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!