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cnapy-org / CNApy

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!
https://cnapy-org.github.io/CNApy-guide/
Apache License 2.0
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EFMTool failure #466

Open dtusso2020 opened 1 year ago

dtusso2020 commented 1 year ago

Hello everyone. I am trying to do a Elementary Flux modes but I got the next error. I am working on windows Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at ch.javasoft.metabolic.efm.util.ColumnUtil.mergeNumeric(ColumnUtil.java:373) at ch.javasoft.metabolic.efm.util.ColumnUtil.mergeNumeric(ColumnUtil.java:364) at ch.javasoft.metabolic.efm.model.nullspace.NullspaceDoubleColumnInspectorModifier.mergeNumeric(NullspaceDoubleColumnInspectorModifier.java:106) at ch.javasoft.metabolic.efm.model.nullspace.NullspaceDoubleColumnInspectorModifier.mergeNumeric(NullspaceDoubleColumnInspectorModifier.java:1) at ch.javasoft.metabolic.efm.column.DoubleColumn.mergeWith(DoubleColumn.java:119) at ch.javasoft.metabolic.efm.column.DoubleColumn.mergeWith(DoubleColumn.java:114) at ch.javasoft.metabolic.efm.adj.incore.AbstractAdjacencyEnumerator.adjacentPairs(AbstractAdjacencyEnumerator.java:76) at ch.javasoft.metabolic.efm.impl.SequentialDoubleDescriptionImpl.iterate(SequentialDoubleDescriptionImpl.java:117) at ch.javasoft.metabolic.efm.impl.AbstractDoubleDescriptionImpl.calculateEfms(AbstractDoubleDescriptionImpl.java:163) at ch.javasoft.metabolic.efm.impl.AbstractDoubleDescriptionImpl.calculateEfms(AbstractDoubleDescriptionImpl.java:130) at ch.javasoft.metabolic.efm.ElementaryFluxModes.calculateCallback(ElementaryFluxModes.java:285) at ch.javasoft.metabolic.efm.main.CalculateFluxModes.start(CalculateFluxModes.java:219) at ch.javasoft.metabolic.efm.main.CalculateFluxModes.start(CalculateFluxModes.java:143) at ch.javasoft.metabolic.efm.main.CalculateFluxModes.main(CalculateFluxModes.java:100) EFMtool failure

How to fix it? Thank you so much.

axelvonkamp commented 1 year ago

How large is your network? EFM enumeration is usually only possible for smaller networks because of combinatorial explosion.