Hi,
I ran MindTheGap on a whole genome sequence data(30x, paired-end 101bp data). The 'find' part has ended in a reasonable time. I ran the 'fill' part similar to the following command:
./MindTheGap fill -graph example.h5 -bkpt example.breakpoints -out example -max-memory 500000 -max-disk 1000000 -nb-cores 84
I increased the -max-memory, -max-disk, and -nb-cores just to speed up the process (The machine has 96 cores (I did not want to use all of the cores), 1TB memory, and more than 2TB disk space).
After ~4,5 - 5 hours, I get this message as time estimate:
[Filling breakpoints ] 1.03 % elapsed: 288 min 1 sec remaining: 27789 min 39 sec
which makes 19 more days! Am I doing something wrong? How can I speed up the 'fill' function?
Thank you very much for you help!