DeepBGC failed with ValueError: missing molecule_type in annotations

Hi,

When I tried to use DeepBGC to analyze a genbank file downloaded from NCBI, I encountered an errror like this:

Using TensorFlow backend.
WARNING 11/02 15:54:49 From /opt/anaconda3/envs/deepbgc/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:74: The name tf.get_default_graph is deprecated. Please use tf.compat.v1.get_default_graph instead.

WARNING 11/02 15:54:49 From /opt/anaconda3/envs/deepbgc/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:517: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead.

WARNING 11/02 15:54:49 From /opt/anaconda3/envs/deepbgc/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:4138: The name tf.random_uniform is deprecated. Please use tf.random.uniform instead.

WARNING 11/02 15:54:49 From /opt/anaconda3/envs/deepbgc/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:133: The name tf.placeholder_with_default is deprecated. Please use tf.compat.v1.placeholder_with_default instead.

WARNING 11/02 15:54:49 From /opt/anaconda3/envs/deepbgc/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.
WARNING 11/02 15:54:50 From /opt/anaconda3/envs/deepbgc/lib/python3.7/site-packages/keras/backend/tensorflow_backend.py:174: The name tf.get_default_session is deprecated. Please use tf.compat.v1.get_default_session instead.

INFO 11/02 15:54:50 Loading model from: /Users/cynthiayo/Library/Application Support/deepbgc/data/0.1.0/classifier/product_class.pkl
/opt/anaconda3/envs/deepbgc/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)
/opt/anaconda3/envs/deepbgc/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 11/02 15:54:52 Loading model from: /Users/cynthiayo/Library/Application Support/deepbgc/data/0.1.0/classifier/product_activity.pkl
INFO 11/02 15:54:52 Processing input file 1/1: sequence.gb
INFO 11/02 15:54:52 ================================================================================
INFO 11/02 15:54:52 Processing record #1: KB946332.1
INFO 11/02 15:54:52 Sequence already contains 802 CDS features, skipping CDS detection
INFO 11/02 15:54:52 Detecting Pfam domains in "KB946332.1" using HMMER hmmscan, this might take a while...
INFO 11/02 15:59:29 HMMER hmmscan Pfam detection done in 0h4m37s
INFO 11/02 16:00:07 Added 1795 Pfam domains (947 unique PFAM_IDs)
INFO 11/02 16:00:07 Detecting BGCs using deepbgc model in KB946332.1
INFO 11/02 16:00:10 Detected 3 BGCs using deepbgc model in KB946332.1
INFO 11/02 16:00:10 Classifying 3 BGCs using product_class model in KB946332.1
INFO 11/02 16:00:10 Classifying 3 BGCs using product_activity model in KB946332.1
INFO 11/02 16:00:10 Saving processed record KB946332.1
ERROR 11/02 16:00:10 missing molecule_type in annotations
Traceback (most recent call last):
File "/opt/anaconda3/envs/deepbgc/lib/python3.7/site-packages/deepbgc/main.py", line 113, in main
run(argv)
File "/opt/anaconda3/envs/deepbgc/lib/python3.7/site-packages/deepbgc/main.py", line 102, in run
args.func.run(**args_dict)
File "/opt/anaconda3/envs/deepbgc/lib/python3.7/site-packages/deepbgc/command/pipeline.py", line 181, in run
writer.write(record)
File "/opt/anaconda3/envs/deepbgc/lib/python3.7/site-packages/deepbgc/output/bgc_genbank.py", line 26, in write
SeqIO.write(cluster_record, self.fd, 'genbank')
File "/opt/anaconda3/envs/deepbgc/lib/python3.7/site-packages/Bio/SeqIO/init.py", line 530, in write
count = writer_class(handle).write_file(sequences)
File "/opt/anaconda3/envs/deepbgc/lib/python3.7/site-packages/Bio/SeqIO/Interfaces.py", line 244, in write_file
count = self.write_records(records, maxcount)
File "/opt/anaconda3/envs/deepbgc/lib/python3.7/site-packages/Bio/SeqIO/Interfaces.py", line 218, in write_records
self.write_record(record)
File "/opt/anaconda3/envs/deepbgc/lib/python3.7/site-packages/Bio/SeqIO/InsdcIO.py", line 981, in write_record
self._write_the_first_line(record)
File "/opt/anaconda3/envs/deepbgc/lib/python3.7/site-packages/Bio/SeqIO/InsdcIO.py", line 744, in _write_the_first_line
raise ValueError("missing molecule_type in annotations")
ValueError: missing molecule_type in annotations
ERROR 11/02 16:00:10 ================================================================================
ERROR 11/02 16:00:10 DeepBGC failed with ValueError: missing molecule_type in annotations
ERROR 11/02 16:00:10 ================================================================================

Could you help me with the problem mentioned here?

Thank you!

Start in deepbgc/output/bgc_genbank.py at the SeqIO.write call shown in the traceback, then trace how the record is created in deepbgc/command/pipeline.py. Reproduce the failure with the reported GenBank input and inspect the record annotations before writing; done means processed GenBank output is written without the missing molecule_type error.