[Help-glpk] [Fwd: Error reading SBML file, GLPK problem?]

[Andrew Makhorin]

-------- Forwarded Message --------
From: Patricia Alvarez <address@hidden>
To: address@hidden
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.