Error running picrust2

alla shevchenko

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Jul 19, 2024, 8:31:33 AM7/19/24

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Hello )
I was trying to use qiime picrust2 full-pipeline plugin

qiime picrust2 full-pipeline
--i-table ASV_table.qza
--i-seq rep-seq.qza
--output-dir picrust-output
--p-placement-tool sepp
--p-threads 5
--p-hsp-method pic
--p-max-nsti 2
--verbose

and got next error. I havent found a working solution.
I have qiime2-2023.5 version
Pathways for files are correct.

error looks this way:

Error running this command:
hsp.py --tree /tmp/tmpkparpvnk/picrust2_out/out.tre --output /tmp/tmpkparpvnk/picrust2_out/KO_predicted.tsv.gz --observed_trait_table /home/alla/mambaforge/envs/qiime2-2023.5/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/ko.txt.gz --hsp_method pic --edge_exponent 0.5 --seed 100 --processes 5

I woul appreciate any help

Thank you

Robyn Wright

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Jul 22, 2024, 11:22:46 AM7/22/24

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Hi there,

Could you try re-running with qiime2-2023.2, as is used in the plugin installation instructions?

Thanks,

Robyn

alla shevchenko

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Jul 22, 2024, 12:21:28 PM7/22/24

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Hello Roby!

Thank you for reply.

I did, and i got next

conda install q2-picrust2=2023.2 \
> -c conda-forge \
> -c bioconda \
> -c gavinmdouglas
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): failed

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/gateways/repodata/__init__.py", line 132, in conda_http_errors
yield
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/gateways/repodata/__init__.py", line 101, in repodata
response.raise_for_status()
File "/home/alla/mambaforge/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://conda.anaconda.org/gavinmdouglas/linux-64/current_repodata.json

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/alla/mambaforge/lib/python3.10/site-packages/requests/models.py", line 971, in json
return complexjson.loads(self.text, **kwargs)
File "/home/alla/mambaforge/lib/python3.10/site-packages/simplejson/__init__.py", line 514, in loads
return _default_decoder.decode(s)
File "/home/alla/mambaforge/lib/python3.10/site-packages/simplejson/decoder.py", line 386, in decode
obj, end = self.raw_decode(s)
File "/home/alla/mambaforge/lib/python3.10/site-packages/simplejson/decoder.py", line 416, in raw_decode
return self.scan_once(s, idx=_w(s, idx).end())
simplejson.errors.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/exceptions.py", line 1124, in __call__
return func(*args, **kwargs)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/cli/main.py", line 69, in main_subshell
exit_code = do_call(args, p)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/cli/conda_argparse.py", line 91, in do_call
return getattr(module, func_name)(args, parser)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/notices/core.py", line 103, in wrapper
return_value = func(*args, **kwargs)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/cli/main_install.py", line 20, in execute
install(args, parser, 'install')
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/cli/install.py", line 264, in install
unlink_link_transaction = solver.solve_for_transaction(
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/core/solve.py", line 132, in solve_for_transaction
unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/core/solve.py", line 175, in solve_for_diff
final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/core/solve.py", line 280, in solve_final_state
ssc = self._collect_all_metadata(ssc)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/common/io.py", line 84, in decorated
return f(*args, **kwds)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/core/solve.py", line 447, in _collect_all_metadata
index, r = self._prepare(prepared_specs)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/core/solve.py", line 1060, in _prepare
reduced_index = get_reduced_index(self.prefix, self.channels,
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/core/index.py", line 267, in get_reduced_index
new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/core/subdir_data.py", line 124, in query_all
result = tuple(chain.from_iterable(executor.map(subdir_query, channel_urls)))
File "/home/alla/mambaforge/lib/python3.10/concurrent/futures/_base.py", line 621, in result_iterator
yield _result_or_cancel(fs.pop())
File "/home/alla/mambaforge/lib/python3.10/concurrent/futures/_base.py", line 319, in _result_or_cancel
return fut.result(timeout)
File "/home/alla/mambaforge/lib/python3.10/concurrent/futures/_base.py", line 451, in result
return self.__get_result()
File "/home/alla/mambaforge/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
raise self._exception
File "/home/alla/mambaforge/lib/python3.10/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/core/subdir_data.py", line 113, in <lambda>
subdir_query = lambda url: tuple(
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/core/subdir_data.py", line 129, in query
self.load()
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/core/subdir_data.py", line 215, in load
_internal_state = self._load()
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/core/subdir_data.py", line 323, in _load
raw_repodata_str = self._repo.repodata(mod_etag_headers)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/gateways/repodata/__init__.py", line 94, in repodata
with conda_http_errors(self._url, filename):
File "/home/alla/mambaforge/lib/python3.10/contextlib.py", line 153, in __exit__
self.gen.throw(typ, value, traceback)
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/gateways/repodata/__init__.py", line 179, in conda_http_errors
raise RepodataIsEmpty(
File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/exceptions.py", line 461, in __init__
body = response.json()
File "/home/alla/mambaforge/lib/python3.10/site-packages/requests/models.py", line 975, in json
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

