On Thu, 2019-03-21 at 21:52 +0100, Andreas Tille wrote: > ChildIOException: > File/directory is a child to another output: > /home/andreas/debian-maintain/salsa/med- > team/0_prospective/kallisto/test/kallisto_out > /home/andreas/debian-maintain/salsa/med- > team/0_prospective/kallisto/test/kallisto_out/abundance.h5 > > > I admit I never used snakemake and may be I'm doing something wrong. > But its not very good in telling the user what's wrong here. Any > hint?
I guess we are talking about https://salsa.debian.org/med-team/kallisto/blob/master/test/Snakefile Try deleting the output "kallisto_out" in case it masks "kallisto_out/abundance.h5" or it might work simply marking it as directory("kallisto_out") as in https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#directories-as-outputs You can then also try to change the overall output (aka all/input reqirements) to direcxtory("kallisto_out") -- Stian Soiland-Reyes The University of Manchester https://www.esciencelab.org.uk/ https://orcid.org/0000-0001-9842-9718