I’m working on finishing some PacBio-sequenced bacterial genomes so I decided to look for repeats at the ends of the sequences and solve them (merge them). I already found the repeats with nucmer and I was trying to visualize them with mummerplot, yet, I could’t run it as I get this error:
Can't use 'defined(%hash)' (Maybe you should just omit the defined()?) at /home/linuxbrew/.linuxbrew/bin/mummerplot line 884.
Apparently is due to a some sort of incompatibility between the syntax of the old and new versions of Perl https://github.com/bioconda/bioconda-recipes/issues/4319 but I couldn’t manage to solve the problem.
I temporarily skipped this step and tried to merge the end-repeats of my genomes by using circlator but I couldn’t launch the program either, this time for this error:
Traceback (most recent call last): File "/home/linuxbrew/.linuxbrew/bin/circlator", line 3, in <module> import argparse ModuleNotFoundError: No module named 'argparse'
In this case I tried to instal the ‘argparse’ Python module but I couldn’t as I don’t have the required permissions.
Probably both are simple issues to solve but I’m stuck on this step so I’d really appreciate your help.