`$ /home/alla/mambaforge/bin/conda install q2-picrust2=2023.2 -c conda-forge -c bioconda -c gavinmdouglas`

environment variables:
CIO_TEST=<not set>
CONDA_DEFAULT_ENV=qiime2-2023.5
CONDA_EXE=/home/alla/mambaforge/bin/conda
CONDA_PREFIX=/home/alla/mambaforge/envs/qiime2-2023.5
CONDA_PREFIX_1=/home/alla/mambaforge
CONDA_PROMPT_MODIFIER=(qiime2-2023.5)
CONDA_PYTHON_EXE=/home/alla/mambaforge/bin/python
CONDA_ROOT=/home/alla/mambaforge
CONDA_SHLVL=2
CURL_CA_BUNDLE=<not set>
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
JAVA_LD_LIBRARY_PATH=/home/alla/mambaforge/envs/qiime2-2023.5/lib/jvm/lib/server
LD_PRELOAD=<not set>
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
PATH=/home/alla/mambaforge/envs/qiime2-
2023.5/bin:/home/alla/mambaforge/condabin:/home/alla/.local/bin:/usr/l
ocal/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr
/local/games:/snap/bin
PYTHONNOUSERSITE=/home/alla/mambaforge/envs/qiime2-2023.5/lib/python*/site-packages/
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
WINDOWPATH=2

active environment : qiime2-2023.5
active env location : /home/alla/mambaforge/envs/qiime2-2023.5
shell level : 2
user config file : /home/alla/.condarc
populated config files : /home/alla/mambaforge/.condarc
/home/alla/.condarc
conda version : 23.1.0
conda-build version : not installed
python version : 3.10.10.final.0
virtual packages : __archspec=1=x86_64
__glibc=2.31=0
__linux=5.15.0=0
__unix=0=0
base environment : /home/alla/mambaforge (writable)
conda av data dir : /home/alla/mambaforge/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://conda.anaconda.org/gavinmdouglas/linux-64
https://conda.anaconda.org/gavinmdouglas/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/alla/mambaforge/pkgs
/home/alla/.conda/pkgs
envs directories : /home/alla/mambaforge/envs
/home/alla/.conda/envs
platform : linux-64
user-agent : conda/23.1.0 requests/2.31.0 CPython/3.10.10 Linux/5.15.0-116-generic ubuntu/20.04.6 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers? [y/N]: y
Upload successful.

Thank you for helping to improve conda.
Opt-in to always sending reports (and not see this message again)
by running

$ conda config --set report_errors true

What should I do?

Thank you)

понедельник, 22 июля 2024 г. в 18:22:46 UTC+3, roby...@gmail.com:

Robyn Wright

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Jul 22, 2024, 12:23:18 PM7/22/24

to picrust-users

Is this inside a fresh conda environment with qiime2-2023.2 installed? It appears to be inside the 2023.5 environment here.

alla shevchenko

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Jul 22, 2024, 12:45:58 PM7/22/24

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Looks like qiime2-2023.2 env doesn't exist, i usually activate qiime2-2023.5

the whole pipeline was working fine before

conda activate qiime2-2023.2

EnvironmentNameNotFound: Could not find conda environment: qiime2-2023.2

You can list all discoverable environments with `conda info --envs

понедельник, 22 июля 2024 г. в 19:23:18 UTC+3, roby...@gmail.com:

alla shevchenko

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Jul 22, 2024, 12:46:01 PM7/22/24

to picrust-users

It looks like I have two of them

conda environments:
#
base * /home/alla/mambaforge
atlas-dev /home/alla/mambaforge/envs/atlas-dev
qiime2-2023.5 /home/alla/mambaforge/envs/qiime2-2023.5
/home/alla/miniconda3
/home/alla/miniconda3/envs/qiime2-2023.2

понедельник, 22 июля 2024 г. в 19:23:18 UTC+3, roby...@gmail.com:

Is this inside a fresh conda environment with qiime2-2023.2 installed? It appears to be inside the 2023.5 environment here.

alla shevchenko

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Jul 22, 2024, 12:46:05 PM7/22/24

to picrust-users

It looks like I have two of them

conda environments:
#
base * /home/alla/mambaforge
atlas-dev /home/alla/mambaforge/envs/atlas-dev
qiime2-2023.5 /home/alla/mambaforge/envs/qiime2-2023.5
/home/alla/miniconda3
/home/alla/miniconda3/envs/qiime2-2023.2

понедельник, 22 июля 2024 г. в 19:23:18 UTC+3, roby...@gmail.com:

Is this inside a fresh conda environment with qiime2-2023.2 installed? It appears to be inside the 2023.5 environment here.

