Why does the core_clusters.txt file contain blank cells in genome columns (columns >=8)?

[jarrettlebov]

Hi, I'm a relatively new user of PanOCT. In viewing some of the output files, I noticed that in the core_clusters.txt file, while the vast majority of rows have no blank cells in the genome columns (columns >= 8), a minority of rows have some blank cells. These empty cells seem to always fall in rows where the "attributes" column contains an "FS", "FG-In", or "FN".

Given the description of core_clusters.txt file in the OUT_FILE_DESCRIPTIONS.txt file ("core_clusters.txt: Tab delimited file. Lists only those clusters which have a representative from every genome in the analysis."), I'm confused how the core_clusters.txt file could have any empty cells.

I apologize if this is a novice question, I can't seem to connect the dots by reading through the documentation on this site, the original 2012 PanOCT paper, or the 2018 pangenome pipeline paper.

Any guidance would be greatly appreciated. I have attached my core_clusters.txt file for reference.

core_clusters.txt