Missing SBO Terms in XML Output with CarveMe

[xuetingyue]

HI,

After running carve Bsubtilis_168.faa --universe bacteria --gapfill M9 --mediadb media_db.tsv -v, I noticed differences between the XML output and the example files provided on the CarveMe GitHub page.

Figure 1: My XML output contains contains <p>FORMULA: xxx</p> and <p>CHARGE: -2</p>.

Figure 2: The example XML file also contains <p>SBOterm xxx</p> , which is missing in my output.

and the XML looks different when viewed in a browser compared to the example file. Is this discrepancy reasonable?

Additionally, when using --cobra, the generated XML has a gene count of 0, whereas --fbc2 does not have this issue. Any insights on why this happens?

Looking forward to your guidance, thank you!