search

biocore / mmvec

Neural networks for microbe-metabolite interaction analysis
BSD 3-Clause "New" or "Revised" License
119 stars 51 forks source link

Trouble running mmvec/Tensorflow #150

Closed CarlaCristinaUranga closed 4 years ago

CarlaCristinaUranga commented 4 years ago

Hi,

I am on an institutional computer, in case this is the issue, but I am not able to run mmvec on my computer. I am totally new to this plugin so please forgive me if this is an obvious issue. When using the qiime2 mmvec plug in, I use the following command:

qiime mmvec paired-omics \ --i-microbes OTU16s.qza \ --i-metabolites OTUprot.qza \ --p-learning-rate 1e-3 \ --o-conditionals ranks.qza \ --o-conditional-biplot biplot.qza

However, I get this error (thank you in advance!):

Traceback (most recent call last): File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/bin/qiime", line 11, in sys.exit(qiime()) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 829, in call return self.main(*args, *kwargs) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 1254, in invoke cmd_name, cmd, args = self.resolve_command(ctx, args) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 1297, in resolve_command cmd = self.get_command(ctx, cmd_name) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py", line 100, in get_command plugin = self._plugin_lookup[name] File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py", line 76, in _plugin_lookup import q2cli.core.cache File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py", line 406, in CACHE = DeploymentCache() File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py", line 61, in init self._state = self._get_cached_state(refresh=refresh) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state self._cache_current_state(current_requirements) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py", line 200, in _cache_current_state state = self._get_current_state() File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py", line 238, in _get_current_state plugin_manager = qiime2.sdk.PluginManager() File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 54, in new self._init(add_plugins=add_plugins) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 81, in _init plugin = entry_point.load() File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/pkg_resources/init.py", line 2471, in load self.require(args, **kwargs) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/pkg_resources/init.py", line 2494, in require items = working_set.resolve(reqs, env, installer, extras=self.extras) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/pkg_resources/init.py", line 790, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (tensorflow-estimator 2.2.0 (/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages), Requirement.parse('tensorflow-estimator==1.15.1'), {'tensorflow'})

mortonjt commented 4 years ago

Hi, it looks like you have tensorflow2 instead, which MMvec is not compatible with. It is recommended to downgrade to tensorflow=1.15. You may have to either run this in an older qiime2 environment <2020.6, or install a separate conda environment with the standalone version.

On Mon, Oct 19, 2020 at 10:05 PM Carla Uranga notifications@github.com wrote:

Hi,

I am on an institutional computer, in case this is the issue, but I am not able to run mmvec on my computer. I am totally new to this plugin so please forgive me if this is an obvious issue. When using the qiime2 mmvec plug in, I use the following command:

qiime mmvec paired-omics --i-microbes OTU16s.qza --i-metabolites OTUprot.qza --p-learning-rate 1e-3 --o-conditionals ranks.qza --o-conditional-biplot biplot.qza

However, I get this error (thank you in advance!):

Traceback (most recent call last): File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/bin/qiime", line 11, in sys.exit(qiime()) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 829, in call return self.main(*args, *kwargs) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 1254, in invoke cmd_name, cmd, args = self.resolve_command(ctx, args) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/click/core.py", line 1297, in resolve_command cmd = self.get_command(ctx, cmd_name) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py", line 100, in get_command plugin = self._plugin_lookup[name] File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py", line 76, in _plugin_lookup import q2cli.core.cache File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py", line 406, in CACHE = DeploymentCache() File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py", line 61, in init self._state = self._get_cached_state(refresh=refresh) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state self._cache_current_state(current_requirements) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py", line 200, in _cache_current_state state = self._get_current_state() File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/core/cache.py", line 238, in _get_current_state plugin_manager = qiime2.sdk.PluginManager() File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 54, in new self._init(add_plugins=add_plugins) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/plugin_manager.py", line 81, in _init plugin = entry_point.load() File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/pkg_resources/ init.py", line 2471, in load self.require(args, *kwargs) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/pkg_resources/ init.py", line 2494, in require items = working_set.resolve(reqs, env, installer, extras=self.extras) File "/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/pkg_resources/ init*.py", line 790, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.ContextualVersionConflict: (tensorflow-estimator 2.2.0 (/Users/curanga/opt/anaconda3/envs/qiime2-2020.8/lib/python3.6/site-packages), Requirement.parse('tensorflow-estimator==1.15.1'), {'tensorflow'})

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/biocore/mmvec/issues/150, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA75VXMABY2VLCH3KYOBGFLSLUEBHANCNFSM4SXOPOWA .

