soft mask genome is necessary？

[bighawkin]

There is one genome that hasn't used the soft mask version when running Cactus. Is it necessary to re-run it? The 20 genomes have already been running for 6 days

[glennhickey]

You should soft mask all input genomes to Progressive Cactus with RepeatMasker. But sometimes it will still run ok if you don't. If it doesn't seem to be running out of memory or stuck forever, then you should be fine to let it keep going.

[bighawkin]

thanks for your answer very much