HelitronScanner running time

Question

[gabri]

Hi All,

I'm running HelitronScanner on my genome assembly with the following command line:

java -jar HelitronScanner.jar scanHead -g Genome.fasta -bs 1000000 -tl 10

-tl 10 = number of CPU

-bs 1000000 = genome slice size

It seems that the process is going very very slow, using less than 1 CPU. Also, I cannot see any kind of temporany output. Is this programm normally very slow? Is the option -bs 1000000 affecting the performance that much?

The manual says: -bs, buffer_size = To avoid excessive memory usage, use -buffer_size 1000000 (1 Mb slice at a time) forwhole genome scans. Otherwise, use -buffer_size 0 instead.

Thank you