foreignsand

Thank you so much! This is really thorough and helpful! I've been using positive and negative points to help refine the mask as suggested in option 3. I'll probably need...

Sure thing. Here they are: ``` $ jupyter serverextension list config dir: /Users/lemurbear/anaconda/etc/jupyter nb_anacondacloud enabled - Validating... Error loading server extension nb_anacondacloud X is nb_anacondacloud importable? nb_conda enabled - Validating......

no worries about the delay! thanks for responding! the results are from a couple of months ago so the total ccs reads should work. great! i'm not entirely sure what...

okay i see what haplotype-resolved assemblies are. i'm providing paired hi-c illumina reads along with the pacbio reads, so hifiasm can resolve parental haplotypes. so in the output, i have...

i uninstalled medaka from within the conda base environment, deactivated the base environment, and reinstalled medaka using pip in the virtual environment and i am still getting the same error:...

of course! here it is: ``` lemurbear@MacBook-Pro-10 bin % . ./medaka/bin/activate (medaka) lemurbear@MacBook-Pro-10 bin % pip install --upgrade pip Requirement already satisfied: pip in ./medaka/lib/python3.8/site-packages (24.3.1) (medaka) lemurbear@MacBook-Pro-10 bin %...

it is an intel-based mac

now i've deleted the original medaka virtual environment and recreated it and am getting a completely different error when trying to reinstall medaka: ``` (medaka) lemurbear@MacBook-Pro-10 bin % pip install...

update: the above error resulted from python3 automatically creating a virtual environment with python 3.12, so i created a virtual environment using the following command: `python3.9 -m venv medaka `...

I'm having the same issue using MitoHiFi as a docker image on my local machine running MacOs Sequoia 15.1.