DeepBGC failed with Exception: Unexpected error detecting protein domains using HMMER hmmscan
Bollie15 opened this issue · comments
Hi, I have some problems about using DeepBGC to identify the BGCs in Mycobacterium tuberculosis H37Rv (high GC Gram+).
Here is my DeepBGC version information:
(base) mima@123456:~/BGC/jieheganjun$ deepbgc info
_____ ____ ____ ____
| _ \ ___ ___ ____ | __ ) / ___) / ___)
| | \ \/ _ \/ _ \ _ \| _ \ | | _ | |
| |_/ / __/ __/ |_) | |_) || |_| || |___
|____/ \___|\___| ___/|____/ \____| \____)
=================|_|===== version 0.1.26 =====
INFO 08/04 16:55:44 Available data files: ['Pfam-A.31.0.hmm', 'Pfam-A.31.0.hmm.h3f', 'Pfam-A.31.0.hmm.h3m', 'Pfam-A.31.0.hmm.h3i', 'Pfam-A.31.0.clans.tsv', 'Pfam-A.31.0.hmm.h3p']
INFO 08/04 16:55:44 ================================================================================
INFO 08/04 16:55:44 Available detectors: ['clusterfinder_retrained', 'clusterfinder_original', 'deepbgc', 'product_class', 'product_activity', 'clusterfinder_geneborder']
INFO 08/04 16:55:44 --------------------------------------------------------------------------------
INFO 08/04 16:55:44 Model: clusterfinder_retrained
INFO 08/04 16:55:44 Loading model from: /home/mima/.local/share/deepbgc/data/0.1.0/detector/clusterfinder_retrained.pkl
WARNING 08/04 16:55:44 Model not supported: ('Package "hmmlearn" needs to be installed to run ClusterFinder HMM. ', 'Install extra dependencies using: \n pip install "deepbgc[hmm]"')
INFO 08/04 16:55:44 --------------------------------------------------------------------------------
INFO 08/04 16:55:44 Model: clusterfinder_original
INFO 08/04 16:55:44 Loading model from: /home/mima/.local/share/deepbgc/data/0.1.0/detector/clusterfinder_original.pkl
WARNING 08/04 16:55:44 Model not supported: ('Package "hmmlearn" needs to be installed to run ClusterFinder HMM. ', 'Install extra dependencies using: \n pip install "deepbgc[hmm]"')
INFO 08/04 16:55:44 --------------------------------------------------------------------------------
INFO 08/04 16:55:44 Model: deepbgc
INFO 08/04 16:55:44 Loading model from: /home/mima/.local/share/deepbgc/data/0.1.0/detector/deepbgc.pkl
Using TensorFlow backend.
WARNING 08/04 16:55:49 From /home/mima/miniconda3/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version.
Instructions for updating:
Colocations handled automatically by placer.
WARNING 08/04 16:55:49 From /home/mima/miniconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:3445: 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`.
INFO 08/04 16:55:50 Type: KerasRNN
INFO 08/04 16:55:50 Version: 0.1.0
INFO 08/04 16:55:50 Timestamp: 1551305667.986168 (2019-02-28T06:14:27.986168)
INFO 08/04 16:55:50 --------------------------------------------------------------------------------
INFO 08/04 16:55:50 Model: product_class
INFO 08/04 16:55:50 Loading model from: /home/mima/.local/share/deepbgc/data/0.1.0/detector/product_class.pkl
/home/mima/miniconda3/lib/python3.7/site-packages/sklearn/base.py:306: UserWarning: Trying to unpickle estimator DecisionTreeClassifier from version 0.18.2 when using version 0.21.3. This might lead to breaking code or invalid results. Use at your own risk.
UserWarning)
/home/mima/miniconda3/lib/python3.7/site-packages/sklearn/base.py:306: UserWarning: Trying to unpickle estimator RandomForestClassifier from version 0.18.2 when using version 0.21.3. This might lead to breaking code or invalid results. Use at your own risk.
UserWarning)
INFO 08/04 16:55:50 Type: RandomForestClassifier
INFO 08/04 16:55:50 Version: 0.1.0
INFO 08/04 16:55:50 Timestamp: 1551781410.019103 (2019-03-05T18:23:30.019103)
INFO 08/04 16:55:50 --------------------------------------------------------------------------------
INFO 08/04 16:55:50 Model: product_activity
INFO 08/04 16:55:50 Loading model from: /home/mima/.local/share/deepbgc/data/0.1.0/detector/product_activity.pkl
INFO 08/04 16:55:50 Type: RandomForestClassifier
INFO 08/04 16:55:50 Version: 0.1.0
INFO 08/04 16:55:50 Timestamp: 1551781433.886473 (2019-03-05T18:23:53.886473)
INFO 08/04 16:55:50 --------------------------------------------------------------------------------
INFO 08/04 16:55:50 Model: clusterfinder_geneborder
INFO 08/04 16:55:50 Loading model from: /home/mima/.local/share/deepbgc/data/0.1.0/detector/clusterfinder_geneborder.pkl
WARNING 08/04 16:55:50 Model not supported: ('Package "hmmlearn" needs to be installed to run ClusterFinder HMM. ', 'Install extra dependencies using: \n pip install "deepbgc[hmm]"')
INFO 08/04 16:55:50 ================================================================================
INFO 08/04 16:55:50 Available classifiers: ['product_class', 'product_activity']
INFO 08/04 16:55:50 --------------------------------------------------------------------------------
INFO 08/04 16:55:50 Model: product_class
INFO 08/04 16:55:50 Loading model from: /home/mima/.local/share/deepbgc/data/0.1.0/classifier/product_class.pkl
INFO 08/04 16:55:50 Type: RandomForestClassifier
INFO 08/04 16:55:50 Version: 0.1.0
INFO 08/04 16:55:50 Timestamp: 1551781410.019103 (2019-03-05T18:23:30.019103)
INFO 08/04 16:55:51 --------------------------------------------------------------------------------
INFO 08/04 16:55:51 Model: product_activity
INFO 08/04 16:55:51 Loading model from: /home/mima/.local/share/deepbgc/data/0.1.0/classifier/product_activity.pkl
INFO 08/04 16:55:51 Type: RandomForestClassifier
INFO 08/04 16:55:51 Version: 0.1.0
INFO 08/04 16:55:51 Timestamp: 1551781433.886473 (2019-03-05T18:23:53.886473)
INFO 08/04 16:55:51 ================================================================================
WARNING 08/04 16:55:51 Some warnings detected, check the output aboveThen type the command deepbgc pipeline ./GCF_000195955.2_ASM19595v2_genomic.fna. Unfortunately, it failed.
