Advice on run time

[seynard]

Hi, I'm trying to build a pangenome across two mammal species. I'm building it on the 2 reference genomes of 2Gb each approximately. How long should I expect progressive cactus to take to give me an output?
Should I perform any pre-treatment on my initial assemblies before running progressive cactus?
Thanks so much in advance for your help

[glennhickey]

Yes, you need to pre-mask genomes before running progressive cactus https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/progressive.md#masking

[seynard]

Thanks a lot for your answer, I tested my genomes with the command
if zgrep -q '^[^>]*[a-z]' ${fasta}; then echo "The FASTA file is soft-masked."; else echo "The FASTA file is NOT soft-masked."; fi
which confirmed that my genomes are soft-masked, is that enough ?
In the mean time the job finished running in 14 days without mistakes for pig and rabbit genomes. I guess that expected.