mortonjt
commented
3 years ago What version of TF are you using? Chances you have TF=2, which is a no go.
You can verify with python -c 'import tensorflow; print(tensorflow.__version__)'
On Sun, Mar 14, 2021 at 1:47 PM JGADuBose @.***> wrote:
Hello. I have been trying to use Songbird for some differential abundance analyses, but I have been unable to get it to work. I have tried running it through the QIIME2 plug-in on qiime2-2019.7, qiime2-2019.10, and qiime2-2020.6. I have also attempted to run it through an independent songbird environment. I have posted the error I get from the QIIME2 plug-in, but the error I get when running the independent version is similar.
**Plugin error from songbird:
num_classes should be positive, got 0 [[node multinomial/Multinomial (defined at /home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/framework/ops.py:1748) ]]
Original stack trace for 'multinomial/Multinomial': File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/bin/qiime", line 11, in sys.exit(qiime()) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 829, in call return self.main(args, kwargs) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 610, in invoke return callback(args, kwargs) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call results = action(arguments) File "", line 2, in multinomial File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable output_types, provenance) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor output_views = self._callable(*view_args) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/songbird/q2/_method.py", line 63, in multinomial model(session, trainX, trainY, testX, testY) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/songbird/multinomial.py", line 70, in call batch_ids = tf.multinomial(tf.ones([1, self.N]), self.batch_size) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/util/deprecation.py", line 324, in new_func return func(args, *kwargs) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/ops/random_ops.py", line 361, in multinomial return multinomial_categorical_impl(logits, num_samples, output_dtype, seed) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/ops/random_ops.py", line 397, in multinomial_categorical_impl logits, num_samples, seed=seed1, seed2=seed2, output_dtype=dtype) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/ops/gen_random_ops.py", line 85, in multinomial seed2=seed2, output_dtype=output_dtype, name=name) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/framework/op_def_library.py", line 794, in _apply_op_helper op_def=op_def) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/util/deprecation.py", line 507, in new_func return func(args,
kwargs) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/framework/ops.py", line 3357, in create_op attrs, op_def, compute_device) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/framework/ops.py", line 3426, in _create_op_internal op_def=op_def) File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/framework/ops.py", line 1748, in init self._traceback = tf_stack.extract_stack()
I have a collaborator who has also attempted to run the stand-alone Songbird, and he has received the following error: ModuleNotFoundError: No module named 'tensorflow.python.types
I have tried adjusting the --min-feature-count and the --min-sample-count so that samples would not be filtered as strictly, just incase the problem was an empty dataset. However, that does not seem to be the issue.
Any advice or help would be greatly appreciated. I am a relatively experienced QIIME2 user. However, this is my first time using Songbird. I noticed that a comment that has stated that tensorflow will be ditched in the next update (which I suspect is the source of our issues), and that this update is in development, so I hope this post doesn't sound pushy or redundant. I'm relatively new to the community and am still figuring a lot of things out. Any insight would be appreciated.
Thank you!
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JGADuBose
Hello. I have been trying to use Songbird for some differential abundance analyses, but I have been unable to get it to work. I have tried running it through the QIIME2 plug-in on qiime2-2019.7, qiime2-2019.10, and qiime2-2020.6. I have also attempted to run it through an independent songbird environment. I have posted the error I get from the QIIME2 plug-in, but the error I get when running the independent version is similar.
Plugin error from songbird:
num_classes should be positive, got 0 [[node multinomial/Multinomial (defined at /home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/framework/ops.py:1748) ]]
Original stack trace for 'multinomial/Multinomial': File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/bin/qiime", line 11, in
sys.exit(qiime())
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 829, in call
return self.main(args, kwargs)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/click/core.py", line 610, in invoke
return callback(args, kwargs)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(arguments)
File "", line 2, in multinomial
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in _callableexecutor
output_views = self._callable(view_args)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/songbird/q2/_method.py", line 63, in multinomial
model(session, trainX, trainY, testX, testY)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/songbird/multinomial.py", line 70, in call
batch_ids = tf.multinomial(tf.ones([1, self.N]), self.batch_size)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/util/deprecation.py", line 324, in new_func
return func(*args, *kwargs)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/ops/random_ops.py", line 361, in multinomial
return multinomial_categorical_impl(logits, num_samples, output_dtype, seed)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/ops/random_ops.py", line 397, in multinomial_categorical_impl
logits, num_samples, seed=seed1, seed2=seed2, output_dtype=dtype)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/ops/gen_random_ops.py", line 85, in multinomial
seed2=seed2, output_dtype=output_dtype, name=name)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/framework/op_def_library.py", line 794, in _apply_op_helper
op_def=op_def)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/util/deprecation.py", line 507, in new_func
return func(args, kwargs)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/framework/ops.py", line 3357, in create_op
attrs, op_def, compute_device)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/framework/ops.py", line 3426, in _create_op_internal
op_def=op_def)
File "/home/jdubose3/miniconda2/envs/qiime2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/framework/ops.py", line 1748, in init
self._traceback = tf_stack.extract_stack()
I have a collaborator who has also attempted to run the stand-alone Songbird, and he has received the following error: ModuleNotFoundError: No module named 'tensorflow.python.types
I have tried adjusting the --min-feature-count and the --min-sample-count so that samples would not be filtered as strictly, just incase the problem was an empty dataset. However, that does not seem to be the issue.
Any advice or help would be greatly appreciated. I am a relatively experienced QIIME2 user. However, this is my first time using Songbird. I noticed that a comment that has stated that tensorflow will be ditched in the next update (which I suspect is the source of our issues), and that this update is in development, so I hope this post doesn't sound pushy or redundant. I'm relatively new to the community and am still figuring a lot of things out. Any insight would be appreciated.
Thank you!