resfinder error

[Former user]

python3 run_resfinder.py -ifa /data1/MFDS_analysis/theragen1130/JH1-60/00.spades/contigs.fasta -s "staphylococcus aureus" -l_p 0.6 -t_p 0.95 --acquired --point -o /data1/MFDS_analysis/theragen1130/JH1-60/02.resfinder -k /data1/tools/resfinder/kma/ -db_res /data1/tools/resfinder/resfinder_db -db_point /data1/tools/resfinder/pointfinder_db/ Traceback (most recent call last): File "/data1/tools/anaconda3/lib/python3.9/site-packages/resfinder/run_resfinder.py", line 537, in <module> sys.exit(main()) File "/data1/tools/anaconda3/lib/python3.9/site-packages/resfinder/run_resfinder.py", line 206, in main std_result.init_database("ResFinder", conf.db_path_res) File "/data1/tools/anaconda3/lib/python3.9/site-packages/cgelib/output/result.py", line 82, in init_database version_in_git, commit = PliersMixin.get_version_commit(db_dir) File "/data1/tools/anaconda3/lib/python3.9/site-packages/cgelib/utils/pliers_mixin.py", line 33, in get_version_commit com2tag[tag.commit.hexsha] = str(tag) File "/data1/tools/anaconda3/lib/python3.9/site-packages/git/refs/tag.py", line 43, in commit obj = self.object File "/data1/tools/anaconda3/lib/python3.9/site-packages/git/refs/tag.py", line 69, in object return Reference._get_object(self) File "/data1/tools/anaconda3/lib/python3.9/site-packages/git/refs/symbolic.py", line 210, in _get_object return Object.new_from_sha(self.repo, hex_to_bin(self.dereference_recursive(self.repo, self.path))) File "/data1/tools/anaconda3/lib/python3.9/site-packages/git/objects/base.py", line 85, in new_from_sha oinfo = repo.odb.info(sha1) File "/data1/tools/anaconda3/lib/python3.9/site-packages/git/db.py", line 43, in info hexsha, typename, size = self._git.get_object_header(bin_to_hex(binsha)) File "/data1/tools/anaconda3/lib/python3.9/site-packages/git/cmd.py", line 1253, in get_object_header return self.__get_object_header(cmd, ref) File "/data1/tools/anaconda3/lib/python3.9/site-packages/git/cmd.py", line 1240, in __get_object_header return self._parse_object_header(cmd.stdout.readline()) File "/data1/tools/anaconda3/lib/python3.9/site-packages/git/cmd.py", line 1198, in _parse_object_header raise ValueError("SHA could not be resolved, git returned: %r" % (header_line.strip())) ValueError: SHA could not be resolved, git returned: b''

[CGE Helpdesk]

Dear Mr./Mrs.

Thank you for your message and for your interest in ResFinder.

The issue seems to be with Git. Please try to update Git to the latest version. Please let me know if the issue persists.

best regards,

Maja, CGE Helpdesk

[Ignacio Montero Ordóñez]

python3 run_resfinder.py -o ./ -s "Escherichia coli" -l 0.6 -t 0.8 --acquired --point -ifq data/test_isolate_01_*
Traceback (most recent call last):
File "/home/microviable/Resfinder/lib/python3.10/site-packages/resfinder/run_resfinder.py", line 568, in <module>
sys.exit(main())
File "/home/microviable/Resfinder/lib/python3.10/site-packages/resfinder/run_resfinder.py", line 228, in main
std_result.init_database("ResFinder", conf.db_path_res)
File "/home/microviable/Resfinder/lib/python3.10/site-packages/cgelib/output/result.py", line 82, in init_database
version_in_git, commit = PliersMixin.get_version_commit(db_dir)
File "/home/microviable/Resfinder/lib/python3.10/site-packages/cgelib/utils/pliers_mixin.py", line 33, in get_version_commit
com2tag[tag.commit.hexsha] = str(tag)
File "/home/microviable/Resfinder/lib/python3.10/site-packages/git/refs/tag.py", line 43, in commit
obj = self.object
File "/home/microviable/Resfinder/lib/python3.10/site-packages/git/refs/tag.py", line 74, in object
return Reference._get_object(self)
File "/home/microviable/Resfinder/lib/python3.10/site-packages/git/refs/symbolic.py", line 219, in _get_object
return Object.new_from_sha(self.repo, hex_to_bin(self.dereference_recursive(self.repo, self.path)))
File "/home/microviable/Resfinder/lib/python3.10/site-packages/git/objects/base.py", line 94, in new_from_sha
oinfo = repo.odb.info(sha1)
File "/home/microviable/Resfinder/lib/python3.10/site-packages/git/db.py", line 40, in info
hexsha, typename, size = self._git.get_object_header(bin_to_hex(binsha))
File "/home/microviable/Resfinder/lib/python3.10/site-packages/git/cmd.py", line 1383, in get_object_header
return self.__get_object_header(cmd, ref)
File "/home/microviable/Resfinder/lib/python3.10/site-packages/git/cmd.py", line 1370, in __get_object_header
return self._parse_object_header(cmd.stdout.readline())
File "/home/microviable/Resfinder/lib/python3.10/site-packages/git/cmd.py", line 1329, in _parse_object_header
raise ValueError("SHA could not be resolved, git returned: %r" % (header_line.strip()))
ValueError: SHA could not be resolved, git returned: b''

‌

How to update git?

[CGE Helpdesk]

Dear User.

To update git please run:

pip install GitPython --upgrade

Best Regards,

Maja, CGE Helpdesk

[CGE Helpdesk]

Duplicate of #105.