Robyn Wright

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Jul 22, 2024, 12:48:04 PM7/22/24

to picrust-users

I would recommend starting fresh and following the install instructions here. You can either delete the previous environments or just give your new one a different name (but you will need to remember to use this new name in all subsequent commands).

alla shevchenko

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Jul 22, 2024, 12:51:47 PM7/22/24

to picrust-users

Thanks

But I have 2023.5 version and picrust2: 2023.2

Itsnt it should be picrust2: 2023.5 ?

qiime info
System versions
Python version: 3.8.16
QIIME 2 release: 2023.5
QIIME 2 version: 2023.5.1
q2cli version: 2023.5.1

Installed plugins
alignment: 2023.5.0
composition: 2023.5.0
cutadapt: 2023.5.1
dada2: 2023.5.0
deblur: 2023.5.0
demux: 2023.5.0
diversity: 2023.5.1
diversity-lib: 2023.5.0
emperor: 2023.5.0
feature-classifier: 2023.5.0
feature-table: 2023.5.0
fragment-insertion: 2023.5.0
gneiss: 2023.5.0
itsxpress: 2.0.0
krona: 1.0.2
longitudinal: 2023.5.0
metadata: 2023.5.0
phylogeny: 2023.5.0
picrust2: 2023.2
quality-control: 2023.5.0
quality-filter: 2023.5.0
rescript: 2023.5.0
sample-classifier: 2023.5.0
taxa: 2023.5.0
types: 2023.5.0
types-genomics: 2023.5.0.dev0+4.gc4f304a
vsearch: 2023.5.0

понедельник, 22 июля 2024 г. в 19:48:04 UTC+3, roby...@gmail.com:

Robyn Wright

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Jul 22, 2024, 12:53:41 PM7/22/24

to picrust-users

What you need to do is: (1) make a new conda environment, (2) install QIIME2 2023.2 in this environment, and then (3) install the PICRUSt2 plugin in this environment.

alla shevchenko

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Jul 22, 2024, 4:50:32 PM7/22/24

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Ok

Thank you very much)

понедельник, 22 июля 2024 г. в 19:53:41 UTC+3, roby...@gmail.com:

alla shevchenko

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Jul 23, 2024, 9:07:04 AM7/23/24

to picrust-users

Hi)

It didn't work, unfortinally

I have the same mistake

301:~$ conda install q2-picrust2=2023.2 \

> -c conda-forge \
> -c bioconda \
> -c gavinmdouglas

File "/home/alla/mambaforge/lib/python3.10/site-packages/conda/notices/core.py", line 109, in wrapper
return func(*args, **kwargs)

CONDA_DEFAULT_ENV=qiime2-2023.2
CONDA_EXE=/home/alla/mambaforge/bin/conda
CONDA_PREFIX=/home/alla/mambaforge/envs/qiime2-2023.2
CONDA_PREFIX_1=/home/alla/mambaforge
CONDA_PROMPT_MODIFIER=(qiime2-2023.2)

CONDA_PYTHON_EXE=/home/alla/mambaforge/bin/python
CONDA_ROOT=/home/alla/mambaforge
CONDA_SHLVL=2
CURL_CA_BUNDLE=<not set>
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path

JAVA_LD_LIBRARY_PATH=/home/alla/mambaforge/envs/qiime2-2023.2/lib/jvm/lib/server

LD_PRELOAD=<not set>
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
PATH=/home/alla/mambaforge/envs/qiime2-

2023.2/bin:/home/alla/mambaforge/condabin:/home/alla/.local/bin:/usr/l

ocal/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr
/local/games:/snap/bin

PYTHONNOUSERSITE=/home/alla/mambaforge/envs/qiime2-2023.2/lib/python*/site-packages/

REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
WINDOWPATH=2

active environment : qiime2-2023.2
active env location : /home/alla/mambaforge/envs/qiime2-2023.2

Upload successful.

понедельник, 22 июля 2024 г. в 23:50:32 UTC+3, alla shevchenko:

Robyn Wright

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Jul 23, 2024, 9:15:44 AM7/23/24

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OK, can you try following these instructions for installing the plugin manually?

alla shevchenko

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Jul 24, 2024, 1:52:23 PM7/24/24

to picrust-users

I am sorry, but it didnt work either

Error: QIIME 2 has no plugin/command named 'picrust2'.

вторник, 23 июля 2024 г. в 16:15:44 UTC+3, roby...@gmail.com:

alla shevchenko

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Aug 1, 2024, 1:50:01 PM8/1/24

to picrust-users

I am sorry, for not providing detailes/

conda install -c bioconda -c conda-forge picrust2
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 23.1.0
latest version: 24.5.0

Please update conda by running

$ conda update -n base -c conda-forge conda

Or to minimize the number of packages updated during conda update use

conda install conda=24.5.0

# All requested packages already installed. conda update -n base -c conda-forge conda
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

environment location: /home/alla/mambaforge

added / updated specs:
- conda

The following packages will be downloaded:

