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?
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--fbc2does not have this issue. Any insights on why this happens?Looking forward to your guidance, thank you!