Entry blaVMB-2_MN865127 contained antibiotic 'ceftiofur' not found in ab class def file.

[Omer Faruk Cetiner]

Hello everyone,

I am trying to run the ResFinder tool on the cluster with this code:

python3 /data/users/ocetiner/resfinder/run_resfinder.py -o ./outdir --species "Other" -l 0.6 -t 0.9 --acquired -ifq *fastq.gz

I always encounter this error.

Entry blaVMB-2_MN865127 contained antibiotic 'ceftiofur' not found in ab class def file.

Additionally, I tried to specify KMA path like this (because I had thought the problem derived from it):

python3 /data/users/ocetiner/resfinder/run_resfinder.py --kmaPATH /data/users/ocetiner/resfinder/cge/kma -o ./outdir --species "Other" -l 0.6 -t 0.9 --acquired -ifq *fastq.gz

and I took this error:

Traceback (most recent call last):
  File "/data/users/ocetiner/resfinder/run_resfinder.py", line 228, in <module>
    _ = subprocess.check_output([kma, "-h"])
  File "/data/users/ocetiner/miniconda/lib/python3.6/subprocess.py", line 356, in check_output
    **kwargs).stdout
  File "/data/users/ocetiner/miniconda/lib/python3.6/subprocess.py", line 423, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/data/users/ocetiner/miniconda/lib/python3.6/subprocess.py", line 729, in __init__
    restore_signals, start_new_session)
  File "/data/users/ocetiner/miniconda/lib/python3.6/subprocess.py", line 1364, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: '/data/users/ocetiner/resfinder/cge/kma/'

‌

Thank you very much,

Omer

[CGE Helpdesk]

Dear Omer,

Thank you for your interest in ResFinder.
I would kindly ask you to submit the data to the ResFinder webserver (https://cge.cbs.dtu.dk/services/ResFinder/) and pass the url link to the results page in an email to [e-mail] referring to issue #55. Then we will look into the issue.

Best regards,
Karen, CGE Helpdesk

[Omer Faruk Cetiner]

Dear Karen,

Thank you for your reply. I'm afraid that these files (extension=fastq.gz, and n=40) are too big to upload to the website.

‌

[CGE Helpdesk]

Dear Omer,

Sorry for the late response. This might not solve the problem entirely, but there might be something wrong with the kma path you’ve specified:

In your case, try to use --kmaPath /data/users/ocetiner/resfinder/cge/kma/kma as the path for kma instead, and let me know if that changes anything.

Kind regards

Malene, CGE Helpdesk

[Omer Faruk Cetiner]

Dear Malene,

It runs correctly now. Thanks to your recommendation.

As for the ceftiofur thing: Alfred Ferrer Florensa, who is a developer the ResFinder, has said me that it is not a bug or error, just hasn't been identified yet.,

Thank you for your cooperation.

Best,

Omer

[CGE Helpdesk]

Dear Omer,
I’m glad, that the issue is solved.

Please do not hesitate to write us again if you have any questions.

Best regards

Malene, CGE Helpdesk.