Hi, welcome. Please understand that a certain minimal amount of information is necessary to make a post meaningful, see https://www.bioconductor.org/help/support/posting-guide/. In your three questions none fulfills these criteria.

• in this one here any context is missing, no code or reproducible example
• in Log of Step 1 it's a wall of code without explanation where it comes from and what exactly is the "fix"
• in Rbam and Rqc files error again no context, code, or data examples or even a sessionInfo()

Please edit these quesions and add the necessary context, code, reproducible examples. Without that it's impossible to help.