Error during detector training
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Description
hello
i faced a problem during detector o my sample
here is the error message, it says i didn't use a negative dataset but actually i used one that is called GeneSwap_Negatives.pfam.tsv
i think deepbgc can't see the negative dataset because of a error o my command. --help didn't tell where or how to put it
'optimizer': 'adam',
'shuffle': True,
'timesteps': 256,
'validation_size': 0,
'verbose': 1,
'weighted': True},
'input_params': { 'features': [ {'type': 'ProteinBorderTransformer'},
{ 'type': 'Pfam2VecTransformer',
'vector_path': 'pfam2vec.csv'}]},
'type': 'KerasRNN'}
INFO 15/05 09:28:22 Loaded 41102 samples and 80777 domains from sample1_deepbgc_prepare_result.tsv
INFO 15/05 09:28:28 Loaded 10128 samples and 706950 domains from GeneSwap_Negatives.pfam.tsv
ERROR 15/05 09:28:33 Got target variable with only one value {0} in: ['sample1_deepbgc_prepare_result.tsv', 'GeneSwap_Negatives.pfam.tsv']
Traceback (most recent call last):
File "/root/esraa/miniconda3/envs/deepbgcv0.1.29/lib/python3.7/site-packages/deepbgc/main.py", line 113, in main
run(argv)
File "/root/esraa/miniconda3/envs/deepbgcv0.1.29/lib/python3.7/site-packages/deepbgc/main.py", line 102, in run
args.func.run(**args_dict)
File "/root/esraa/miniconda3/envs/deepbgcv0.1.29/lib/python3.7/site-packages/deepbgc/command/train.py", line 60, in run
train_samples, train_y = util.read_samples(inputs, target)
File "/root/esraa/miniconda3/envs/deepbgcv0.1.29/lib/python3.7/site-packages/deepbgc/util.py", line 574, in read_samples
'Did you provide positive and negative samples?')
ValueError: ("Got target variable with only one value {0} in: ['sample1_deepbgc_prepare_result.tsv', 'GeneSwap_Negatives.pfam.tsv']", 'At least two values are required to train a model. ', 'Did you provide positive and negative samples?')
ERROR 15/05 09:28:33 ================================================================================
ERROR 15/05 09:28:33 DeepBGC failed with ValueError: Got target variable with only one value {0} in: ['sample1_deepbgc_prepare_result.tsv', 'GeneSwap_Negatives.pfam.tsv']
ERROR 15/05 09:28:33 ================================================================================
ERROR 15/05 09:28:33 At least two values are required to train a model.
ERROR 15/05 09:28:33 Did you provide positive and negative samples?
ERROR 15/05 09:28:33 ================================================================================
my cmmand:
deepbgc train --model templates/deepbgc.json --output MyDeepBGCDetector.pkl sample1_deepbgc_prepare_result.tsv GeneSwap_Negatives.pfam.tsv --config PFAM2VEC pfam2vec
.csv -v ClusterFinder_Annotated_Contigs.full.gbk
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Research direction
Reproduce the shown deepbgc train command, then inspect deepbgc/command/train.py and deepbgc/util.py, especially read_samples, as named in the traceback. Determine how the two TSV inputs are assigned target values and document or correct the behavior so training accepts distinct positive and negative samples.
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Assessment
- Tech stack
- python
- Domain
- cli, machine-learning
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100