Comments (3)
Hi Lucas, you called it. The references had been re-indexed as part of another pipeline and snakemake wanted to recall everything that happened before that .
from grenepipe.
you already closed the issue before I could answer - does that mean that you have solved it already? If not, feel free to re-open as needed!
In short, from what you posted, its hard to guess the reason why this is happening. The snakemake command line interface however offers an option for this, which accurately is called --reason
. If you add this option together with the dry-run option (-n
), you should get a (very long...) listing that tells you for each rule executing why this is invoked. You should then be able to figure out which updates snakemake things are necessary, and why your variant calls need to be re-run.
My gut feeling is that some timestamps of input files got updated somehow or something stupid like that, and that hence snakemake thinks those files are changed and so their downstream rules need updating... If that's the case, you can fix this by manually changing the timestamps. But let's see what's going on there first ;-)
So long
Lucas
from grenepipe.
Haha yes, happened to me before as well, no worries. Glad you figured it out ;-)
from grenepipe.
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