package | build
---------------------------|-----------------
archspec-0.2.3 | pyhd8ed1ab_0 48 KB conda-forge
bedtools-2.31.1 | hf5e1c6e_2 1.5 MB bioconda
boltons-24.0.0 | pyhd8ed1ab_0 291 KB conda-forge
bottleneck-1.4.0 | py310h261611a_1 123 KB conda-forge
brotli-1.1.0 | hd590300_1 19 KB conda-forge
brotli-bin-1.1.0 | hd590300_1 19 KB conda-forge
brotli-python-1.1.0 | py310hc6cd4ac_1 341 KB conda-forge
c-ares-1.32.3 | h4bc722e_0 176 KB conda-forge
cffi-1.16.0 | py310h2fee648_0 236 KB conda-forge
conda-24.5.0 | py310hff52083_0 939 KB conda-forge
conda-libmamba-solver-24.7.0| pyhd8ed1ab_0 40 KB conda-forge
conda-package-handling-2.3.0| pyh7900ff3_0 250 KB conda-forge
conda-package-streaming-0.10.0| pyhd8ed1ab_0 19 KB conda-forge
contourpy-1.2.1 | py310hd41b1e2_0 236 KB conda-forge
curl-8.7.1 | hdbd6064_0 86 KB
cycler-0.12.1 | pyhd8ed1ab_0 13 KB conda-forge
distro-1.9.0 | pyhd8ed1ab_0 41 KB conda-forge
fmt-10.2.1 | h00ab1b0_0 189 KB conda-forge
fonttools-4.53.1 | py310h5b4e0ec_0 2.3 MB conda-forge
frozendict-2.4.4 | py310hc51659f_0 48 KB conda-forge
future-1.0.0 | pyhd8ed1ab_0 356 KB conda-forge
hmmer-3.4 | hdbdd923_1 11.1 MB bioconda
humanfriendly-10.0 | pyhd8ed1ab_6 72 KB conda-forge
importlib-metadata-8.2.0 | pyha770c72_0 27 KB conda-forge
isa-l-2.31.0 | h4bc722e_2 156 KB conda-forge
jsonpointer-3.0.0 | py310hff52083_0 16 KB conda-forge
kiwisolver-1.4.5 | py310hd41b1e2_1 71 KB conda-forge
libarchive-3.7.4 | hfca40fe_0 851 KB conda-forge
libblas-3.9.0 |23_linux64_openblas 15 KB conda-forge
libcblas-3.9.0 |23_linux64_openblas 14 KB conda-forge
libcurl-8.7.1 | h251f7ec_0 424 KB
libidn2-2.3.7 | hd590300_0 124 KB conda-forge
liblapack-3.9.0 |23_linux64_openblas 14 KB conda-forge
libmamba-1.5.8 | had39da4_0 1.6 MB conda-forge
libmambapy-1.5.8 | py310h39ff949_0 302 KB conda-forge
libopenblas-0.3.27 |pthreads_hac2b453_1 5.3 MB conda-forge
libxml2-2.12.7 | hc051c1a_1 688 KB conda-forge
lzo-2.10 | hd590300_1001 167 KB conda-forge
mamba-1.5.8 | py310h51d5547_0 51 KB conda-forge
markdown-3.6 | pyhd8ed1ab_0 76 KB conda-forge
markupsafe-2.1.5 | py310h2372a71_0 24 KB conda-forge
matplotlib-base-3.9.1 | py310h0b1de36_0 6.7 MB conda-forge
mdurl-0.1.2 | pyhd8ed1ab_0 14 KB conda-forge
menuinst-2.1.1 | py310hff52083_0 134 KB conda-forge
networkx-3.3 | pyhd8ed1ab_1 1.1 MB conda-forge
numexpr-2.10.0 |py310h3ea09b0_100 132 KB conda-forge
numpy-1.26.4 | py310hb13e2d6_0 6.7 MB conda-forge
openjdk-8.0.412 | hd590300_1 88.3 MB conda-forge
openjpeg-2.5.2 | h488ebb8_0 334 KB conda-forge
pillow-10.2.0 | py310h01dd4db_0 39.3 MB conda-forge
pycosat-0.6.6 | py310h2372a71_0 85 KB conda-forge
pygments-2.18.0 | pyhd8ed1ab_0 859 KB conda-forge
pyparsing-3.1.2 | pyhd8ed1ab_0 87 KB conda-forge
python_abi-3.10 | 4_cp310 6 KB conda-forge
pyyaml-6.0.1 | py310h2372a71_1 167 KB conda-forge
qhull-2020.2 | h434a139_5 540 KB conda-forge
reproc-14.2.4.post0 | hd590300_1 33 KB conda-forge
reproc-cpp-14.2.4.post0 | h59595ed_1 25 KB conda-forge
rich-13.7.1 | pyhd8ed1ab_0 180 KB conda-forge
rich-click-1.8.3 | pyhd8ed1ab_0 33 KB conda-forge
ruamel.yaml-0.18.6 | py310h2372a71_0 199 KB conda-forge
ruamel.yaml.clib-0.2.8 | py310h2372a71_0 133 KB conda-forge
simplejson-3.19.2 | py310h2372a71_0 107 KB conda-forge
tqdm-4.66.4 | pyhd8ed1ab_0 87 KB conda-forge
typing_extensions-4.12.2 | pyha770c72_0 39 KB conda-forge
unicodedata2-15.1.0 | py310h2372a71_0 365 KB conda-forge
yaml-cpp-0.8.0 | h59595ed_0 200 KB conda-forge
zipp-3.19.2 | pyhd8ed1ab_0 20 KB conda-forge
zstandard-0.23.0 | py310h64cae3c_0 398 KB conda-forge
------------------------------------------------------------
Total: 174.3 MB

