Regarding PICRUST2 Installation

Tulsi Joishy

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Dec 6, 2018, 9:38:36 AM12/6/18

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Dear Gavin

I am having trouble in installing PICRUSt2 pipeline.

I got this error.

conda-env update -n qiime2-2018.11 -f picrust2-env.yaml

Solving environment: failed

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

Traceback (most recent call last):

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/urllib3/response.py", line 302, in _error_catcher

yield

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/urllib3/response.py", line 601, in read_chunked

chunk = self._handle_chunk(amt)

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/urllib3/response.py", line 557, in _handle_chunk

value = self._fp._safe_read(amt)

File "/home/qiime2/miniconda3/lib/python3.6/http/client.py", line 614, in _safe_read

raise IncompleteRead(b''.join(s), amt)

http.client.IncompleteRead: IncompleteRead(8208 bytes read, 2032 more expected)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/requests/models.py", line 745, in generate

for chunk in self.raw.stream(chunk_size, decode_content=True):

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/urllib3/response.py", line 432, in stream

for line in self.read_chunked(amt, decode_content=decode_content):

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/urllib3/response.py", line 626, in read_chunked

self._original_response.close()

File "/home/qiime2/miniconda3/lib/python3.6/contextlib.py", line 99, in __exit__

self.gen.throw(type, value, traceback)

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/urllib3/response.py", line 320, in _error_catcher

raise ProtocolError('Connection broken: %r' % e, e)

urllib3.exceptions.ProtocolError: ('Connection broken: IncompleteRead(8208 bytes read, 2032 more expected)', IncompleteRead(8208 bytes read, 2032 more expected))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/conda/exceptions.py", line 819, in __call__

return func(*args, **kwargs)

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/conda_env/cli/main.py", line 74, in do_call

exit_code = getattr(module, func_name)(args, parser)

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/conda_env/cli/main_update.py", line 126, in execute

installer.install(prefix, specs, args, env)

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/conda_env/installers/conda.py", line 35, in install

unlink_link_transaction = solver.solve_for_transaction(prune=getattr(args, 'prune', False))

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/conda/core/solve.py", line 506, in solve_for_transaction

force_remove, force_reinstall)

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/conda/core/solve.py", line 439, in solve_for_diff

final_precs = self.solve_final_state(deps_modifier, prune, ignore_pinned, force_remove)

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/conda/core/solve.py", line 180, in solve_final_state

index, r = self._prepare(prepared_specs)

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/conda/core/solve.py", line 580, in _prepare

self.subdirs, prepared_specs)

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/conda/core/index.py", line 215, in get_reduced_index

new_records = query_all(spec)

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/conda/core/index.py", line 184, in query_all

return tuple(concat(future.result() for future in as_completed(futures)))

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/conda/core/subdir_data.py", line 95, in query

self.load()

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/conda/core/subdir_data.py", line 149, in load

_internal_state = self._load()

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/conda/core/subdir_data.py", line 227, in _load

mod_etag_headers.get('_mod'))

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/conda/core/subdir_data.py", line 437, in fetch_repodata_remote_request

timeout=timeout)

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/requests/sessions.py", line 521, in get

return self.request('GET', url, **kwargs)

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/requests/sessions.py", line 508, in request

resp = self.send(prep, **send_kwargs)

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/requests/sessions.py", line 658, in send

r.content

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/requests/models.py", line 823, in content

self._content = bytes().join(self.iter_content(CONTENT_CHUNK_SIZE)) or bytes()

File "/home/qiime2/miniconda3/lib/python3.6/site-packages/requests/models.py", line 748, in generate

raise ChunkedEncodingError(e)

requests.exceptions.ChunkedEncodingError: ('Connection broken: IncompleteRead(8208 bytes read, 2032 more expected)', IncompleteRead(8208 bytes read, 2032 more expected))

`$ /home/qiime2/miniconda3/bin/conda-env update -n qiime2-2018.11 -f picrust2-env.yaml`

environment variables:

CIO_TEST=<not set>

CONDA_AUTO_UPDATE_CONDA=false

CONDA_DEFAULT_ENV=qiime2-2018.11

CONDA_EXE=/home/qiime2/miniconda3/bin/conda

CONDA_PREFIX=/home/qiime2/miniconda3/envs/qiime2-2018.11

CONDA_PROMPT_MODIFIER=(qiime2-2018.11)

CONDA_PYTHON_EXE=/home/qiime2/miniconda3/bin/python

CONDA_ROOT=/home/qiime2/miniconda3

CONDA_SHLVL=1

PATH=/home/qiime2/miniconda3/envs/qiime2-2018.11/bin:/home/qiime2/miniconda

3/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/u

sr/sbin:/home/qiime2/.local/bin:/home/qiime2/bin

PYTHONNOUSERSITE=/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python*/site-packages/

QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins

REQUESTS_CA_BUNDLE=<not set>

SSL_CERT_FILE=<not set>

active environment : qiime2-2018.11

active env location : /home/qiime2/miniconda3/envs/qiime2-2018.11

shell level : 1

user config file : /home/qiime2/.condarc

populated config files :

conda version : 4.5.8

conda-build version : not installed

python version : 3.6.5.final.0

base environment : /home/qiime2/miniconda3 (writable)

channel URLs : https://repo.anaconda.com/pkgs/main/linux-64

https://repo.anaconda.com/pkgs/main/noarch

https://repo.anaconda.com/pkgs/free/linux-64

https://repo.anaconda.com/pkgs/free/noarch

https://repo.anaconda.com/pkgs/r/linux-64

https://repo.anaconda.com/pkgs/r/noarch

https://repo.anaconda.com/pkgs/pro/linux-64

https://repo.anaconda.com/pkgs/pro/noarch

package cache : /home/qiime2/miniconda3/pkgs

/home/qiime2/.conda/pkgs

envs directories : /home/qiime2/miniconda3/envs

/home/qiime2/.conda/envs

platform : linux-64

user-agent : conda/4.5.8 requests/2.18.4 CPython/3.6.5 Linux/3.10.0-693.5.2.el7.x86_64 centos/7 glibc/2.17

UID:GID : 1004:1004

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]:

No report sent. To permanently opt-out, use

$ conda config --set report_errors false

Can you please suggest me whats wrong??

