The logging output of FLAIR is not helpful and obscures real issues
FLAIR fills stdout with various progress meters. Since 1) these are for several internal steps of FLAIR, not the whole run, and 2) one doesn't run something that takes this long from a terminal, it just creates hundreds of lines of noise that obscure real issues. Please delete the progress bars. These are negatively helpful.
The stderr/stdout messages vs the fair.err file results in messages split between two destinations. The is means one has to look it two places to understand what is happening.
Please just use python logger
minimap2 log messages fill up the log, please turn these off
The logging output of FLAIR is not helpful and obscures real issues