Comments (4)
Hi @chengyou96. Can you share the output of deepbgc info
?
from deepbgc.
Sure. Here it is:
INFO 22/03 16:06:09 Loading model from: /Users/cynthiayo/Library/Application Support/deepbgc/data/0.1.0/detector/deepbgc.pkl
from deepbgc.
Did you have solved this problem yet?
from deepbgc.
having the same issue here.
here is the output of deepbgc info
_____ ____ ____ ____
| _ \ ___ ___ ____ | __ ) / ___) / ___)
| | \ \/ _ \/ _ \ _ \| _ \ | | _ | |
| |_/ / __/ __/ |_) | |_) || |_| || |___
|____/ \___|\___| ___/|____/ \____| \____)
=================|_|===== version 0.1.18 =====
INFO 29/01 14:08:32 Available data files: ['Pfam-A.31.0.hmm.h3m', 'Pfam-A.31.0.hmm', 'Pfam-A.31.0.hmm.h3i', 'Pfam-A.31.0.hmm.h3p', 'Pfam-A.31.0.hmm.h3f', 'Pfam-A.31.0.clans.tsv']
INFO 29/01 14:08:32 ================================================================================
INFO 29/01 14:08:32 Available detectors: ['clusterfinder_original', 'clusterfinder_geneborder', 'deepbgc', 'clusterfinder_retrained']
INFO 29/01 14:08:32 --------------------------------------------------------------------------------
INFO 29/01 14:08:32 Model: clusterfinder_original
INFO 29/01 14:08:32 Loading model from: /home/karencgs/.local/share/deepbgc/data/0.1.0/detector/clusterfinder_original.pkl
INFO 29/01 14:08:33 Type: ClusterFinderHMM
INFO 29/01 14:08:33 Version: 0.1.0
INFO 29/01 14:08:33 Timestamp: 1551449904.5101252 (2019-03-01T09:18:24.510125)
INFO 29/01 14:08:33 --------------------------------------------------------------------------------
INFO 29/01 14:08:33 Model: clusterfinder_geneborder
INFO 29/01 14:08:33 Loading model from: /home/karencgs/.local/share/deepbgc/data/0.1.0/detector/clusterfinder_geneborder.pkl
INFO 29/01 14:08:33 Type: GeneBorderHMM
INFO 29/01 14:08:33 Version: 0.1.0
INFO 29/01 14:08:33 Timestamp: 1551449863.1564941 (2019-03-01T09:17:43.156494)
INFO 29/01 14:08:33 --------------------------------------------------------------------------------
INFO 29/01 14:08:33 Model: deepbgc
INFO 29/01 14:08:33 Loading model from: /home/karencgs/.local/share/deepbgc/data/0.1.0/detector/deepbgc.pkl
Using TensorFlow backend.
WARNING 29/01 14:08:44 From /home/karencgs/deepbcg/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:3733: calling dropout (from tensorflow.python.ops.nn_ops) with keep_prob is deprecated and will be removed in a future version.
Instructions for updating:
Please use `rate` instead of `keep_prob`. Rate should be set to `rate = 1 - keep_prob`.
WARNING 29/01 14:08:44 From /home/karencgs/deepbcg/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:207: The name tf.global_variables is deprecated. Please use tf.compat.v1.global_variables instead.
WARNING 29/01 14:08:44 From /home/karencgs/deepbcg/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:216: The name tf.is_variable_initialized is deprecated. Please use tf.compat.v1.is_variable_initialized instead.
WARNING 29/01 14:08:45 From /home/karencgs/deepbcg/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:223: The name tf.variables_initializer is deprecated. Please use tf.compat.v1.variables_initializer instead.
INFO 29/01 14:08:45 Type: KerasRNN
INFO 29/01 14:08:45 Version: 0.1.0
INFO 29/01 14:08:45 Timestamp: 1551305667.986168 (2019-02-27T17:14:27.986168)
INFO 29/01 14:08:45 --------------------------------------------------------------------------------
INFO 29/01 14:08:45 Model: clusterfinder_retrained
INFO 29/01 14:08:45 Loading model from: /home/karencgs/.local/share/deepbgc/data/0.1.0/detector/clusterfinder_retrained.pkl
INFO 29/01 14:08:45 Type: DiscreteHMM
INFO 29/01 14:08:45 Version: 0.1.0
INFO 29/01 14:08:45 Timestamp: 1551449925.734045 (2019-03-01T09:18:45.734045)
INFO 29/01 14:08:45 ================================================================================
INFO 29/01 14:08:45 Available classifiers: ['product_class', 'product_activity']
INFO 29/01 14:08:45 --------------------------------------------------------------------------------
INFO 29/01 14:08:45 Model: product_class
INFO 29/01 14:08:45 Loading model from: /home/karencgs/.local/share/deepbgc/data/0.1.0/classifier/product_class.pkl
/home/karencgs/deepbcg/lib/python3.7/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.ensemble.forest module is deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.ensemble. Anything that cannot be imported from sklearn.ensemble is now part of the private API.
warnings.warn(message, FutureWarning)
/home/karencgs/deepbcg/lib/python3.7/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.tree.tree module is deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.tree. Anything that cannot be imported from sklearn.tree is now part of the private API.
warnings.warn(message, FutureWarning)
/home/karencgs/deepbcg/lib/python3.7/site-packages/sklearn/base.py:334: UserWarning: Trying to unpickle estimator DecisionTreeClassifier from version 0.18.2 when using version 0.23.0. This might lead to breaking code or invalid results. Use at your own risk.
UserWarning)
/home/karencgs/deepbcg/lib/python3.7/site-packages/sklearn/base.py:334: UserWarning: Trying to unpickle estimator RandomForestClassifier from version 0.18.2 when using version 0.23.0. This might lead to breaking code or invalid results. Use at your own risk.
UserWarning)
INFO 29/01 14:08:45 Type: RandomForestClassifier
INFO 29/01 14:08:45 Version: 0.1.0
INFO 29/01 14:08:45 Timestamp: 1551781410.019103 (2019-03-05T05:23:30.019103)
INFO 29/01 14:08:45 --------------------------------------------------------------------------------
INFO 29/01 14:08:45 Model: product_activity
INFO 29/01 14:08:45 Loading model from: /home/karencgs/.local/share/deepbgc/data/0.1.0/classifier/product_activity.pkl
INFO 29/01 14:08:45 Type: RandomForestClassifier
INFO 29/01 14:08:45 Version: 0.1.0
INFO 29/01 14:08:45 Timestamp: 1551781433.886473 (2019-03-05T05:23:53.886473)
INFO 29/01 14:08:45 ================================================================================
INFO 29/01 14:08:45 All OK
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Related Issues (20)
- Where I can get the code of e-deepBGC? HOT 1
- bug in get_proteins_by_id affecting pfam annotator HOT 4
- Visualization HOT 1
- run Deepbgc in fungal genomes HOT 1
- WARNING: Tensor flow backened message when running deepbgc info into the CLI HOT 1
- how to get a cluster?
- installation error HOT 1
- how to create negative samples? HOT 1
- fit_generator
- what "inhibitor" means???
- Could deepBGC be used for special gene clusters?
- Hmmer and Prodigal Package Access Problem HOT 1
- Bugs for protein input HOT 1
- running "deepbgc info" issue
- Use https instead of ftp protocol for Pfam database download HOT 1
- Looking for individual genes
- ImportError: Missing required dependencies ['numpy'] HOT 1
- User Warning
- deepbgc info crash - same as Issue #39
- ValueError: End location (8780) must be greater than or equal to start location (9428)
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from deepbgc.