Cynobacteria universe

[Buiboni]

Hi, First of all I want to say that CarveMe is really an amazing tool! Thanks for making it so easy to use!

I am using it to reconstruct various networks but with the new version I could not use the cyanobactera universe. The error comes from the lack of objective function. But even when using the objective function from the bacteria universe there is no photosynthetic apparel. As you improved a lot the bacteria universe, I do not know if there is some modification on the photosynthetic side of the cyanobacteria.

I am using the latest version of CarveMe (1.5.1).

Best, Antoine

PS: The issue of missing objective function also occur when building the "Bigg" universe.

[cdanielmachado]

Hi Antoine,

Sorry for the late reply. I have an automated benchmark for gram-positive and gram-negative bacteria but not for cyanobacteria. So it is possible that during the last manual curation some changes have created problems for the cyanobacteria universal model. I will look into it, but I am quite busy at the moment so it could take some time. For the moment I am afraid you might have to use CarveMe 1.4.

Best, Daniel

[ntromas]

Hi Daniel,

I also tried to use the cyanobacteria universe and got this error:

The host system is detected to have 134 GB of RAM. It is recommended to use this parameter for better performance: -c1 Traceback (most recent call last): File "/home/nico/miniconda3/bin/carve", line 33, in sys.exit(load_entry_point('carveme==1.5.1', 'console_scripts', 'carve')()) File "/home/nico/miniconda3/lib/python3.8/site-packages/carveme/cli/carve.py", line 349, in main maincall( File "/home/nico/miniconda3/lib/python3.8/site-packages/carveme/cli/carve.py", line 202, in maincall model = carve_model(universe_model, scores, inplace=(not gapfill), default_score=default_score, File "/home/nico/miniconda3/lib/python3.8/site-packages/carveme/reconstruction/carving.py", line 231, in carve_model sol = minmax_reduction(model, scores, default_score=default_score, uptake_score=uptake_score, soft_score=soft_score, File "/home/nico/miniconda3/lib/python3.8/site-packages/carveme/reconstruction/carving.py", line 99, in minmax_reduction biomass = model.biomass_reaction File "/home/nico/miniconda3/lib/python3.8/site-packages/reframed/core/cbmodel.py", line 190, in biomass_reaction self._detect_biomass_reaction() File "/home/nico/miniconda3/lib/python3.8/site-packages/reframed/core/cbmodel.py", line 213, in _detect_biomass_reaction raise RuntimeError(f"No biomass reaction identified from model objective.") RuntimeError: No biomass reaction identified from model objective.

Just wonder if it is still an issue with the last version of CarveMe or not.

Cheers!

Nico