Hello,
is it possible that the -m parameter is ignored in the initial assembly step?
In https://github.com/mdsufz/MuDoGeR/blob/master/src/modules/mudoger-module-1.sh it seems that it is either set to the default of 100gb or the value from the khmer prediction is used.
I'm running mudoger --module preprocess --meta metadata.tsv -o output_folder -t 20 -m 1500 --metaspades
and still the memory threshold for spades is taken from the khmer file, and for some samples it seems spades is failing at the assembly step due to insufficient memory.
Also it seems that the khmer step ignores the number of threads set and is utilizing all available cores instead.
Hello,
is it possible that the
-mparameter is ignored in the initial assembly step?In https://github.com/mdsufz/MuDoGeR/blob/master/src/modules/mudoger-module-1.sh it seems that it is either set to the default of 100gb or the value from the khmer prediction is used.
I'm running
mudoger --module preprocess --meta metadata.tsv -o output_folder -t 20 -m 1500 --metaspadesand still the memory threshold for spades is taken from the khmer file, and for some samples it seems spades is failing at the assembly step due to insufficient memory.
Also it seems that the khmer step ignores the number of threads set and is utilizing all available cores instead.