Open UmerFarooq17 opened 2 months ago
This is caused by a change in Biopython I believe:
"propertynofuzzy_start Start position (integer, approximated if fuzzy, read only) (OBSOLETE).
This is now an alias for int(feature.start), which should be used in preference – unless you are trying to support old versions of Biopython.
propertynofuzzy_end End position (integer, approximated if fuzzy, read only) (OBSOLETE).
This is now an alias for int(feature.end), which should be used in preference – unless you are trying to support old versions of Biopython."
This problem seems to be fixed by a simple find and replace of nofuzzy_start and nofuzzy_end
Ex: sed -i.bak "s/nofuzzy_start/start/g" /home/vinson/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/library.py
sed -i.bak "s/nofuzzy_end/end/g" /home/vinson/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/library.py
Just downgrade biopython <1.80.
Just downgrade biopython <1.80.
Is remote phobius stopping at about 90% of the way also a known issue caused by this incompatibility with biopython < 1.80?
Are you using the latest release? yes. version 1.8.17
Describe the bug When tunning funannotate annotate command with required options, it drops in errors within the python library.py file. AttributeError: 'SimpleLocation' object has no attribute 'nofuzzy_start'
What command did you issue?
funannotate annotate --input ./ --fasta 47514_clean_sort.fna --species 'Fusarium oxysporum' --strain 47514 --isolate 47514 --cpus 16 2>&1 | tee -a 07.annotate.log
Logfiles
OS/Install Information