Can not run any command in Qiime2 env after installing Songbird

Hi,

I have PacBio 16S sequences and I use qiime2-2022.2, everything was good until I installed Songbird, then I tried to import new sequences from another project, but it failed producing this error message:

installing songbird made an issue to import data An unexpected error has occurred:

No module named 'tensorflow.contrib'

I checked tensorflow version as follows:

$pip freeze | grep tensorflow
tensorflow==2.13.0
tensorflow-estimator==2.13.0
tensorflow-io-gcs-filesystem==0.33.0

Also, whenever I activate qiime2-2022.2 env, I got this warning message:

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

2023-08-15 08:33:36.880401: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.

2023-08-15 08:33:36.909950: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.

2023-08-15 08:33:36.910304: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.

To enable the following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.

2023-08-15 08:33:37.425176: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT

Traceback (most recent call last):

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/util.py", line 224, in get_plugin_manager

return qiime2.sdk.PluginManager.reuse_existing()

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 58, in reuse_existing

raise UninitializedPluginManagerError

qiime2.sdk.plugin_manager.UninitializedPluginManagerError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "/home/miniconda3/envs/qiime2-2022.2/bin/qiime", line 11, in

sys.exit(qiime())

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py", line 829, in call

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

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py", line 781, in main

with self.make_context(prog_name, args, **extra) as ctx:

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py", line 700, in make_context

self.parse_args(ctx, args)

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/click/command.py", line 43, in parse_args

return super().parse_args(ctx, args)

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py", line 1209, in parse_args

echo(ctx.get_help(), color=ctx.color)

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py", line 570, in get_help

return self.command.get_help(self)

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py", line 975, in get_help

self.format_help(ctx, formatter)

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/click/core.py", line 1003, in format_help

self.format_options(ctx, formatter)

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/click/command.py", line 157, in format_options

for subcommand in self.list_commands(ctx):

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 92, in list_commands

plugins = sorted(self._plugin_lookup)

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 76, in _plugin_lookup

import q2cli.core.cache

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/core/cache.py", line 285, in

CACHE = DeploymentCache()

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/core/cache.py", line 61, in init

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

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state

self._cache_current_state(current_requirements)

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/core/cache.py", line 205, in _cache_current_state

state = self._get_current_state()

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/core/cache.py", line 253, in _get_current_state

plugin_manager = q2cli.util.get_plugin_manager()

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/util.py", line 236, in get_plugin_manager

return qiime2.sdk.PluginManager()

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 67, in new

self._init(add_plugins=add_plugins)

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 105, in _init

plugin = entry_point.load()

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/pkg_resources/init.py", line 2465, in load

return self.resolve()

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/pkg_resources/init.py", line 2471, in resolve

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

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/songbird/q2/init.py", line 2, in

from ._method import multinomial

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/songbird/q2/_method.py", line 8, in

from songbird.multinomial import MultRegression

File "/home/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/songbird/multinomial.py", line 3, in

from tensorflow.contrib.distributions import Multinomial, Normal

ModuleNotFoundError: No module named 'tensorflow.contrib'

So, I tried to install the latest version of qiime2 (qiime2-2023.5) to skip this issue using conda but I got the error below:

ERROR conda.core.link:_execute(730): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0'.
Rolling back transaction: done
class: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0
location of failed script: /home/miniconda3/envs/qiime2-2023.5/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

==> script output <==
stdout:
stderr: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
++ dirname -- /home/miniconda3/envs/qiime2-2023.5/bin/installBiocDataPackage.sh

  • SCRIPT_DIR=/home/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages
  • json=/home/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
    ++ yq '."genomeinfodbdata-1.2.9".fn' /home/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
  • FN='"GenomeInfoDbData_1.2.9.tar.gz"'
  • IFS=
  • read -r value
    ++ yq '."genomeinfodbdata-1.2.9".urls[]' /home/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
  • URLS+=($value)
  • IFS=
  • read -r value
  • URLS+=($value)
  • IFS=
  • read -r value
  • URLS+=($value)
  • IFS=
  • read -r value
    ++ yq '."genomeinfodbdata-1.2.9".md5' /home/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
  • MD5='"7cc138cfb74665fdfa8d1c244eac4879"'
  • STAGING=/home/miniconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9
  • mkdir -p /home/miniconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9
  • TARBALL='/home/miniconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
  • SUCCESS=0
  • for URL in ${URLS[@]}
    ++ echo '"https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz"'
    ++ tr -d '"'
  • URL=https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
    ++ echo '"7cc138cfb74665fdfa8d1c244eac4879"'
    ++ tr -d '"'
  • MD5=7cc138cfb74665fdfa8d1c244eac4879
  • curl -L https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
    % Total % Received % Xferd Average Speed Time Time Time Current
    Dload Upload Total Spent Left Speed
    100 416 100 416 0 0 3367 0 --:--:-- --:--:-- --:--:-- 3382
    0 0 0 0 0 0 0 0 --:--:-- 0:02:11 --:--:-- 0
    curl: (7) Failed to connect to mghp.osn.xsede.org port 443 after 131408 ms: Couldn't connect to server

return code: 7

kwargs:
{}

Traceback (most recent call last):
File "/home/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1114, in call
return func(*args, **kwargs)
File "/home/miniconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 80, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/home/miniconda3/lib/python3.9/site-packages/conda_env/cli/main_create.py", line 143, in execute
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/home/miniconda3/lib/python3.9/site-packages/conda_env/installers/conda.py", line 59, in install
unlink_link_transaction.execute()
File "/home/miniconda3/lib/python3.9/site-packages/conda/core/link.py", line 281, in execute
self._execute(tuple(concat(interleave(self.prefix_action_groups.values()))))
File "/home/miniconda3/lib/python3.9/site-packages/conda/core/link.py", line 744, in _execute
raise CondaMultiError(tuple(concatv(
conda.CondaMultiErrorclass: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0
location of failed script: /home/miniconda3/envs/qiime2-2023.5/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==

