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sanger-pathogens / circlator

A tool to circularize genome assemblies
http://sanger-pathogens.github.io/circlator/
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Error running fixstart with Docker:latest #185

Closed erinyoung closed 6 months ago

erinyoung commented 1 year ago

I am getting an error when using the latest Docker image (sangerpathogens/circlator:latest). I am trying to run fixstart. I get no errors when using a conda installation.

The following command failed with exit code 255
bash run_nucmer.sh

The output was:

ERROR: The following critical files could not be used
p.delta
p.mgaps
p.aaqry
p.aaref
Check your paths and file permissions and try again
ERROR: Could not parse delta file, p.delta
error no: 400
ERROR: Could not parse delta file, p.delta.filter
error no: 402

Traceback (most recent call last):
  File "/usr/local/lib/python3.5/dist-packages/pymummer-0.11.0-py3.5.egg/pymummer/syscall.py", line 20, in run
  File "/usr/lib/python3.5/subprocess.py", line 626, in check_output
    **kwargs).stdout
  File "/usr/lib/python3.5/subprocess.py", line 708, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'bash run_nucmer.sh' returned non-zero exit status 255

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/bin/circlator", line 4, in <module>
    __import__('pkg_resources').run_script('circlator==1.5.5', 'circlator')
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 719, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1504, in run_script
    exec(code, namespace, namespace)
  File "/usr/local/lib/python3.5/dist-packages/circlator-1.5.5-py3.5.egg/EGG-INFO/scripts/circlator", line 58, in <module>
    exec('circlator.tasks.' + task + '.run()')
  File "<string>", line 1, in <module>
  File "/usr/local/lib/python3.5/dist-packages/circlator-1.5.5-py3.5.egg/circlator/tasks/fixstart.py", line 26, in run
    fixer.run()
  File "/usr/local/lib/python3.5/dist-packages/circlator-1.5.5-py3.5.egg/circlator/start_fixer.py", line 310, in run
    promer_mincluster=self.promer_mincluster,
  File "/usr/local/lib/python3.5/dist-packages/circlator-1.5.5-py3.5.egg/circlator/start_fixer.py", line 133, in _find_circular_using_promer
    prunner.run()
  File "/usr/local/lib/python3.5/dist-packages/pymummer-0.11.0-py3.5.egg/pymummer/nucmer.py", line 144, in run
  File "/usr/local/lib/python3.5/dist-packages/pymummer-0.11.0-py3.5.egg/pymummer/syscall.py", line 26, in run
pymummer.syscall.Error: ('Error running command:', 'bash run_nucmer.sh')`, size: 2394 (max: 255)