Annotation format and column meaning

[SchwarzMarek]

Hello, thanks for the pipeline I' want to use different reference and needed to convert annotations as suggested in documentation. To get the feel about the annotation format, I've looked at the M.abscessus annotations; I' not sure what does the following columns mean and if/how this information is used in the pipeline and what are acceptable values:

What I've seen in the file:

status_region             [status 3]
status_function          [annotated]
region_number                    [5]
function_number                  [6]

Also, since genome can have multiple sequences (chromosomes or incomplete assembly with multiple contigs/scaffolds), how would this be specified in this pipeline, as it appears that no chromosome identification is present in the *.txt annotation file.?