CarlaCristinaUranga commented 4 years ago

Wow thank you for your fast reply! I am having trouble with the standalone version. I would love to use the standalone version, but I get this error:

Traceback (most recent call last): File "/Users/curanga/opt/anaconda3/envs/mmvec/bin/mmvec", line 17, in import tensorflow as tf File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow/init.py", line 99, in from tensorflow_core import * File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_core/init.py", line 36, in from tensorflow._api.v1 import compat File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_core/_api/v1/compat/init.py", line 23, in from tensorflow._api.v1.compat import v1 File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_core/_api/v1/compat/v1/init.py", line 672, in from tensorflow_estimator.python.estimator.api._v1 import estimator File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_estimator/init.py", line 10, in from tensorflow_estimator._api.v1 import estimator File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_estimator/_api/v1/estimator/init.py", line 10, in from tensorflow_estimator._api.v1.estimator import experimental File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_estimator/_api/v1/estimator/experimental/init.py", line 10, in from tensorflow_estimator.python.estimator.canned.dnn import dnn_logit_fn_builder File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_estimator/python/estimator/canned/dnn.py", line 33, in from tensorflow_estimator.python.estimator import estimator File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_estimator/python/estimator/estimator.py", line 53, in from tensorflow_estimator.python.estimator import util as estimator_util File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_estimator/python/estimator/util.py", line 75, in class _DatasetInitializerHook(tf.compat.v1.train.SessionRunHook): AttributeError: module 'tensorflow' has no attribute 'compat'

mortonjt commented 4 years ago

Something is weird with the install - did you use pip or conda? Did you create a separate conda environment as outlined in the readme?

On Mon, Oct 19, 2020 at 10:17 PM Carla Uranga notifications@github.com wrote:

Wow thank you for your fast reply! I am having trouble with the standalone version. I would love to use the standalone version, but I get this error:

Traceback (most recent call last): File "/Users/curanga/opt/anaconda3/envs/mmvec/bin/mmvec", line 17, in import tensorflow as tf File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow/ init.py", line 99, in from tensorflow_core import File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_core/ init.py", line 36, in from tensorflow._api.v1 import compat File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_core/_api/v1/compat/ init.py", line 23, in from tensorflow._api.v1.compat import v1 File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_core/_api/v1/compat/v1/ init.py", line 672, in from tensorflow_estimator.python.estimator.api._v1 import estimator File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_estimator/ init.py", line 10, in from tensorflow_estimator._api.v1 import estimator File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_estimator/_api/v1/estimator/ init.py", line 10, in from tensorflow_estimator._api.v1.estimator import experimental File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_estimator/_api/v1/estimator/experimental/ init*.py", line 10, in from tensorflow_estimator.python.estimator.canned.dnn import dnn_logit_fn_builder File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_estimator/python/estimator/canned/dnn.py", line 33, in from tensorflow_estimator.python.estimator import estimator File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_estimator/python/estimator/estimator.py", line 53, in from tensorflow_estimator.python.estimator import util as estimator_util File "/Users/curanga/opt/anaconda3/envs/mmvec/lib/python3.7/site-packages/tensorflow_estimator/python/estimator/util.py", line 75, in class _DatasetInitializerHook(tf.compat.v1.train.SessionRunHook): AttributeError: module 'tensorflow' has no attribute 'compat'

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/biocore/mmvec/issues/150#issuecomment-712577908, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA75VXJTVKIO5ELM4OESJYDSLUFO7ANCNFSM4SXOPOWA .

CarlaCristinaUranga commented 4 years ago

Hi so I started with a fresh install using pip install mmvec and this is the output:

(base) mgardnerlt-osx:FINAL_PROTEOMICS curanga$ mmvec paired-omics \

    --microbe-file OTU16s.biom \
    --metabolite-file OTUprot.biom \
    --summary-dir summary

/Users/curanga/opt/anaconda3/lib/python3.7/site-packages/biom_format-2.1.8.dev0-py3.7-macosx-10.9-x86_64.egg/biom/table.py:4068: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version. Use a regular DataFrame whose columns are SparseArrays instead.