The following NEW packages will be INSTALLED:

archspec conda-forge/noarch::archspec-0.2.3-pyhd8ed1ab_0
boltons conda-forge/noarch::boltons-24.0.0-pyhd8ed1ab_0
conda-libmamba-so~ conda-forge/noarch::conda-libmamba-solver-24.7.0-pyhd8ed1ab_0
distro conda-forge/noarch::distro-1.9.0-pyhd8ed1ab_0
frozendict conda-forge/linux-64::frozendict-2.4.4-py310hc51659f_0
gettext-tools conda-forge/linux-64::gettext-tools-0.22.5-h59595ed_2
h2 conda-forge/noarch::h2-4.1.0-pyhd8ed1ab_0
hpack conda-forge/noarch::hpack-4.0.0-pyh9f0ad1d_0
hyperframe conda-forge/noarch::hyperframe-6.0.1-pyhd8ed1ab_0
jsonpatch conda-forge/noarch::jsonpatch-1.33-pyhd8ed1ab_0
jsonpointer conda-forge/linux-64::jsonpointer-3.0.0-py310hff52083_0
libasprintf conda-forge/linux-64::libasprintf-0.22.5-h661eb56_2
libasprintf-devel conda-forge/linux-64::libasprintf-devel-0.22.5-h661eb56_2
libgettextpo conda-forge/linux-64::libgettextpo-0.22.5-h59595ed_2
libgettextpo-devel conda-forge/linux-64::libgettextpo-devel-0.22.5-h59595ed_2
libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1
menuinst conda-forge/linux-64::menuinst-2.1.1-py310hff52083_0
platformdirs conda-forge/noarch::platformdirs-4.2.2-pyhd8ed1ab_0
qhull conda-forge/linux-64::qhull-2020.2-h434a139_5
truststore conda-forge/noarch::truststore-0.8.0-pyhd8ed1ab_0

The following packages will be REMOVED:

alsa-lib-1.2.9-hd590300_0
cairo-1.16.0-hbbf8b49_1016
cryptography-41.0.2-py310h75e40e8_0
expat-2.5.0-hcb278e6_1
font-ttf-dejavu-sans-mono-2.37-hab24e00_0
font-ttf-inconsolata-3.000-h77eed37_0
font-ttf-source-code-pro-2.038-h77eed37_0
font-ttf-ubuntu-0.83-hab24e00_0
fontconfig-2.14.2-h14ed4e7_0
fonts-conda-ecosystem-1-0
fonts-conda-forge-1-0
giflib-5.2.1-h0b41bf4_3
graphite2-1.3.13-h58526e2_1001
harfbuzz-7.3.0-hdb3a94d_0
libcups-2.3.3-h36d4200_3
libexpat-2.5.0-hcb278e6_1
libglib-2.76.4-hebfc3b9_0
pcre2-10.40-hc3806b6_0
pixman-0.40.0-h36c2ea0_0
pyopenssl-23.2.0-pyhd8ed1ab_1
toolz-0.12.0-pyhd8ed1ab_0
xorg-fixesproto-5.0-h7f98852_1002
xorg-inputproto-2.3.2-h7f98852_1002
xorg-kbproto-1.0.7-h7f98852_1002
xorg-libice-1.1.1-hd590300_0
xorg-libsm-1.2.4-h7391055_0
xorg-libx11-1.8.6-h8ee46fc_0
xorg-libxext-1.3.4-h0b41bf4_2
xorg-libxfixes-5.0.3-h7f98852_1004
xorg-libxi-1.7.10-h7f98852_0
xorg-libxrender-0.9.11-hd590300_0
xorg-libxt-1.3.0-hd590300_1
xorg-libxtst-1.2.3-h7f98852_1002
xorg-recordproto-1.14.2-h7f98852_1002
xorg-renderproto-0.11.1-h7f98852_1002
xorg-xextproto-7.3.0-h0b41bf4_1003
xorg-xproto-7.0.31-h7f98852_1007

The following packages will be UPDATED:

