Traceback (most recent call last):
File "/mnt/shared/scratch/awebb/apps/conda/envs/ENSEMBL_submission_env/bin/EMBLmyGFF3", line 10, in <module>
sys.exit(main())
File "/mnt/shared/scratch/awebb/apps/conda/envs/ENSEMBL_submission_env/lib/python3.10/site-packages/EMBLmyGFF3/EMBLmyGFF3.py", line 1361, in main
for record in GFF.parse(infile, base_dict=seq_dict):
File "/mnt/shared/scratch/awebb/apps/conda/envs/ENSEMBL_submission_env/lib/python3.10/site-packages/BCBio/GFF/GFFParser.py", line 793, in parse
for rec in parser.parse_in_parts(gff_files, base_dict, limit_info,
File "/mnt/shared/scratch/awebb/apps/conda/envs/ENSEMBL_submission_env/lib/python3.10/site-packages/BCBio/GFF/GFFParser.py", line 337, in parse_in_parts
cur_dict = self._results_to_features(cur_dict, results)
File "/mnt/shared/scratch/awebb/apps/conda/envs/ENSEMBL_submission_env/lib/python3.10/site-packages/BCBio/GFF/GFFParser.py", line 376, in _results_to_features
base = self._add_parent_child_features(base, results.get('parent', []),
File "/mnt/shared/scratch/awebb/apps/conda/envs/ENSEMBL_submission_env/lib/python3.10/site-packages/BCBio/GFF/GFFParser.py", line 448, in _add_parent_child_features
child_feature = self._get_feature(child_dict)
File "/mnt/shared/scratch/awebb/apps/conda/envs/ENSEMBL_submission_env/lib/python3.10/site-packages/BCBio/GFF/GFFParser.py", line 591, in _get_feature
new_feature = SeqFeature.SeqFeature(location, feature_dict['type'],
TypeError: SeqFeature.__init__() got an unexpected keyword argument 'strand'
General info:
EMBLmyGFF3 v2.3
installed with: conda v. 23.3.1, mostly as described in readme:
Dear developers.
General info:
EMBLmyGFF3 v2.3
installed with: conda v. 23.3.1, mostly as described in readme:
and run within that environment
OS: CentOS, Rocky Linux 8.8 (Green Obsidian)
the commands:
The gff3 file was generated by EVidenceModeler and incomplete genes were removed by AGAT.
I can't quite work out what in there triggers the error.