Comments (6)
Hi @andreagp96, What operating system are you working on?
from dragonflye.
Hello! I'm working on macOS (Ventura v13.6.4) :)
from dragonflye.
Do you by chance have access to "Docker Desktop"?
from dragonflye.
Mmm, I don't have access to "Docker Desktop". However, I was able to resolve the issue by modifying the dragonflye script using VIM. I added the command "polish" in line 414 as follows:
run_cmd("polypolish polish $POLISHED_FASTA $SAM_R1 $SAM_R2 > $round_dir/polypolish-$i.fasta", "short read polishing - polypolish ($i of $polypolish)");
instead of:
run_cmd("polypolish $POLISHED_FASTA $SAM_R1 $SAM_R2 > $round_dir/polypolish-$i.fasta", "short read polishing - polypolish ($i of $polypolish)");
Hoping this info is useful.
Kind regards,
Andrea
from dragonflye.
This is super helpful! Thank you so much! I did not realize some changes in the most recent version of polypolish: https://github.com/rrwick/Polypolish/releases/tag/v0.6.0
I will update Dragonflye to pin the minimum version of polypolish to 0.6.0
from dragonflye.
Happy to help!!
Thank you for your time and dedication,
Andrea
from dragonflye.
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