Recon-all shutting down after long run? because of flair?

recon-all is not an MRtrix command but a FreeSurfer command. You can seek support for FreeSurfer at: FreeSurferSupport - Free Surfer Wiki

Two minor points in addition to what Ben said:

  • Your subject name is visible in the screenshot. If this is confidential data you might want to redact that part of the screenshot.
  • The second screenshot does not show the log file. Instead, you had a typo when opening the file: recol-all.log (notice the L instead of n). Maybe the right log file can point you towards a solution.

thank you so much!