Regards

Tulsi

Gavin Douglas

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Dec 6, 2018, 2:53:11 PM12/6/18

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Hi there,

It looks like this error is realted to the urrlib3 package so it’s difficult for me to give specific recommendations. You could try re-installing the qiime2 conda environment - did you just install a fresh environment or had there already been changes?

Thanks,

Gavin

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Tulsi Joishy

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Dec 7, 2018, 1:28:27 AM12/7/18

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Dear Gavin,

Thank you for the response, we have conda 4.5.8 and we installed it few months back, python 3.5. How should i go for PICRUST2 now please tell.

Regards

Tulsi

--

REGARDS ,
Tulsi Kumari Joishy

Tulsi Joishy

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Dec 7, 2018, 2:05:18 AM12/7/18

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Hi Gavin,

Could install it by installing the package you mentioned. m getting this error now:

(qiime2-2018.11) [qiime2@localhost picrust2-2.0.3-b]$ qiime picrust2 custom-tree-pipeline --i-table /home/qiime2/Dairy consumers/PICRUSt2/Picrust2_output/placements.qza \

> --i-tree /home/qiime2/Dairy consumers/PICRUSt2/Picrust2_output/tree.qza \

> --output-dir q2-picrust2_output \

> --p-threads 15 --p-hsp-method pic \

> --p-max-nsti 2

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

Traceback (most recent call last):

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/bin/qiime", line 11, in <module>

sys.exit(qiime())

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 764, in __call__

return self.main(*args, **kwargs)

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 717, in main

rv = self.invoke(ctx)

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 1132, in invoke

cmd_name, cmd, args = self.resolve_command(ctx, args)

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 1171, in resolve_command

cmd = self.get_command(ctx, cmd_name)

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py", line 99, in get_command

plugin = self._plugin_lookup[name]

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py", line 75, in _plugin_lookup

import q2cli.cache

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/cache.py", line 301, in <module>

CACHE = DeploymentCache()

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/cache.py", line 61, in __init__

self._state = self._get_cached_state(refresh=refresh)

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/cache.py", line 107, in _get_cached_state

self._cache_current_state(current_requirements)

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/cache.py", line 200, in _cache_current_state

state = self._get_current_state()

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/cache.py", line 238, in _get_current_state

plugin_manager = qiime2.sdk.PluginManager()

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 44, in __new__

self._init()

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/plugin_manager.py", line 59, in _init

plugin = entry_point.load()

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2332, in load

return self.resolve()

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2338, in resolve

module = __import__(self.module_name, fromlist=['__name__'], level=0)

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_picrust2-0.0.2-py3.5.egg/q2_picrust2/__init__.py", line 9, in <module>

from ._full_pipeline import full_pipeline

File "/home/qiime2/miniconda3/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_picrust2-0.0.2-py3.5.egg/q2_picrust2/_full_pipeline.py", line 9, in <module>

import picrust2.pipeline

ImportError: No module named 'picrust2'

Can you please suggest me in this regards.

Best

Tulsi

On Fri, Dec 7, 2018 at 1:23 AM Gavin Douglas <gavinm...@gmail.com> wrote:

Gavin Douglas

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Dec 7, 2018, 6:45:11 AM12/7/18

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Hi there,

That error means that PICRUSt2 is not installed. Can you confirm that you ran all the installation commands, including the pip command?

Gavin

Tulsi Joishy

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Dec 7, 2018, 7:12:57 AM12/7/18

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Dear Gavin,

have two questions:

1) I have this error while installing pip. What should i do?

(qiime2-2018.11) [qiime2@localhost ~]$ source activate picrust2

(picrust2) [qiime2@localhost ~]$ pip install --editable

Usage:

pip install [options] <requirement specifier> [package-index-options] ...

pip install [options] -r <requirements file> [package-index-options] ...

pip install [options] [-e] <vcs project url> ...

pip install [options] [-e] <local project path> ...

pip install [options] <archive url/path> ...

--editable option requires 1 argument

2) and also do we need to install EPA-NG, GAPPA for custom tre pipeline? m getting this error? m so lost..please help.

[qiime2@localhost Dairy consumers]$ qiime picrust2 custom-tree-pipeline --i-table /home/qiime2/Dairy_consumers/PICRUSt2/Picrust2_output/table.qza --i-tree /home/qiime2/Dairy_consumers/PICRUSt2/Picrust2_output/tree.qza --output-dir q2-p2_output --p-threads 15 --p-hsp-method mp --p-max-nsti 2

Error running this command:

hsp.py -i 16S -t /tmp/tmp9vzeaco9/placed_seqs.tre -p 1 -n -o /tmp/tmp9vzeaco9/picrust2_out/16S_predicted -m mp

Regards

Tulsi

Gavin Douglas

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Dec 7, 2018, 8:59:14 AM12/7/18

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Hi there,

1) You’re missing the “.” character at the end:

pip install --editable .

2) No you don’t need those programs. Did you use place your ASVs into the PICRUSt2 reference tree with q2-fragment-insertion? If not then you should re-run that step with the files described in the tutorial. Otherwise, if you don’t mind sending me the table.qza and tree.qza files privately I’m happy to troubleshoot the issue.

Gavin

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