I am trying to model the biochemical interaction between a photosynthetic bacterium and another commonly found bacterium. However, mmetana fails to find a minimal growth medium. I have attached the data for reproducibility ("testcase.tar.gz").
The file bin.6.xml contains the metabolomic model for the photosynthetic bacterium.
The file bin.5.xml contains the metabolomic model for the potential symbiont.
The models were produced using gapseq.
The file media_db.tsv contains the MF2 medium.
I have tried both the "default" notation and the gapseq-like notation of components in MF2_gapseq_smetana.tsv, but neither worked.
To reproduce:
extract the testcase.tar.gz file
run command smetana --molweight --verbose --solver gurobi -d bin.*.xml -o test1 -m MF2 --mediadb media_db.tsv. The 1.2.0 version of smetana was used.
The error i get:
`smetana --molweight --verbose --solver gurobi -d bin.*.xml -o test1 -m MF2 --mediadb media_db.tsv
Loading community: all
Running SCS for community all on medium MF2...
/mnt/workspace/miniconda3/envs/snakemake/lib/python3.11/site-packages/reframed/core/cbmodel.py:211: UserWarning: Suspicious biomass identifier: R_EX_cpd11416_c0
warn(f"Suspicious biomass identifier: {self._biomass_reaction}")
Set parameter Username
Academic license - for non-commercial use only - expires 2025-06-19
/mnt/workspace/miniconda3/envs/snakemake/lib/python3.11/site-packages/smetana/smetana.py:104: UserWarning: SCS: Failed to find a solution for growth of bin.5
warn('SCS: Failed to find a solution for growth of ' + org_id)
/mnt/workspace/miniconda3/envs/snakemake/lib/python3.11/site-packages/smetana/smetana.py:104: UserWarning: SCS: Failed to find a solution for growth of bin.6
warn('SCS: Failed to find a solution for growth of ' + org_id)
Running MUS for community all on medium MF2...
/mnt/workspace/miniconda3/envs/snakemake/lib/python3.11/site-packages/reframed/core/elements.py:62: UserWarning: Atomic weight not listed for elements: {'Z'}
warn(f"Atomic weight not listed for elements: {missing}")
/mnt/workspace/miniconda3/envs/snakemake/lib/python3.11/site-packages/smetana/smetana.py:160: UserWarning: MUS: Failed to find a minimal growth medium for bin.5
warn('MUS: Failed to find a minimal growth medium for ' + org_id)
/mnt/workspace/miniconda3/envs/snakemake/lib/python3.11/site-packages/smetana/smetana.py:160: UserWarning: MUS: Failed to find a minimal growth medium for bin.6
warn('MUS: Failed to find a minimal growth medium for ' + org_id)
For bin.6, this medium should support growth. I have tested it with BacArena, and the medium allows the growth of bin.6. How can I move forward? Thank you in advance.
Hi,
I am trying to model the biochemical interaction between a photosynthetic bacterium and another commonly found bacterium. However, mmetana fails to find a minimal growth medium. I have attached the data for reproducibility ("testcase.tar.gz").
The file bin.6.xml contains the metabolomic model for the photosynthetic bacterium. The file bin.5.xml contains the metabolomic model for the potential symbiont. The models were produced using gapseq. The file media_db.tsv contains the MF2 medium. I have tried both the "default" notation and the gapseq-like notation of components in MF2_gapseq_smetana.tsv, but neither worked.
To reproduce:
smetana --molweight --verbose --solver gurobi -d bin.*.xml -o test1 -m MF2 --mediadb media_db.tsv.The 1.2.0 version of smetana was used. The error i get: `smetana --molweight --verbose --solver gurobi -d bin.*.xml -o test1 -m MF2 --mediadb media_db.tsv Loading community: all Running SCS for community all on medium MF2... /mnt/workspace/miniconda3/envs/snakemake/lib/python3.11/site-packages/reframed/core/cbmodel.py:211: UserWarning: Suspicious biomass identifier: R_EX_cpd11416_c0 warn(f"Suspicious biomass identifier: {self._biomass_reaction}") Set parameter Username Academic license - for non-commercial use only - expires 2025-06-19 /mnt/workspace/miniconda3/envs/snakemake/lib/python3.11/site-packages/smetana/smetana.py:104: UserWarning: SCS: Failed to find a solution for growth of bin.5 warn('SCS: Failed to find a solution for growth of ' + org_id) /mnt/workspace/miniconda3/envs/snakemake/lib/python3.11/site-packages/smetana/smetana.py:104: UserWarning: SCS: Failed to find a solution for growth of bin.6 warn('SCS: Failed to find a solution for growth of ' + org_id) Running MUS for community all on medium MF2... /mnt/workspace/miniconda3/envs/snakemake/lib/python3.11/site-packages/reframed/core/elements.py:62: UserWarning: Atomic weight not listed for elements: {'Z'} warn(f"Atomic weight not listed for elements: {missing}") /mnt/workspace/miniconda3/envs/snakemake/lib/python3.11/site-packages/smetana/smetana.py:160: UserWarning: MUS: Failed to find a minimal growth medium for bin.5 warn('MUS: Failed to find a minimal growth medium for ' + org_id) /mnt/workspace/miniconda3/envs/snakemake/lib/python3.11/site-packages/smetana/smetana.py:160: UserWarning: MUS: Failed to find a minimal growth medium for bin.6 warn('MUS: Failed to find a minimal growth medium for ' + org_id)For bin.6, this medium should support growth. I have tested it with BacArena, and the medium allows the growth of bin.6. How can I move forward? Thank you in advance.
Best, Gediminas
testcase.tar.gz