See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.

return constructor(mat, index=index, columns=columns) /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/pandas/core/sparse/frame.py:257: FutureWarning: SparseSeries is deprecated and will be removed in a future version. Use a Series with sparse values instead.

>>> series = pd.Series(pd.SparseArray(...))

See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.

sparse_index=BlockIndex(N, blocs, blens), /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/pandas/core/generic.py:4583: FutureWarning: SparseSeries is deprecated and will be removed in a future version. Use a Series with sparse values instead.

>>> series = pd.Series(pd.SparseArray(...))

See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.

return self._constructor(new_data).finalize(self) /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/pandas/core/sparse/frame.py:854: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version. Use a regular DataFrame whose columns are SparseArrays instead.

See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.

default_kind=self._default_kind, /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/pandas/core/frame.py:3471: FutureWarning: SparseSeries is deprecated and will be removed in a future version. Use a Series with sparse values instead.

>>> series = pd.Series(pd.SparseArray(...))

See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.

return klass(values, index=self.index, name=items, fastpath=True) /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/pandas/core/sparse/frame.py:785: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version. Use a regular DataFrame whose columns are SparseArrays instead.

See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.

return self._constructor(new_arrays, index=index, columns=columns).finalize( /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/pandas/core/ops/init.py:1641: FutureWarning: SparseSeries is deprecated and will be removed in a future version. Use a Series with sparse values instead.

>>> series = pd.Series(pd.SparseArray(...))

See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.

return self._constructor(new_values, index=self.index, name=self.name) /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/pandas/core/sparse/frame.py:339: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version. Use a regular DataFrame whose columns are SparseArrays instead.

See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.

default_fill_value=self.default_fill_value, /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/pandas/core/generic.py:6289: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version. Use a regular DataFrame whose columns are SparseArrays instead.

See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.

return self._constructor(new_data).finalize(self) /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/pandas/core/generic.py:5884: FutureWarning: SparseSeries is deprecated and will be removed in a future version. Use a Series with sparse values instead.

>>> series = pd.Series(pd.SparseArray(...))

See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.

return self._constructor(new_data).finalize(self) /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/pandas/core/generic.py:3606: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version. Use a regular DataFrame whose columns are SparseArrays instead.

See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.

result = self._constructor(new_data).finalize(self) WARNING:tensorflow:From /Users/curanga/opt/anaconda3/bin/mmvec:160: The name tf.ConfigProto is deprecated. Please use tf.compat.v1.ConfigProto instead.

WARNING:tensorflow:From /Users/curanga/opt/anaconda3/bin/mmvec:161: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.

2020-10-19 21:58:19.943709: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA 2020-10-19 21:58:19.976740: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x7f9a5b7428b0 initialized for platform Host (this does not guarantee that XLA will be used). Devices: 2020-10-19 21:58:19.976759: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version WARNING:tensorflow:From /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/mmvec/multimodal.py:90: The name tf.log is deprecated. Please use tf.math.log instead.

WARNING:tensorflow:From /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/mmvec/multimodal.py:91: multinomial (from tensorflow.python.ops.random_ops) is deprecated and will be removed in a future version. Instructions for updating: Use tf.random.categorical instead. WARNING:tensorflow:From /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/mmvec/multimodal.py:102: The name tf.random_normal is deprecated. Please use tf.random.normal instead.

WARNING:tensorflow:From /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/mmvec/multimodal.py:118: Normal.init (from tensorflow.python.ops.distributions.normal) is deprecated and will be removed after 2019-01-01. Instructions for updating: The TensorFlow Distributions library has moved to TensorFlow Probability (https://github.com/tensorflow/probability). You should update all references to use tfp.distributions instead of tf.distributions. WARNING:tensorflow:From /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/tensorflow_core/python/ops/distributions/normal.py:160: Distribution.init (from tensorflow.python.ops.distributions.distribution) is deprecated and will be removed after 2019-01-01. Instructions for updating: The TensorFlow Distributions library has moved to TensorFlow Probability (https://github.com/tensorflow/probability). You should update all references to use tfp.distributions instead of tf.distributions. WARNING:tensorflow:From /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/mmvec/multimodal.py:135: Multinomial.init (from tensorflow.python.ops.distributions.multinomial) is deprecated and will be removed after 2019-01-01. Instructions for updating: The TensorFlow Distributions library has moved to TensorFlow Probability (https://github.com/tensorflow/probability). You should update all references to use tfp.distributions instead of tf.distributions. WARNING:tensorflow:From /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/mmvec/multimodal.py:183: The name tf.summary.scalar is deprecated. Please use tf.compat.v1.summary.scalar instead.

