When using the mdl-printcytoseed command, we are not getting correct model information printed to the appropriate cytoseed files.
The program is returning no information or an error in the mdl-printcytoseed subroutine in ModelDriver.pm when calling "get_model_data" and "biomass_reaction_details" in the following code:
open(FH, ">".$cmdir."/model_data") or ModelSEED::utilities::ERROR("Could not open file: $!\n");
my $md = $fbaObj->get_model_data({ "id" => [$args->{model}] });
print FH $dumper->dump($md->{$args->{model}});
close FH;
print "Model data printed...\n";
open(FH, ">".$cmdir."/biomass_reaction_details") or ModelSEED::utilities::ERROR("Could not open file: $!\n");
print FH $dumper->dump($fbaObj->get_biomass_reaction_data({ "model" => [$args->{model}] }));
close FH;
print "Biomass data printed...\n";
Output for model data is:
--- ~
When the biomass is accessed, it returns:
error:
- iYusMp.906 either nonexistant or nonaccessible
This error is being generated from code in FBAMODEL.pm
Accessing other data in the model appears to work (for instance, compound data, reaction data).
Additionally, accessing the compound data seems to be taking about 20 minutes to process this call:
my $cids = $fbaObj->get_compound_id_list({ "id" => [$args->{model}] });
open(FH, ">".$cmdir."/compound_details") or ModelSEED::utilities::ERROR("Could not open file: $!\n");
my $cpds = $fbaObj->get_compound_data({ "id" => $cids->{$args->{model}} });
print FH $dumper->dump($cpds);
close FH;
print "Compound data printed...\n";
Seems like that is very long, especially for a small genome/model.
When using the mdl-printcytoseed command, we are not getting correct model information printed to the appropriate cytoseed files.
The program is returning no information or an error in the mdl-printcytoseed subroutine in ModelDriver.pm when calling "get_model_data" and "biomass_reaction_details" in the following code:
Output for model data is:
--- ~
When the biomass is accessed, it returns:
error:
This error is being generated from code in FBAMODEL.pm
Accessing other data in the model appears to work (for instance, compound data, reaction data).
Additionally, accessing the compound data seems to be taking about 20 minutes to process this call:
my $cids = $fbaObj->get_compound_id_list({ "id" => [$args->{model}] });
open(FH, ">".$cmdir."/compound_details") or ModelSEED::utilities::ERROR("Could not open file: $!\n");
my $cpds = $fbaObj->get_compound_data({ "id" => $cids->{$args->{model}} });
print FH $dumper->dump($cpds);
close FH;
print "Compound data printed...\n";
Seems like that is very long, especially for a small genome/model.