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linsalrob / PhiSpy

Prediction of prophages from bacterial genomes
MIT License
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ValueError: missing molecule_type in annotations #43

Closed snehamurthy21 closed 3 years ago

snehamurthy21 commented 3 years ago

Hi

i am getting this error when i run with output choice 255

/.local/lib/python3.8/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

Could you please help me resolve it

pdec commented 3 years ago

Hi,

sure but could you provide information about the PhiSpy version you're using and the version of Biopython package you have installed?

You can get this information by running: PhiSpy.py --version and pip3 list | grep biopython

Thanks, Przemek

snehamurthy21 commented 3 years ago

PhiSpy.py --version 4.1.22 pip3 list | grep biopython biopython 1.78

pdec commented 3 years ago

Great, thanks!

PhiSpy v4.1.22 does not support Biopython v1.78 and above.

You can either downgrade Biopython to v1.77 by running pip3 install biopython==1.77 or install the current PhiSpy version from GitHub repo - v4.2.5, which works well with Biopython v.1.78.

Best, Przemek

snehamurthy21 commented 3 years ago

Thank you for your help It worked great with biopython==1.77

pdec commented 3 years ago

That's great!