WARNING:tensorflow:From /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/mmvec/multimodal.py:185: The name tf.summary.histogram is deprecated. Please use tf.compat.v1.summary.histogram instead.

WARNING:tensorflow:From /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/mmvec/multimodal.py:189: The name tf.summary.merge_all is deprecated. Please use tf.compat.v1.summary.merge_all instead.

WARNING:tensorflow:From /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/mmvec/multimodal.py:191: The name tf.summary.FileWriter is deprecated. Please use tf.compat.v1.summary.FileWriter instead.

WARNING:tensorflow:From /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/mmvec/multimodal.py:196: The name tf.train.AdamOptimizer is deprecated. Please use tf.compat.v1.train.AdamOptimizer instead.

WARNING:tensorflow:From /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/tensorflow_core/python/ops/clip_ops.py:301: where (from tensorflow.python.ops.array_ops) is deprecated and will be removed in a future version. Instructions for updating: Use tf.where in 2.0, which has the same broadcast rule as np.where WARNING:tensorflow:From /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/mmvec/multimodal.py:206: The name tf.global_variables_initializer is deprecated. Please use tf.compat.v1.global_variables_initializer instead.

WARNING:tensorflow:From /Users/curanga/opt/anaconda3/lib/python3.7/site-packages/mmvec/multimodal.py:243: The name tf.train.Saver is deprecated. Please use tf.compat.v1.train.Saver instead.

0it [00:00, ?it/s] Traceback (most recent call last): File "/Users/curanga/opt/anaconda3/bin/mmvec", line 233, in mmvec() File "/Users/curanga/opt/anaconda3/lib/python3.7/site-packages/click/core.py", line 764, in call return self.main(args, kwargs) File "/Users/curanga/opt/anaconda3/lib/python3.7/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/Users/curanga/opt/anaconda3/lib/python3.7/site-packages/click/core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/Users/curanga/opt/anaconda3/lib/python3.7/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, ctx.params) File "/Users/curanga/opt/anaconda3/lib/python3.7/site-packages/click/core.py", line 555, in invoke return callback(args, **kwargs) File "/Users/curanga/opt/anaconda3/bin/mmvec", line 176, in paired_omics checkpoint_interval=checkpoint_interval) File "/Users/curanga/opt/anaconda3/lib/python3.7/site-packages/mmvec/multimodal.py", line 274, in fit self.U = rU UnboundLocalError: local variable 'rU' referenced before assignment

mortonjt commented 4 years ago

ok cool. So it looks like you are able to get something installed :) Now it seems to be more of a problem of running it. This type of error occurs when everything gets filtered out. This can occur for extremely small sample sizes (the min-feature-count is default 10, if you have less than 10 samples MMvec will have problems).

CarlaCristinaUranga commented 4 years ago

Ugh really? I have 9 samples! Bummer! So do you have any suggestions for how to deal with small datasets? This is a huge problem! Thank you for your honesty.

Best, Carla

On Tue, Oct 20, 2020, 7:55 AM Jamie Morton notifications@github.com wrote:

ok cool. So it looks like you are able to get something installed :) Now it seems to be more of a problem of running it. This type of error occurs when everything gets filtered out. This can occur for extremely small sample sizes (the min-feature-count is default 10, if you have less than 10 samples MMvec will have problems).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biocore/mmvec/issues/150#issuecomment-712912627, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFK6HC7VPTUVEHRIEAKHGO3SLWQFLANCNFSM4SXOPOWA .

mortonjt commented 4 years ago

sorry, we can't do much with 9 samples with mmvec. I actually don't know of any program that can currently do it, with the exception of highly customized Bayesian inference. The tricky thing with small datasets is you basically need to know the exact answer ahead of time, and are using the data just to verify if your answer is correct.

