Gapfilling a model after gapseq adapt?

[LucoDevro]

Hi there,

Is it possible to gapfill a model after running adapt? The reason why I'm asking this is that I'm trying to construct new strain-specific models starting from a pan-species reference model that I build using gapseq.

To construct the pan-model, I didn't use your new panDraft module but started a de novo gapseq workflow up to the draft stage and this starting from representative proteins sequences from an upstream pangenome tool.

To then get the new strain-specific model, I'm using BBH from Diamond to select present reactions from the pan-model and remove all the other ones from of the pan-model using gapseq adapt. I'd like then to gapfill the new draft strain-model using the fill module to get it produce biomass, but it throws an obscure error.

gapseq fill -m pan_model-adapt.RDS -n M9_glc_medium_an.csv -c pan_model-rxnWeights.RDS -g pan_model-rxnXgenes.RDS -f out 
Loading required package: glpkAPI
using GLPK version 5.0
Warning message:
glpkAPI is used but cplexAPI is recommended because it is much faster 
Loading model files pan_model-adapt.RDS 
Error in data.frame(..., check.names = FALSE) : 
  arguments imply differing number of rows: 0, 1
Calls: cbind -> cbind -> data.frame
Execution halted

This is the output of gapseq -v

gapseq version: 1.3.1 fb7fbcb7
Sequence DB md5sum: 17e92c9 (2023-12-12, Bacteria)
Sequence DB md5sum: 8bb9575 (2023-12-12, Archaea)

And this of gapseq test
test.txt

For your information, I also have similar errors related with special characters as in #173, but I'm ignoring all errors that seem related to this as suggested there (and #213 is related to #173 I guess, and exactly my case as well, it's the same md5sum). Hope the failing gapfilling is not a downstream effect of this.