==> script output <==
stdout:
stderr: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
++ dirname -- /home/miniconda3/envs/qiime2-2023.5/bin/installBiocDataPackage.sh

  • SCRIPT_DIR=/home/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages
  • json=/home/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
    ++ yq '."genomeinfodbdata-1.2.9".fn' /home/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
  • FN='"GenomeInfoDbData_1.2.9.tar.gz"'
  • IFS=
  • read -r value
    ++ yq '."genomeinfodbdata-1.2.9".urls[]' /home/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
  • URLS+=($value)
  • IFS=
  • read -r value
  • URLS+=($value)
  • IFS=
  • read -r value
  • URLS+=($value)
  • IFS=
  • read -r value
    ++ yq '."genomeinfodbdata-1.2.9".md5' /home/miniconda3/envs/qiime2-2023.5/bin/../share/bioconductor-data-packages/dataURLs.json
  • MD5='"7cc138cfb74665fdfa8d1c244eac4879"'
  • STAGING=/home/miniconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9
  • mkdir -p /home/miniconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9
  • TARBALL='/home/miniconda3/envs/qiime2-2023.5/share/genomeinfodbdata-1.2.9/"GenomeInfoDbData_1.2.9.tar.gz"'
  • SUCCESS=0
  • for URL in ${URLS[@]}
    ++ echo '"https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz"'
    ++ tr -d '"'
  • URL=https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
    ++ echo '"7cc138cfb74665fdfa8d1c244eac4879"'
    ++ tr -d '"'
  • MD5=7cc138cfb74665fdfa8d1c244eac4879
  • curl -L https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
    % Total % Received % Xferd Average Speed Time Time Time Current
    Dload Upload Total Spent Left Speed
    100 416 100 416 0 0 3367 0 --:--:-- --:--:-- --:--:-- 3382
    0 0 0 0 0 0 0 0 --:--:-- 0:02:11 --:--:-- 0
    curl: (7) Failed to connect to mghp.osn.xsede.org port 443 after 131408 ms: Couldn't connect to server

return code: 7

kwargs:
{}

: <exception str() failed>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/miniconda3/bin/conda-env", line 7, in
sys.exit(main())
File "/home/miniconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 91, in main
return conda_exception_handler(do_call, args, parser)
File "/home/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1404, in conda_exception_handler
return_value = exception_handler(func, *args, **kwargs)
File "/home/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1117, in call
return self.handle_exception(exc_val, exc_tb)
File "/home/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1148, in handle_exception
return self.handle_application_exception(exc_val, exc_tb)
File "/home/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1162, in handle_application_exception
self._print_conda_exception(exc_val, exc_tb)
File "/home/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1166, in _print_conda_exception
print_conda_exception(exc_val, exc_tb)
File "/home/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1091, in print_conda_exception
stderrlog.error("\n%r\n", exc_val)
File "/home/miniconda3/lib/python3.9/logging/init.py", line 1475, in error
self._log(ERROR, msg, args, **kwargs)
File "/home/miniconda3/lib/python3.9/logging/init.py", line 1589, in _log
self.handle(record)
File "/home/miniconda3/lib/python3.9/logging/init.py", line 1598, in handle
if (not self.disabled) and self.filter(record):
File "/home/miniconda3/lib/python3.9/logging/init.py", line 806, in filter
result = f.filter(record)
File "/home/miniconda3/lib/python3.9/site-packages/conda/gateways/logging.py", line 51, in filter
record.msg = record.msg % new_args
File "/home/miniconda3/lib/python3.9/site-packages/conda/init.py", line 101, in repr
errs.append(e.repr())
File "/home/miniconda3/lib/python3.9/site-packages/conda/init.py", line 58, in repr
return '%s: %s' % (self.class.name, str(self))
File "/home/miniconda3/lib/python3.9/site-packages/conda/init.py", line 62, in str
return str(self.message % self._kwargs)
ValueError: unsupported format character 'T' (0x54) at index 2102

Your support is appreciated!

Hello @Eman. It looks like you might have a similar issue to some other users on the forum. Can you try following the instructions in this post and let me know if it works?

I think the re-installation of Anaconda should fix this issue. However, does removing Anaconda and then re-installing it delete all installed environments since I have different environments for different installed software?

Thanks!

@Eman I believe it will yes. For a less nuclear option, try running the command conda clean --all. That will not remove anything from any environment, but it will remove a bunch of things conda has cached which may help. It is also entirely possible that the people in the other post simply got lucky. The issue here seems to be that a server which hosts some of our 3rd party dependencies is down. It is possible they got lucky and created their environments when the server was up for a while before going back down.

It works now after uninstalling miniconda3 and re-installing it, but of course, this removed all environments with their software. But I am happy it is working now:).

Thank you!

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