I'm using hard constraints to force some reactions to be present in my model, but for some reason the reactions are not included in the output model (but the reactions are present in the universe model).
The command I used is:
carve proteinSeq.txt -v --hard hardConstraints.tsv -u archaea
The hardConstraints.tsv file has only three lines:
R_12DGR140tipp -1000 1000
R_2AGPGAT160 -1000 1000
R_2DGULRx -1000 1000
I did not receive any error message. Below you find the last lines printed by CarveMe:
"""
Closing the database file... [0.014s]
Deallocating taxonomy... [0s]
Total time = 15.244s
Reported 2709 pairwise alignments, 2709 HSPs.
1402 queries aligned.
Loading universe model...
Scoring reactions...
Reconstructing a single model
Done.
"""
When I don't use hard constraints (i.e. "carve proteinSeq.txt -v -u archaea") I have a different model, but the reactions present on "hardConstraints.tsv" are not part of this difference.
I'm using hard constraints to force some reactions to be present in my model, but for some reason the reactions are not included in the output model (but the reactions are present in the universe model).
The command I used is: carve proteinSeq.txt -v --hard hardConstraints.tsv -u archaea
The hardConstraints.tsv file has only three lines: R_12DGR140tipp -1000 1000 R_2AGPGAT160 -1000 1000 R_2DGULRx -1000 1000
I did not receive any error message. Below you find the last lines printed by CarveMe:
""" Closing the database file... [0.014s] Deallocating taxonomy... [0s] Total time = 15.244s Reported 2709 pairwise alignments, 2709 HSPs. 1402 queries aligned. Loading universe model... Scoring reactions... Reconstructing a single model Done. """
When I don't use hard constraints (i.e. "carve proteinSeq.txt -v -u archaea") I have a different model, but the reactions present on "hardConstraints.tsv" are not part of this difference.
I'm using CarveMe version 1.5.1
Am I dong something wrong?