"Version of nucmer too low. I found ., but must be at least 3.1."

[MattPinder]

Thank you for addressing my previous issue with nucmer detection (#122). However, having installed v1.5.5, I'm now having a different nucmer-related problem. Once again, circlator progcheck finds the correct version of nucmer, however circlator all is detecting the version incorrectly (as opposed to not finding it at all previously). This is the error message I receive:

Traceback (most recent call last): File "/usr/local/packages/anaconda3-4.4.0/bin/circlator", line 4, in <module> __import__('pkg_resources').run_script('circlator==1.5.5', 'circlator') File "/usr/local/packages/anaconda3-4.4.0/lib/python3.6/site-packages/setuptools-27.2.0-py3.6.egg/pkg_resources/__init__.py", line 744, in run_script File "/usr/local/packages/anaconda3-4.4.0/lib/python3.6/site-packages/setuptools-27.2.0-py3.6.egg/pkg_resources/__init__.py", line 1499, in run_script File "/home/local/packages/anaconda3-4.4.0/lib/python3.6/site-packages/circlator-1.5.5-py3.6.egg/EGG-INFO/scripts/circlator", line 58, in <module> exec('circlator.tasks.' + task + '.run()') File "<string>", line 1, in <module> File "/usr/local/packages/anaconda3-4.4.0/lib/python3.6/site-packages/circlator-1.5.5-py3.6.egg/circlator/tasks/all.py", line 74, in run circlator.versions.get_all_versions(None, raise_error=True, assembler=options.assembler) File "/usr/local/packages/anaconda3-4.4.0/lib/python3.6/site-packages/circlator-1.5.5-py3.6.egg/circlator/versions.py", line 15, in get_all_versions external_progs.check_all_progs(verbose=False, raise_error=raise_error, filehandle=filehandle, debug=debug, assembler=assembler) File "/usr/local/packages/anaconda3-4.4.0/lib/python3.6/site-packages/circlator-1.5.5-py3.6.egg/circlator/external_progs.py", line 105, in check_all_progs make_and_check_prog(prog, verbose=verbose, raise_error=raise_error, filehandle=filehandle, debug=debug, required=prog==assembler) File "/usr/local/packages/anaconda3-4.4.0/lib/python3.6/site-packages/circlator-1.5.5-py3.6.egg/circlator/external_progs.py", line 82, in make_and_check_prog handle_error('Version of ' + name + ' too low. I found ' + p.version + ', but must be at least ' + min_versions[name] + '. Found here:\n' + p.from_which, raise_error=raise_error) File "/usr/local/packages/anaconda3-4.4.0/lib/python3.6/site-packages/circlator-1.5.5-py3.6.egg/circlator/external_progs.py", line 53, in handle_error raise Error(message + '\nCannot continue') circlator.external_progs.Error: Version of nucmer too low. I found ., but must be at least 3.1. Found here: /usr/local/packages/MUMmer3.23/nucmer Cannot continue

Once again, any guidance would be greatly appreciated.

[kimnegrette3]

Hi! did you solve this issue? I'm having the exact same problem now. Any help is really appreciated. Thanks!

[MattPinder]

Going back through my notes, it appears that my last reference to Circlator was 'Waiting on reply from devs'... If I return to this and have any success in installing it, I'll be sure to post my solution here. I hope you'll have more luck than I did in the meantime

[kimnegrette3]

Hi @MattPinder! Thak you for taking the time to reply! In case you need to run circlator again, I think I managed to solve this nucmer problem. I downloaded the bioconda package and modified the external_progs.py file in the "prog_to_version_cmd" section so the nucmer line finally looks like this:

'nucmer': ('--version', re.compile(r'^NUCmer (NUCleotide MUMmer) version ([0-9.]+)')),

Then deleted all files on " __ pycache __" folder and run again. This is something like the solution proposed on #110

That solved the initial problem, but I'm still waiting for the complete pipeline to finish. Hope it works till the end.