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nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
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Error in running #332

Closed sekhwal closed 2 years ago

sekhwal commented 2 years ago

hi, I am getting following error when I run the Gubbins. $ generate_ska_alignment.py --reference NC_336.1.fasta --fasta PMEN3_isolates.list --out out.aln

Error------------

Traceback (most recent call last): File "/home/anaconda3/envs/gubbins/lib/python3.9/site-packages/pkg_resources/init.py", line 579, in _build_master ws.require(requires) File "/home/anaconda3/envs/gubbins/lib/python3.9/site-packages/pkg_resources/init.py", line 897, in require needed = self.resolve(parse_requirements(requirements)) File "/home/anaconda3/envs/gubbins/lib/python3.9/site-packages/pkg_resources/init.py", line 788, in resolve raise VersionConflict(dist, req).with_context(dependent_req) pkg_resources.VersionConflict: (gubbins 3.1.6 (/home/anaconda3/envs/gubbins/lib/python3.9/site-packages), Requirement.parse('gubbins==3.1.4'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/anaconda3/envs/gubbins/bin/generate_ska_alignment.py", line 4, in import('pkg_resources').run_script('gubbins==3.1.4', 'generate_ska_alignment.py') File "/home/anaconda3/envs/gubbins/lib/python3.9/site-packages/pkg_resources/init.py", line 3247, in def _initialize_master_working_set(): File "/home/anaconda3/envs/gubbins/lib/python3.9/site-packages/pkg_resources/init.py", line 3221, in _call_aside f(*args, **kwargs) File "/home/anaconda3/envs/gubbins/lib/python3.9/site-packages/pkg_resources/init.py", line 3259, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/home/anaconda3/envs/gubbins/lib/python3.9/site-packages/pkg_resources/init.py", line 581, in _build_master return cls._build_from_requirements(requires) File "/home/anaconda3/envs/gubbins/lib/python3.9/site-packages/pkg_resources/init.py", line 594, in _build_from_requirements dists = ws.resolve(reqs, Environment()) File "/home/anaconda3/envs/gubbins/lib/python3.9/site-packages/pkg_resources/init.py", line 783, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'gubbins==3.1.4' distribution was not found and is required by the application

nickjcroucher commented 2 years ago

The script can't find the installed gubbins package. It would be worth trying the latest version (3.1.6) in a clean conda environment - I think there were some teething problems with these scripts finding the package.

sekhwal commented 2 years ago

I created new conda environment and installed Gubbins. However, once I run the program, it shows the same error. Please let me know where I can find the new version of this script.

nickjcroucher commented 2 years ago

@jdaeth274 has identified the likely problem - something odd happened to the script code when ensuring it installed properly, you can get the original from https://raw.githubusercontent.com/nickjcroucher/gubbins/c9bdb6b83fb9e75b1e34e2c32da22e46d0296364/python/scripts/generate_ska_alignment.py.