Dear Developer, Thank you so much for your ongoing maintenance of GapSeq. I apologize for bothering you again with an issue I encountered in the software.
After running the gapseq adapt command, although it indicates reactions were added, I cannot locate the corresponding metabolites in the files. This prevents me from performing FBA calculations. I am using Gapseq version 2.0.0.
./gapseq adapt -m AR1365-CDS.RDS -w cpd01200:TRUE -b AR1365/faa/AR1365-CDS-all-Reactions.tbl
Loading model files AR1365-CDS.RDS
[1] "adapt model to growth table"
[1] "EX_cpd01200_e0"
[1] "Added exchange reaction for:cpd01200"
Try to gapfill Palatinose cpd01200
Utilized candidate reactions: 58
Gapfill summary:
Added reactions: 14
Added core reactions: 5
Final growth rate: 0.3125
Added reactions: rxn08972_c0 rxn10043_c0 rxn17267_c0 rxn40053_c0 rxn90031_c0 rxn90032_c0 rxn90090_c0 rxn90093_c0 rxn90103_c0
[1] "Save output file ./AR1365-CDS-adapt.RDS"
[1] "Writing SBML file ./AR1365-CDS-adapt.xml"
When I checked the generated XML, I couldn't find the substance cpd01200.
Dear Developer, Thank you so much for your ongoing maintenance of GapSeq. I apologize for bothering you again with an issue I encountered in the software.
After running the
gapseq adaptcommand, although it indicates reactions were added, I cannot locate the corresponding metabolites in the files. This prevents me from performing FBA calculations. I am using Gapseq version 2.0.0.When I checked the generated XML, I couldn't find the substance cpd01200.