FRED-2 / OptiType

Precision HLA typing from next-generation sequencing data

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[External] GLPK error 4.5x

b-schubert opened this issue · comments

With Pyomo 5.x the following error occurs for GLPK <= 4.5x (see Pyomo/pyomo#146)

Writing MIP solution to `/tmp/tmpDUGZvJ.glpk.raw'... 474 lines were written ERROR: Expecting 's' row after 'c' rows Traceback (most recent call last): File "OptiTypePipeline.py", line 405, in <module> result = op.solve(args.enumerate) File "/home/travis/build/FRED-2/OptiType/model.py", line 153, in solve res = self.__solver.solve(self.__instance, options={}, tee=self.__verbosity) File "/home/travis/virtualenv/python2.7.9/lib/python2.7/site-packages/pyomo/opt/base/solvers.py", line 610, in solve result = self._postsolve() File "/home/travis/virtualenv/python2.7.9/lib/python2.7/site-packages/pyomo/opt/solver/shellcmd.py", line 268, in _postsolve results = self.process_output(self._rc) File "/home/travis/virtualenv/python2.7.9/lib/python2.7/site-packages/pyomo/opt/solver/shellcmd.py", line 330, in process_output self.process_soln_file(results) File "/home/travis/virtualenv/python2.7.9/lib/python2.7/site-packages/pyomo/solvers/plugins/solvers/GLPK.py", line 362, in process_soln_file raise ValueError(msg) ValueError: Error parsing solution data file, line 2

Internally resolved for Travis-CI tests in PR #57