run_resfinder.py Dockerfile test error

Issue #81 resolved
guoyuh created an issue

hi ,verythanks resfinder.

‌ because of apt source ,I modyfied dockerfile with baseimages from ‘FROM debian:stretch' to 'FROM ubuntu:18.04’,and it finally build success.

‌ when run testfiles with docker follow the tutories,it return me a error message:

\$ docker run --rm -it -v $(pwd)/db_resfinder/:/usr/src/db_resfinder -v $(pwd)/results/:/usr/src/results resfinder -ifa /usr/src/tests/data/test_isolate_01.fa -acq -db_res /usr/src/db_resfinder -o /usr/src/results
Traceback (most recent call last):
File "/usr/src/run_resfinder.py", line 338, in <module>
args.db_path_res)
File "/usr/src/cge/standardize_results.py", line 288, in load_database_metadata
version, commit = Generator.get_version_commit(db_dir)
File "/usr/src/cge/out/util/generator.py", line 38, in get_version_commit
com2tag[tag.commit.hexsha] = str(tag)
File "/usr/local/lib/python3.6/dist-packages/git/refs/tag.py", line 29, in commit
obj = self.object
File "/usr/local/lib/python3.6/dist-packages/git/refs/symbolic.py", line 190, in _get_object
return Object.new_from_sha(self.repo, hex_to_bin(self.dereference_recursive(self.repo, self.path)))
File "/usr/local/lib/python3.6/dist-packages/git/objects/base.py", line 83, in new_from_sha
oinfo = repo.odb.info(sha1)
File "/usr/local/lib/python3.6/dist-packages/git/db.py", line 43, in info
hexsha, typename, size = self._git.get_object_header(bin_to_hex(binsha))
File "/usr/local/lib/python3.6/dist-packages/git/cmd.py", line 1189, in get_object_header
return self.__get_object_header(cmd, ref)
File "/usr/local/lib/python3.6/dist-packages/git/cmd.py", line 1178, in __get_object_header
return self._parse_object_header(cmd.stdout.readline())
File "/usr/local/lib/python3.6/dist-packages/git/cmd.py", line 1138, 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''

Comments (2)

  1. CGE Helpdesk

    Hello,
    Thank you for your message and for using ResFinder.

    I was not able to reproduce your error with either FROM debian:stretch' or 'FROM ubuntu:18.04’

    I did find someone having similar issues which suggest to update git, see link for the full discussion: https://github.com/gitpython-developers/GitPython/issues/1016
    They also suggest that the issue might be that git is running into a different owner than the repository.

    Inside repo, you can try this command:
    git config --global -add safe.directory <repo_path>

    I hope this helps.
    Best regards Maja, CGE Helpdesk

  2. Log in to comment