(base) mima@123456:~/BGC/jieheganjun$ deepbgc pipeline ./GCF_000195955.2_ASM19595v2_genomic.fna
_____ ____ ____ ____
| _ \ ___ ___ ____ | __ ) / ___) / ___)
| | \ \/ _ \/ _ \ _ \| _ \ | | _ | |
| |_/ / __/ __/ |_) | |_) || |_| || |___
|____/ \___|\___| ___/|____/ \____| \____)
=================|_|===== version 0.1.26 =====
INFO 08/04 16:32:36 Loading model from: /home/mima/.local/share/deepbgc/data/0.1.0/detector/deepbgc.pkl
Using TensorFlow backend.
WARNING 08/04 16:32:36 From /home/mima/miniconda3/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version.
Instructions for updating:
Colocations handled automatically by placer.
WARNING 08/04 16:32:36 From /home/mima/miniconda3/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:3445: 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`.
INFO 08/04 16:32:37 Loading model from: /home/mima/.local/share/deepbgc/data/0.1.0/classifier/product_class.pkl
/home/mima/miniconda3/lib/python3.7/site-packages/sklearn/base.py:306: UserWarning: Trying to unpickle estimator DecisionTreeClassifier from version 0.18.2 when using version 0.21.3. This might lead to breaking code or invalid results. Use at your own risk.
UserWarning)
/home/mima/miniconda3/lib/python3.7/site-packages/sklearn/base.py:306: UserWarning: Trying to unpickle estimator RandomForestClassifier from version 0.18.2 when using version 0.21.3. This might lead to breaking code or invalid results. Use at your own risk.
UserWarning)
INFO 08/04 16:32:37 Loading model from: /home/mima/.local/share/deepbgc/data/0.1.0/classifier/product_activity.pkl
INFO 08/04 16:32:37 Processing input file 1/1: ./GCF_000195955.2_ASM19595v2_genomic.fna
INFO 08/04 16:32:37 ================================================================================
INFO 08/04 16:32:37 Processing record #1: NC_000962.3
WARNING 08/04 16:32:37 Updating record alphabet to generic_dna
INFO 08/04 16:32:37 Finding genes in record: NC_000962.3
INFO 08/04 16:32:47 Detecting Pfam domains in "NC_000962.3" using HMMER hmmscan, this might take a while...
WARNING 08/04 16:42:14 == HMMER hmmscan Error: ================
WARNING 08/04 16:42:14
WARNING 08/04 16:42:14 == End HMMER hmmscan Error. ============
ERROR 08/04 16:42:14 Unexpected error detecting protein domains using HMMER hmmscan
Traceback (most recent call last):
File "/home/mima/miniconda3/lib/python3.7/site-packages/deepbgc/main.py", line 113, in main
run(argv)
File "/home/mima/miniconda3/lib/python3.7/site-packages/deepbgc/main.py", line 102, in run
args.func.run(**args_dict)
File "/home/mima/miniconda3/lib/python3.7/site-packages/deepbgc/command/pipeline.py", line 177, in run
step.run(record)
File "/home/mima/miniconda3/lib/python3.7/site-packages/deepbgc/pipeline/annotator.py", line 35, in run
pfam_annotator.annotate()
File "/home/mima/miniconda3/lib/python3.7/site-packages/deepbgc/pipeline/pfam.py", line 97, in annotate
self._run_hmmscan(protein_path, domtbl_path)
File "/home/mima/miniconda3/lib/python3.7/site-packages/deepbgc/pipeline/pfam.py", line 73, in _run_hmmscan
raise Exception("Unexpected error detecting protein domains using HMMER hmmscan")
Exception: Unexpected error detecting protein domains using HMMER hmmscan
ERROR 08/04 16:42:14 ================================================================================
ERROR 08/04 16:42:14 DeepBGC failed with Exception: Unexpected error detecting protein domains using HMMER hmmscan
ERROR 08/04 16:42:14 ================================================================================I don't know how to solve this problem, so please help me. (By the way, I have tried put this genome sequences into antiSMASH, and it works). Thanks in advance.
Hi @Bollie15, I tried running deepbgc on those sequences and I didn't get any error. Can you try running again? Looks like hmmscan has crashed, maybe enough memory was not available?