Keep getting an error as 'ASCII file unsupported' which terminates the code
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When running a function from the efmtoool by ETH Zurich - to produce a print out of code - I am recieving the error printed below. The term 'stoich' it refers to is a sparse double - 72*95 matrix in size. How can i eliminate this error?
Warning: Saving sparse arrays to an ASCII file is unsupported.
Variable 'stoich' not written to file.
> In CalculateFluxModes>CalculateStoich (line 203)
In CalculateFluxModes (line 109)
In EFMTool_test (line 21)
java call arguments:
-kind stoichiometry -stoich tmp/stoich.txt -rev tmp/revs.txt -meta tmp/mnames.txt -reac tmp/rnames.txt -arithmetic double -zero 1e-10 -out matlab tmp/efms.mat -compression default -log console -level INFO -tmpdir /Users/b5019437/Documents/MATLAB/pHd/EFM Methods/efmtool/tmp -maxthreads -1 -normalize min -adjacency-method pattern-tree-minzero -rowordering MostZerosOrAbsLexMin
2020-11-23 15:14:45.560 main INFO | logger initialized
2020-11-23 15:14:45.561 main INFO | =====================================================
2020-11-23 15:14:45.561 main INFO | efmtool version 4.7.1, 2009-12-04 18:30:05
2020-11-23 15:14:45.561 main INFO | Copyright (c) 2009, Marco Terzer, Zurich, Switzerland
2020-11-23 15:14:45.561 main INFO | This is free software, !!! NO WARRANTY !!!
2020-11-23 15:14:45.561 main INFO | See LICENCE.txt for redistribution conditions
2020-11-23 15:14:45.561 main INFO | =====================================================
java.lang.NegativeArraySizeException
at ch.javasoft.metabolic.parse.StoichParser.parseStoich(StoichParser.java:226)
at ch.javasoft.metabolic.parse.StoichParser.parse(StoichParser.java:112)
at ch.javasoft.metabolic.parse.ConfiguredParser.parseStoichiometry(ConfiguredParser.java:405)
at ch.javasoft.metabolic.parse.ConfiguredParser.parse(ConfiguredParser.java:219)
at ch.javasoft.metabolic.parse.ConfiguredParser.parseConfig(ConfiguredParser.java:201)
at ch.javasoft.metabolic.efm.main.CalculateFluxModes.start(CalculateFluxModes.java:217)
at ch.javasoft.metabolic.efm.main.CalculateFluxModes.start(CalculateFluxModes.java:143)
at ch.javasoft.metabolic.efm.main.CalculateFluxModes.matlab(CalculateFluxModes.java:109)
ch.javasoft.metabolic.efm.main.CalculateFluxModes with following arguments: -kind stoichiometry -stoich tmp/stoich.txt -rev tmp/revs.txt -meta tmp/mnames.txt -reac tmp/rnames.txt -arithmetic double -zero 1e-10 -out matlab tmp/efms.mat -compression default -log console -level INFO -tmpdir /Users/b5019437/Documents/MATLAB/pHd/EFM Methods/efmtool/tmp -maxthreads -1 -normalize min -adjacency-method pattern-tree-minzero -rowordering MostZerosOrAbsLexMin
>>
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Rik
am 23 Nov. 2020
The solution is in the error message: "Saving sparse arrays to an ASCII file is unsupported."
Either use full to convert your sparse double to a normal double, or don't use an ASCII file.
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