CarlaCristinaUranga commented 4 years ago

Ok, thank you! Well, using qiime2-2020.6 I get this error, is it also due to the small dataset?:

(qiime2-2020.6) mgardnerlt-osx:FINAL_PROTEOMICS curanga$ qiime mmvec paired-omics \

    --i-microbes OTU16s.qza \

    --i-metabolites OTUprot.qza \

    --p-learning-rate 1e-3 \

    --o-conditionals ranks.qza \

    --o-conditional-biplot biplot.qza

Plugin error from mmvec:

Debug info has been saved to /var/folders/_9/dvqyx4xcx3wwstdv74lh0xw00003ms/T/qiime2-q2cli-err-o96m83cq.log

On Tue, Oct 20, 2020 at 10:06 AM Jamie Morton notifications@github.com wrote:

sorry, we can't do much with 9 samples with mmvec. I actually don't know of any program that can currently do it, with the exception of highly customized Bayesian inference. The tricky thing with small datasets is you basically need to know the exact answer ahead of time, and are using the data just to verify if your answer is correct.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biocore/mmvec/issues/150#issuecomment-713008335, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFK6HC4UL7J4OESY4RFN3STSLW7THANCNFSM4SXOPOWA .

mortonjt commented 4 years ago

yes, its the same error.

On Tue, Oct 20, 2020 at 11:14 AM Carla Uranga notifications@github.com wrote:

Ok, thank you! Well, using qiime2-2020.6 I get this error, is it also due to the small dataset?:

(qiime2-2020.6) mgardnerlt-osx:FINAL_PROTEOMICS curanga$ qiime mmvec paired-omics \

--i-microbes OTU16s.qza \

--i-metabolites OTUprot.qza \

--p-learning-rate 1e-3 \

--o-conditionals ranks.qza \

--o-conditional-biplot biplot.qza

Plugin error from mmvec:

  • local variable 'rU' referenced before assignment*

*Debug info has been saved to

/var/folders/_9/dvqyx4xcx3wwstdv74lh0xw00003ms/T/qiime2-q2cli-err-o96m83cq.log*

On Tue, Oct 20, 2020 at 10:06 AM Jamie Morton notifications@github.com wrote:

sorry, we can't do much with 9 samples with mmvec. I actually don't know of any program that can currently do it, with the exception of highly customized Bayesian inference. The tricky thing with small datasets is you basically need to know the exact answer ahead of time, and are using the data just to verify if your answer is correct.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biocore/mmvec/issues/150#issuecomment-713008335, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AFK6HC4UL7J4OESY4RFN3STSLW7THANCNFSM4SXOPOWA

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/biocore/mmvec/issues/150#issuecomment-713012848, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA75VXKPPBPSFKN7KFHMETDSLXAQJANCNFSM4SXOPOWA .

CarlaCristinaUranga commented 4 years ago

Ok, I will research other options for co-occurrence analysis for small datasets. No more mmvec for me right now. Thank you Jamie you are very much appreciated.

Best wishes, Carla

On Tue, Oct 20, 2020 at 10:19 AM Jamie Morton notifications@github.com wrote:

yes, its the same error.

On Tue, Oct 20, 2020 at 11:14 AM Carla Uranga notifications@github.com wrote:

Ok, thank you! Well, using qiime2-2020.6 I get this error, is it also due to the small dataset?:

(qiime2-2020.6) mgardnerlt-osx:FINAL_PROTEOMICS curanga$ qiime mmvec paired-omics \

--i-microbes OTU16s.qza \

--i-metabolites OTUprot.qza \

--p-learning-rate 1e-3 \

--o-conditionals ranks.qza \

--o-conditional-biplot biplot.qza

Plugin error from mmvec:

  • local variable 'rU' referenced before assignment*

*Debug info has been saved to

/var/folders/_9/dvqyx4xcx3wwstdv74lh0xw00003ms/T/qiime2-q2cli-err-o96m83cq.log*

On Tue, Oct 20, 2020 at 10:06 AM Jamie Morton notifications@github.com wrote:

sorry, we can't do much with 9 samples with mmvec. I actually don't know of any program that can currently do it, with the exception of highly customized Bayesian inference. The tricky thing with small datasets is you basically need to know the exact answer ahead of time, and are using the data just to verify if your answer is correct.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biocore/mmvec/issues/150#issuecomment-713008335, or unsubscribe <

https://github.com/notifications/unsubscribe-auth/AFK6HC4UL7J4OESY4RFN3STSLW7THANCNFSM4SXOPOWA

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/biocore/mmvec/issues/150#issuecomment-713012848, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AA75VXKPPBPSFKN7KFHMETDSLXAQJANCNFSM4SXOPOWA

.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/biocore/mmvec/issues/150#issuecomment-713015500, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFK6HC4SCJLSUEIAOU4ZINLSLXBA5ANCNFSM4SXOPOWA .