panacus hsitgrowth returns NaN for first line of output with 0.

[freshspaceoctopus]

Hello, I have constructed a pangenome using minigraph-cactus, and was trying to use panacus to get the histogram values.

I have about 849 assemblies used for my pangenome. I used the following command

haplo=ab.paths.haplotypes.txt RUST_LOG=info panacus histgrowth -t8 -l 1,2,1,1,1 -q 0,0,1,0.5,0.1 -S -a -s ${haplo} ab.gfa > ab.histgrowth.node.tsv

and this is part of the truncated results:

panacus hist growth growth growth growth growth count node node node node node node coverage 1 2 1 1 1 quorum 0 0 1 0.5 0.1 0 18892 NaN NaN NaN NaN NaN 1 719272 913762 912915 913762 913762 913762 2 375826 1069307 1067612 758218 1069307 1069307 3 227182 1162781 1160240 696148 882358 1162781 4 156027 1235106 1231717 655229 945808 1235106 ( ... )

I think there may be an issue with having too many paths? Thank you in advance.

[heringerp]

No, this line is not an issue and is in fact expected. The line starting with 0 tells you that there are 18892 nodes with a coverage of 0. If you have added 0 paths to the graph there is no graph and thus the concept of growth does not make sense yet. That is why NaN is inserted as a placeholder.