Monitoring Performance

If you’re running ScaleHD in verbose mode (-v/–verbose), the pipeline will print to the terminal any updates on stages for each sample that is being processed. This involves a colour code, for success (green), warning/information (yellow) and failure (red). However, if you’re more interested in progress for each individual sample as it is being processed, you will need to look at additional software. Personally, I find it easiest to use the program htop, which you can read about here: https://hisham.hm/htop/. Running htop will allow you to see what third-party binaries that ScaleHD has launched (i.e. what stage of the sample processing it is on), as well as resource usage.

Normally, we just leave a job running overnight and return to it being finished (or almost finished) the next morning.