-------- Forwarded Message -------- From: Patricia Alvarez <[email protected]> To: [email protected] Subject: Error reading SBML file, GLPK problem? Date: Fri, 13 Oct 2017 10:48:29 +0200
Hello, I'm trying to reconstruct a first draft of a model with Pathway Tools, using the annotation file Genbank and the genome FASTA curate of NCBI. Then, I export it as SBML format to use it in CobraPy. If I read the model in this way, I get no errors: from libsbml import * reader= SBMLReader() model= reader.readSBML(filename) print model.getNumErrors() print model.printErrors() However, If I use "read_sbml_model" function, the kernel die and I obtain this error. I think it's related with the solver GLPK, but I'm only reading the model. glp_set_col_name: j = 1877; column name too long Error detected in file api/prob1.c at line 506 Aborted (core' generated)` In addition, I validated the SBML file in http://sbml.org/Facilities/Validator/ and it's OK. I took a look at the XML file and all the reactions have the bounds defined, although they aren't curated yet. CobraPy experts suggest me maybe the problem it's because IDs variables are very long (close to 256 characters) and GLPLK cannot supported it. But I don't know how to identify that IDs in the file (if these is the problem, of course...) How can I read the model? What should I do? How I can fix it? I attached the file for more info. I would appreciate any advice. Thank you very much. _______________________________________________ Help-glpk mailing list [email protected] https://lists.gnu.org/mailman/listinfo/help-glpk
