Long runtime

[David-Flurin]

Hi!

I'm wondering about the time Pindel takes on our machine for a whole genome analysis. When I run Pindel for a 90x-coverage file and use 22 Cores, it takes about 4 days to completion. I'm aware that it has to take longer for higher coverage, but this seems a bit unreasonable compared to the 4.5 hours runtime which is mentioned in the initial Pindel paper. Further I have not seen that any other people had an issue with the runtime.
The command I'm using is:

./pindel -f ref_file.fa -i configfile -T 22 -o output

In the configfile is only one BAM file mentioned.
Do you have any idea why its taking so long? Do you have suggestions how to improve the runtime?

I would greatly appreciate your help!

Thanks,
David