bedtools 2.31.1-hf5e1c6e_0 --> 2.31.1-hf5e1c6e_2
bottleneck anaconda::bottleneck-1.3.5-py310ha9d4~ --> conda-forge::bottleneck-1.4.0-py310h261611a_1
brotli 1.0.9-h166bdaf_9 --> 1.1.0-hd590300_1
brotli-bin 1.0.9-h166bdaf_9 --> 1.1.0-hd590300_1
brotli-python 1.0.9-py310hd8f1fbe_9 --> 1.1.0-py310hc6cd4ac_1
bzip2 1.0.8-h7f98852_4 --> 1.0.8-h4bc722e_7
c-ares 1.19.1-hd590300_0 --> 1.32.3-h4bc722e_0
ca-certificates 2023.11.17-hbcca054_0 --> 2024.7.4-hbcca054_0
certifi 2023.11.17-pyhd8ed1ab_0 --> 2024.7.4-pyhd8ed1ab_0
cffi 1.15.1-py310h255011f_3 --> 1.16.0-py310h2fee648_0
charset-normalizer 3.2.0-pyhd8ed1ab_0 --> 3.3.2-pyhd8ed1ab_0
click 8.1.6-unix_pyh707e725_0 --> 8.1.7-unix_pyh707e725_0
conda 23.1.0-py310hff52083_0 --> 24.5.0-py310hff52083_0
conda-package-han~ 2.2.0-pyh38be061_0 --> 2.3.0-pyh7900ff3_0
conda-package-str~ 0.9.0-pyhd8ed1ab_0 --> 0.10.0-pyhd8ed1ab_0
contourpy 1.1.0-py310hd41b1e2_0 --> 1.2.1-py310hd41b1e2_0
curl conda-forge::curl-7.88.1-hdc1c0ab_1 --> pkgs/main::curl-8.7.1-hdbd6064_0
cycler 0.11.0-pyhd8ed1ab_0 --> 0.12.1-pyhd8ed1ab_0
fmt 9.1.0-h924138e_0 --> 10.2.1-h00ab1b0_0
fonttools 4.42.0-py310h2372a71_0 --> 4.53.1-py310h5b4e0ec_0
freetype 2.12.1-hca18f0e_1 --> 2.12.1-h267a509_2
future 0.18.3-pyhd8ed1ab_0 --> 1.0.0-pyhd8ed1ab_0
gettext 0.21.1-h27087fc_0 --> 0.22.5-h59595ed_2
hmmer 3.4-hdbdd923_0 --> 3.4-hdbdd923_1
humanfriendly conda-forge/linux-64::humanfriendly-1~ --> conda-forge/noarch::humanfriendly-10.0-pyhd8ed1ab_6
icu 72.1-hcb278e6_0 --> 73.2-h59595ed_0
idna 3.4-pyhd8ed1ab_0 --> 3.7-pyhd8ed1ab_0
importlib-metadata 6.8.0-pyha770c72_0 --> 8.2.0-pyha770c72_0
isa-l 2.30.0-ha770c72_4 --> 2.31.0-h4bc722e_2
jinja2 3.1.2-pyhd8ed1ab_1 --> 3.1.4-pyhd8ed1ab_0
kiwisolver 1.4.4-py310hbf28c38_1 --> 1.4.5-py310hd41b1e2_1
lcms2 2.15-haa2dc70_1 --> 2.16-hb7c19ff_0
ld_impl_linux-64 2.40-h41732ed_0 --> 2.40-hf3520f5_7
libarchive 3.6.2-h039dbb9_1 --> 3.7.4-hfca40fe_0
libblas 3.9.0-17_linux64_openblas --> 3.9.0-23_linux64_openblas
libbrotlicommon 1.0.9-h166bdaf_9 --> 1.1.0-hd590300_1
libbrotlidec 1.0.9-h166bdaf_9 --> 1.1.0-hd590300_1
libbrotlienc 1.0.9-h166bdaf_9 --> 1.1.0-hd590300_1
libcblas 3.9.0-17_linux64_openblas --> 3.9.0-23_linux64_openblas
libcurl conda-forge::libcurl-7.88.1-hdc1c0ab_1 --> pkgs/main::libcurl-8.7.1-h251f7ec_0
libdeflate 1.18-h0b41bf4_0 --> 1.20-hd590300_0
libev 4.33-h516909a_1 --> 4.33-hd590300_2
libgcc-ng 13.1.0-he5830b7_0 --> 14.1.0-h77fa898_0
libgfortran-ng 13.1.0-h69a702a_0 --> 14.1.0-h69a702a_0
libgfortran5 13.1.0-h15d22d2_0 --> 14.1.0-hc5f4f2c_0
libgomp 13.1.0-he5830b7_0 --> 14.1.0-h77fa898_0
libiconv 1.17-h166bdaf_0 --> 1.17-hd590300_2
libidn2 2.3.4-h166bdaf_0 --> 2.3.7-hd590300_0
libjpeg-turbo 2.1.5.1-h0b41bf4_0 --> 3.0.0-hd590300_1
liblapack 3.9.0-17_linux64_openblas --> 3.9.0-23_linux64_openblas
libmamba 1.4.1-hcea66bb_0 --> 1.5.8-had39da4_0
libmambapy 1.4.1-py310h1428755_0 --> 1.5.8-py310h39ff949_0
libnghttp2 1.52.0-h61bc06f_0 --> 1.58.0-h47da74e_1
