ValueError("missing molecule_type in annotations")

[ramadatta]

Hi,

Thanks for the nice tool. I am using a gbk file generated by prokka tool. But I run into following error:

locus2genoplotr -l GMCHABGO_03197 -r renamed_C01871_unicycler.gbk -o single_plot -v -rs 45000 
/home/prakki/anaconda3/envs/locus2genoplotr/lib/python3.9/site-packages/Bio/GenBank/Scanner.py:1554: BiopythonParserWarning: Malformed LOCUS line found - is this correct?
:'LOCUS       C01871_unicycler.fasta_1_length=69062\t6906207 bp   DNA linear\n'
  warnings.warn(
/home/prakki/anaconda3/envs/locus2genoplotr/lib/python3.9/site-packages/Bio/GenBank/Scanner.py:1554: BiopythonParserWarning: Malformed LOCUS line found - is this correct?
:'LOCUS       C01871_unicycler.fasta_2_length=39694\t39694 bp   DNA linear\n'
  warnings.warn(
extraction from 3429462 to 3490275
match, True
/home/prakki/anaconda3/envs/locus2genoplotr/lib/python3.9/site-packages/Bio/SeqIO/InsdcIO.py:726: BiopythonWarning: Increasing length of locus line to allow long name. This will result in fields that are not in usual positions.
  warnings.warn(
Traceback (most recent call last):
  File "/home/prakki/anaconda3/envs/locus2genoplotr/bin/locus2genoplotr", line 8, in <module>
    sys.exit(main())
  File "/home/prakki/anaconda3/envs/locus2genoplotr/lib/python3.9/site-packages/locus2genoplotr/__init__.py", line 62, in main
    gbk_list = L.write_genbank_subrecords([L.ref_sub_record])
  File "/home/prakki/anaconda3/envs/locus2genoplotr/lib/python3.9/site-packages/locus2genoplotr/locus2genoplotr.py", line 273, in write_genbank_subrecords
    SeqIO.write(record, fastastr, 'genbank')
  File "/home/prakki/anaconda3/envs/locus2genoplotr/lib/python3.9/site-packages/Bio/SeqIO/__init__.py", line 524, in write
    count = writer_class(handle).write_file(sequences)
  File "/home/prakki/anaconda3/envs/locus2genoplotr/lib/python3.9/site-packages/Bio/SeqIO/Interfaces.py", line 234, in write_file
    count = self.write_records(records, maxcount)
  File "/home/prakki/anaconda3/envs/locus2genoplotr/lib/python3.9/site-packages/Bio/SeqIO/Interfaces.py", line 208, in write_records
    self.write_record(record)
  File "/home/prakki/anaconda3/envs/locus2genoplotr/lib/python3.9/site-packages/Bio/SeqIO/InsdcIO.py", line 994, in write_record
    self._write_the_first_line(record)
  File "/home/prakki/anaconda3/envs/locus2genoplotr/lib/python3.9/site-packages/Bio/SeqIO/InsdcIO.py", line 749, in _write_the_first_line
    raise ValueError("missing molecule_type in annotations")
ValueError: missing molecule_type in annotations

can help how this can be resolved.

[tpillone]

Hi @ramadatta,

This problem is caused by the latest versions of biopython, you can solve it by downgrading biopython to version 1.77

conda activate locus2genoplotr
conda install biopython=1.77