Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error creating tmp dir with no-stream and relative paths #48

Closed
johnlees opened this issue Jul 6, 2019 · 0 comments
Closed

Error creating tmp dir with no-stream and relative paths #48

johnlees opened this issue Jul 6, 2019 · 0 comments
Assignees
Labels
bug Something isn't working

Comments

@johnlees
Copy link
Member

johnlees commented Jul 6, 2019

e.g. run with --no-stream --ref-db ../query_db
Will fail with:

  File "PopPUNK/mash.py", line 462, in queryDatabase
    suffix=".tmp", dir="./" + os.path.basename(dbPrefix))
  File "tempfile.py", line 340, in mkstemp
    return _mkstemp_inner(dir, prefix, suffix, flags, output_type)
  File "tempfile.py", line 258, in _mkstemp_inner
    fd = _os.open(file, flags, 0o600)
FileNotFoundError: [Errno 2] No such file or directory: './query_db/query_dby6aic3ql.tmp'

Need to fix lines:

    if no_stream:
            tmpHandle, tmpName = mkstemp(prefix=os.path.basename(dbPrefix),
                                         suffix=".tmp", dir="./" + os.path.basename(dbPrefix))
            mash_cmd += " > " + tmpName
@johnlees johnlees self-assigned this Jul 6, 2019
@johnlees johnlees added the bug Something isn't working label Jul 6, 2019
ccoulombe pushed a commit to ccoulombe/PopPUNK that referenced this issue Oct 28, 2022
Add functions to iteratively move boundary
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

1 participant