libnsl 2.0.0-h7f98852_0 --> 2.0.1-hd590300_0
libopenblas 0.3.23-pthreads_h80387f5_0 --> 0.3.27-pthreads_hac2b453_1
libpng 1.6.39-h753d276_0 --> 1.6.43-h2797004_0
libsqlite 3.42.0-h2797004_0 --> 3.46.0-hde9e2c9_0
libstdcxx-ng 13.1.0-hfd8a6a1_0 --> 14.1.0-hc0a3c3a_0
libtiff 4.5.1-h8b53f26_0 --> 4.6.0-h1dd3fc0_3
libwebp-base 1.3.1-hd590300_0 --> 1.4.0-hd590300_0
libxml2 2.11.4-h0d562d8_0 --> 2.12.7-hc051c1a_1
lzo 2.10-h516909a_1000 --> 2.10-hd590300_1001
mamba 1.4.1-py310h51d5547_0 --> 1.5.8-py310h51d5547_0
markdown 3.4.4-pyhd8ed1ab_0 --> 3.6-pyhd8ed1ab_0
markupsafe 2.1.3-py310h2372a71_0 --> 2.1.5-py310h2372a71_0
matplotlib-base 3.7.2-py310hf38f957_0 --> 3.9.1-py310h0b1de36_0
mdurl 0.1.0-pyhd8ed1ab_0 --> 0.1.2-pyhd8ed1ab_0
munkres bioconda::munkres-1.0.7-py_1 --> conda-forge::munkres-1.1.4-pyh9f0ad1d_0
ncurses 6.4-hcb278e6_0 --> 6.5-h59595ed_0
networkx 3.1-pyhd8ed1ab_0 --> 3.3-pyhd8ed1ab_1
numexpr 2.8.7-py310hc2d3c2e_104 --> 2.10.0-py310h3ea09b0_100
numpy 1.25.2-py310ha4c1d20_0 --> 1.26.4-py310hb13e2d6_0
openjpeg 2.5.0-hfec8fc6_2 --> 2.5.2-h488ebb8_0
openssl 3.2.0-hd590300_1 --> 3.3.1-h4bc722e_2
packaging 23.1-pyhd8ed1ab_0 --> 24.1-pyhd8ed1ab_0
perl 5.32.1-4_hd590300_perl5 --> 5.32.1-7_hd590300_perl5
pillow 10.0.0-py310h582fbeb_0 --> 10.2.0-py310h01dd4db_0
pluggy 1.2.0-pyhd8ed1ab_0 --> 1.5.0-pyhd8ed1ab_0
pycosat 0.6.4-py310h5764c6d_1 --> 0.6.6-py310h2372a71_0
pycparser 2.21-pyhd8ed1ab_0 --> 2.22-pyhd8ed1ab_0
pygments 2.16.1-pyhd8ed1ab_0 --> 2.18.0-pyhd8ed1ab_0
pyparsing 3.0.9-pyhd8ed1ab_0 --> 3.1.2-pyhd8ed1ab_0
python-dateutil 2.8.2-pyhd8ed1ab_0 --> 2.9.0-pyhd8ed1ab_0
python-tzdata anaconda::python-tzdata-2023.3-pyhd3e~ --> conda-forge::python-tzdata-2024.1-pyhd8ed1ab_0
python_abi 3.10-3_cp310 --> 3.10-4_cp310
pytz anaconda/linux-64::pytz-2023.3.post1-~ --> conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0
pyyaml 6.0-py310h5764c6d_5 --> 6.0.1-py310h2372a71_1
reproc 14.2.4-h0b41bf4_0 --> 14.2.4.post0-hd590300_1
reproc-cpp 14.2.4-hcb278e6_0 --> 14.2.4.post0-h59595ed_1
requests 2.31.0-pyhd8ed1ab_0 --> 2.32.3-pyhd8ed1ab_0
rich 13.5.1-pyhd8ed1ab_0 --> 13.7.1-pyhd8ed1ab_0
rich-click 1.6.1-pyhd8ed1ab_0 --> 1.8.3-pyhd8ed1ab_0
ruamel.yaml 0.17.32-py310h2372a71_0 --> 0.18.6-py310h2372a71_0
ruamel.yaml.clib 0.2.7-py310h1fa729e_1 --> 0.2.8-py310h2372a71_0
simplejson 3.19.1-py310h1fa729e_0 --> 3.19.2-py310h2372a71_0
tk 8.6.12-h27826a3_0 --> 8.6.13-noxft_h4845f30_101
tqdm 4.65.0-pyhd8ed1ab_1 --> 4.66.4-pyhd8ed1ab_0
typing_extensions 4.7.1-pyha770c72_0 --> 4.12.2-pyha770c72_0
tzdata 2023c-h71feb2d_0 --> 2024a-h0c530f3_0
unicodedata2 15.0.0-py310h5764c6d_0 --> 15.1.0-py310h2372a71_0
urllib3 2.0.4-pyhd8ed1ab_0 --> 2.2.2-pyhd8ed1ab_1
wheel 0.41.1-pyhd8ed1ab_0 --> 0.43.0-pyhd8ed1ab_1
yaml-cpp 0.7.0-h27087fc_2 --> 0.8.0-h59595ed_0
zipp 3.16.2-pyhd8ed1ab_0 --> 3.19.2-pyhd8ed1ab_0
zstandard 0.19.0-py310h1275a96_2 --> 0.23.0-py310h64cae3c_0
zstd 1.5.2-hfc55251_7 --> 1.5.6-ha6fb4c9_0

