dominik-handler

unpackdb stalls

2

## Expected Behavior splitting of MSAs works multi-threaded might be related to #189 ## Current Behavior on larger final.a3m files unpackdb stalls and does not continue when executed via colabfold_search...

## Expected Behavior MSAs generated locally and on the ipynb should be identical ## Current Behavior local MSA coverage  ipynb MSA coverage  ## Steps to Reproduce (for bugs)...

intersect using split creates weird behavior in v2.30 compared to v2.28

1

Hi, I observed some weird behavior when I use bedtools intersect using split and single-exon intervals in v2.30. It seems this de-activates the function of -f (overlaps of length 5)...

Python 3

5

Hi, I saw that you have the branch 2to3 to migrate HiCAssembler to python 3. As it is getting quite difficult to install all dependencies for python 2.7 I wanted...

Hi, it happened to me that the pipeline crashes in the last step of outputting the final fasta file with an error like this: ``` DEBUG:HiCAssembler:reordering matrix DEBUG:HiCAssembler:{0: [], 1:...

Incompatible dependencies for ambertools/openmmforcefields

3

Hi, while installing Cfold locally I came across the following dependency problems: Could not solve for environment specs The following packages are incompatible ├─ ambertools ==23.3 py312h1577c9a_6 is requested and...