Open lxsteiner opened 1 year ago
Hi,
I would also be interested in not using the --isolate
option of spades.py automatically with Unicycler. Indeed, for some reads I get errors with Unicycler (Errors finished abnormally, OS return value: -9
) and spades.py (Errors finished abnormally, OS return value: -6
) maybe because of the --isolate
option. Without the --isolate
option, the assembly works with spades.py.
Unicycler v0.5.0 and Spades 3.15.5 in Conda
Regards,
https://github.com/rrwick/Unicycler/blob/69e712eb95c4b9f8a46aade467260260a9ce7a91/unicycler/spades_func.py#L226
Based on the code, it seems like the --isolate parameter is "automatically" applied at the start of the assembly command. Is there a reason why this is preferred or was set like this?
From the SPAdes manual:
Unfortunately, "More details..." doesn't really give me more details and doesn't mention the
--isolate
flag at all, only--careful
which is how I incidently found that--isolate
was applied at the beginning. I tried to pass--careful
via--spades_options "--careful"
and ran into an error:I think that commenting out the line might just solve my issue with passing
--careful
, but I'm curious why--isolate
was needed.Thanks!