The following packages will be DOWNGRADED:

openjdk 20.0.0-h8e330f5_0 --> 8.0.412-hd590300_1

Proceed ([y]/n)? y

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in /home/alla/mambaforge/envs/qiime2-2023.2/lib/python3.8/site-packages (from PICRUSt2==2.5.2) (1.23.5)
Requirement already satisfied: h5py in /home/alla/mambaforge/envs/qiime2-2023.2/lib/python3.8/site-packages (from PICRUSt2==2.5.2) (2.10.0)
Requirement already satisfied: joblib in /home/alla/mambaforge/envs/qiime2-2023.2/lib/python3.8/site-packages (from PICRUSt2==2.5.2) (1.2.0)
Requirement already satisfied: biom-format in /home/alla/mambaforge/envs/qiime2-2023.2/lib/python3.8/site-packages (from PICRUSt2==2.5.2) (2.1.12)
Requirement already satisfied: pandas>=0.20.0 in /home/alla/mambaforge/envs/qiime2-2023.2/lib/python3.8/site-packages (from biom-format->PICRUSt2==2.5.2) (1.5.3)
Requirement already satisfied: cython>=0.29 in /home/alla/mambaforge/envs/qiime2-2023.2/lib/python3.8/site-packages (from biom-format->PICRUSt2==2.5.2) (0.29.33)
Requirement already satisfied: click in /home/alla/mambaforge/envs/qiime2-2023.2/lib/python3.8/site-packages (from biom-format->PICRUSt2==2.5.2) (8.1.3)
Requirement already satisfied: scipy>=1.3.1 in /home/alla/mambaforge/envs/qiime2-2023.2/lib/python3.8/site-packages (from biom-format->PICRUSt2==2.5.2) (1.8.1)
Requirement already satisfied: six in /home/alla/mambaforge/envs/qiime2-2023.2/lib/python3.8/site-packages (from h5py->PICRUSt2==2.5.2) (1.16.0)
Requirement already satisfied: python-dateutil>=2.8.1 in /home/alla/mambaforge/envs/qiime2-2023.2/lib/python3.8/site-packages (from pandas>=0.20.0->biom-format->PICRUSt2==2.5.2) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /home/alla/mambaforge/envs/qiime2-2023.2/lib/python3.8/site-packages (from pandas>=0.20.0->biom-format->PICRUSt2==2.5.2) (2022.7.1)
Installing collected packages: PICRUSt2
Attempting uninstall: PICRUSt2
Found existing installation: PICRUSt2 2.5.2
Uninstalling PICRUSt2-2.5.2:
Successfully uninstalled PICRUSt2-2.5.2
Running setup.py develop for PICRUSt2
Successfully installed PICRUSt2-2.5.2

qiime dev refresh-cache
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.

qiime picrust2 --help

Error: QIIME 2 has no plugin/command named 'picrust2'.

среда, 24 июля 2024 г. в 20:52:23 UTC+3, alla shevchenko:

Robyn Wright

unread,

Aug 2, 2024, 8:11:23 AM8/2/24

to picrust-users

Can you show the full output with you installing qiime2-2023.2 please? This should look like:

wget https://data.qiime2.org/distro/core/qiime2-2023.2-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n qiime2-2023.2 --file qiime2-2023.2-py38-osx-conda.yml
conda activate qiime2-2023.2
conda config --env --set subdir osx-64
conda activate qiime2-2023.2
conda install -c bioconda -c conda-forge picrust2 wget https://github.com/gavinmdouglas/q2-picrust2/archive/refs/tags/2023.2_0.zip
unzip 2023.2_0.zip
cd q2-picrust2-2023.2_0
pip install -e . qiime dev refresh-cache qiime picrust2 --help

So it seems like you may have been missing the wget/unzip/cd commands?

Robyn

Robyn Wright

unread,

Aug 23, 2024, 10:00:50 AM8/23/24

to picrust-users

Hello,

I’m not sure if that worked for you or not, but there is now a version available for qiime2-2024.5 so it may be worth trying that.

Robyn

alla shevchenko

unread,

Oct 29, 2024, 11:15:49 AM10/29/24

to picrust-users

Hello Robyn!

I have installed the qiime2-amplicon-2024.5

And tried to install picrust2, but still nothing seems to work

(qiime2-amplicon-2024.5) m_t:/disk1/16s$ conda install -c bioconda -c conda-forge picrust2
/home/m_t/miniconda3/lib/python3.12/site-packages/conda/base/context.py:198: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.

To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:

conda config --add channels defaults

For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html

deprecated.topic(
/home/m_t/miniconda3/lib/python3.12/site-packages/conda/base/context.py:198: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.

To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:

conda config --add channels defaults

For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html

deprecated.topic(
Channels:
- bioconda
- conda-forge
- defaults
- https://packages.qiime2.org/qiime2/2024.5/amplicon/released
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

# All requested packages already installed.

qiime picrust2 --help
Error: QIIME 2 has no plugin/command named 'picrust2'.

I can't figure this out

Any suggestions?

Thank you

Best,

Alla

пятница, 23 августа 2024 г. в 17:00:50 UTC+3, roby...@gmail.com:

Robyn Wright

unread,

Oct 29, 2024, 11:27:01 AM10/29/24

to picrust-users

Hi there,

For installation within QIIME2, you'll need to follow the QIIME2 installation instructions: https://old-library.qiime2.org/plugins/q2-picrust2/13/ - note that it appears that the location of this page just changed, so I guess I'll need to figure out where that is supposed to be hosted now, but those instructions should work for now, anyway.

Robyn

alla shevchenko

unread,

Oct 29, 2024, 12:05:06 PM10/29/24

to picrust-users

Thank you very much!

It worked

Best,

Alla

вторник, 29 октября 2024 г. в 18:27:01 UTC+3, roby...@gmail.com:

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