1.0.3             r42hc72bb7e_1    conda-forge
r-sass                    0.4.5             r42h38f115c_0    conda-forge
r-scales                  1.2.1             r42hc72bb7e_1    conda-forge
r-scs                     3.0_1             r42h5f7b363_1    conda-forge
r-selectr                 0.4_2             r42hc72bb7e_2    conda-forge
r-sitmo                   2.0.2             r42h7525677_1    conda-forge
r-snow                    0.4_4             r42hc72bb7e_1    conda-forge
r-sp                      1.6_0             r42h133d619_0    conda-forge
r-statmod                 1.5.0             r42h74f4db8_0    conda-forge
r-stringi                 1.7.12            r42h1ae9187_0    conda-forge
r-stringr                 1.5.0             r42h785f33e_0    conda-forge
r-survival                3.5_3             r42h133d619_0    conda-forge
r-sys                     3.4.1             r42h06615bd_0    conda-forge
r-systemfonts             1.0.4             r42h0ff29ef_1    conda-forge
r-textshaping             0.3.6             r42hbb20487_4    conda-forge
r-tibble                  3.1.8             r42h06615bd_1    conda-forge
r-tidyr                   1.3.0             r42h38f115c_0    conda-forge
r-tidyselect              1.2.0             r42hc72bb7e_0    conda-forge
r-tidytree                0.4.2             r42hc72bb7e_0    conda-forge
r-tidyverse               1.3.2             r42hc72bb7e_1    conda-forge
r-timechange              0.2.0             r42h38f115c_0    conda-forge
r-tinytex                 0.44              r42hc72bb7e_0    conda-forge
r-tzdb                    0.3.0             r42h7525677_1    conda-forge
r-utf8                    1.2.3             r42h133d619_0    conda-forge
r-uuid                    1.1_0             r42h06615bd_1    conda-forge
r-uwot                    0.1.14            r42h7525677_1    conda-forge
r-vctrs                   0.5.2             r42h38f115c_0    conda-forge
r-vegan                   2.6_4             r42hb20cf53_0    conda-forge
r-vipor                   0.4.5           r42hc72bb7e_1004    conda-forge
r-viridis                 0.6.2             r42hc72bb7e_1    conda-forge
r-viridislite             0.4.1             r42hc72bb7e_1    conda-forge
r-vroom                   1.6.1             r42h38f115c_0    conda-forge
r-withr                   2.5.0             r42hc72bb7e_1    conda-forge
r-xfun                    0.37              r42h38f115c_0    conda-forge
r-xml2                    1.3.3             r42h044e5c7_2    conda-forge
r-xtable                  1.8_4             r42hc72bb7e_4    conda-forge
r-yaml                    2.3.7             r42h133d619_0    conda-forge
r-yulab.utils             0.0.6             r42hc72bb7e_0    conda-forge
raxml                     8.2.12               hec16e2b_4    bioconda
readline                  8.1.2                h8228510_1    conda-forge
requests                  2.28.2             pyhd8ed1ab_1    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
samtools                  1.16.1               h6899075_1    bioconda
scikit-bio                0.5.7            py38h6c62de6_0    conda-forge
scikit-learn              0.24.1           py38h658cfdd_0    conda-forge
scipy                     1.8.1            py38h8ce737c_3    conda-forge
seaborn                   0.12.2               hd8ed1ab_0    conda-forge
seaborn-base              0.12.2             pyhd8ed1ab_0    conda-forge
sed                       4.8                  he412f7d_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
sepp                      4.3.10           py38h3252c3a_2    bioconda
setuptools                67.4.0             pyhd8ed1ab_0    conda-forge
sip                       6.7.7            py38h8dc9893_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
sortmerna                 2.0                  he860b03_4    bioconda
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
statsmodels               0.13.5           py38h26c90d9_2    conda-forge
sysroot_linux-64          2.12                he073ed8_15    conda-forge
tbb                       2021.8.0             hf52228f_0    conda-forge
terminado                 0.17.1             pyh41d4057_0    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tktable                   2.10                 hb7b940f_3    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
tornado                   6.2              py38h0a891b7_1    conda-forge
tqdm                      4.64.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.9.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.4.0                hd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
tzlocal                   2.1                pyh9f0ad1d_0    conda-forge
umap-learn                0.5.3            py38h578d9bd_0    conda-forge
unicodedata2              15.0.0           py38h0a891b7_0    conda-forge
unifrac                   1.1.1            py38h17adfb0_1    bioconda
unifrac-binaries          1.1.1                h15a0faf_4    bioconda
urllib3                   1.26.14            pyhd8ed1ab_0    conda-forge
vsearch                   2.22.1               hf1761c0_0    bioconda
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.5.1              pyhd8ed1ab_0    conda-forge
wget                      1.20.3               ha56f1ee_1    conda-forge
wheel                     0.38.4             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.5              pyhd8ed1ab_0    conda-forge
woltka                    0.1.5                    pypi_0    pypi
wrapt                     1.15.0           py38h1de0b5d_0    conda-forge
xcb-util                  0.4.0                h516909a_0    conda-forge
xcb-util-image            0.4.0                h166bdaf_0    conda-forge
xcb-util-keysyms          0.4.0                h516909a_0    conda-forge
xcb-util-renderutil       0.3.9                h166bdaf_0    conda-forge
xcb-util-wm               0.4.1                h516909a_0    conda-forge
xkeyboard-config          2.38                 h0b41bf4_0    conda-forge
xmltodict                 0.13.0             pyhd8ed1ab_0    conda-forge
xopen                     1.7.0            py38h578d9bd_1    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                h0b41bf4_2    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             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xyzservices               2023.2.0           pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yq                        3.1.1              pyhd8ed1ab_0    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.15.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               h166bdaf_4    conda-forge
zstandard                 0.19.0           py38h5945529_1    conda-forge
zstd                      1.5.2                h3eb15da_6    conda-forge

Thoughts?

Ah actually, I just noticed. Your conda bin is on your path HOWEVER your conda environment bin is not. This is unusual given the fact that your qiime commands did work, and your qiime info and conda list look good. To be clear, you have made sure to activate your conda environment prior to running all of these commands correct?

Can you activate your conda environment then run echo $PATH? I'm not sure exactly what is going on here, but it doesn't seem like conda is setting things up quite correctly. This could be related to some sort of configuration settings on your cluster.

When you have a conda environment active, I'm expecting to see something like the output from the second echo $PATH below. A conda/env/bin at the head of the path.


The thing that gets me is that should need to be on the head of the path for qiime info or any other qiime command to work as well. Your best bet may be to (if you are able) remove and recreate the environment.

1 Like

Hi Oddant,

Yes the other commands were with my activated qiime environment.
And when I do echo Path within the env I get this:

(qiime2-2023.2) [sdegregori@barnacle2]~% echo $PATH
/home/sdegregori/miniconda3/envs/qiime2-2023.2/bin:/home/sdegregori/miniconda3/condabin:/usr/lib64/qt-3.3/bin:/home/sdegregori/perl5/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/slurm-20.11.7/bin:/opt/slurm-20.11.7/sbin:/opt/slurm-20.11.7/bin:/opt/slurm-20.11.7/sbin

It seems like the qiime2 env is the first thing that comes up in my Path.
Based off this would you recommend just reinstalling qiime2 in a new conda environment?
Cheers,
Sam

Yes I would advise trying that. If that does not work, there could be some sort of permissions issue, and I would check with the admins of the cluster.

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