not enough memory Unresolved

[Sheila Rodríguez]

Hello Cecile,

Thanks for developing PhyloNet and helping us troubleshoot through this group.

I'm trying to use the software for the first time and I keep getting the same error (see below).

I tried your solution to the problem "Not enough memory" from here https://phylogenomics.rice.edu/html/phylonetTroubleshooting2.html but it didn't work for me. Hope you can help me.

Thanks in advance,

Sheila

From my terminal, I tried the following:

java -jar -Xmx4G PhyloNetv3_8_2.jar MPL/InferNetwork_MPL_pl8_0_393.nex

also, 8G and 12G and still the same error.

>> My mac: Processor: 2.3 GHz Intel Core i9

                      Memory 16 GB 2400 MHz DDR4

>> Java: java version "15.0.2" 2021-01-19

               Java(TM) SE Runtime Environment (build 15.0.2+7-27)

               Java HotSpot(TM) 64-Bit Server VM (build 15.0.2+7-27, mixed mode, sharing)

>> My data: 393 IQTree-generated trees --- 10 ingroup taxa --- 1 outgroup --- 

>> My .nex file:

#NEXUS
BEGIN Trees;
Tree gt0 = ((((((Gambusia:0.0170357743,Pseudoxiphophorus:0.0176974271):0.0099131778,Neoheterandria:0.029365,Heterandria:0.0384303,(Girardinus:0.0184635091,Quintana:0.0130039246)99:0.0113028)91:0.00231539,(Limia:0.0237257023,Phalloceros:0.028164478)70:0.0032726426)52:0.0112633297,Tomeurus:0.0589380421)92:0.0259470276,Xenodexia:0.0540513091)99:0,Anableps:0.1230131159);
...

Tree gt392 ();

END;
BEGIN PHYLONET;
InferNetwork_MPL (all) 0 -pl 8 -x 10 -po;

END;

ERROR:

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

   at java.base/java.util.Hashtable.addEntry(Hashtable.java:451)

   at java.base/java.util.Hashtable.put(Hashtable.java:493)

   at edu.rice.cs.bioinfo.programs.phylonet.structs.tree.model.sti.STINode.<init>(STINode.java:62)

   at edu.rice.cs.bioinfo.programs.phylonet.structs.tree.model.sti.STITree.copyNode(STITree.java:192)

   at edu.rice.cs.bioinfo.programs.phylonet.structs.tree.model.sti.STITree.copyNode(STITree.java:199)

   at edu.rice.cs.bioinfo.programs.phylonet.structs.tree.model.sti.STITree.copyNode(STITree.java:199)

   at edu.rice.cs.bioinfo.programs.phylonet.structs.tree.model.sti.STITree.<init>(STITree.java:154)

   at edu.rice.cs.bioinfo.programs.phylonet.structs.tree.model.sti.STITree.<init>(STITree.java:133)

   at edu.rice.cs.bioinfo.programs.phylonet.structs.tree.util.Trees.getAllBinaryResolution(Trees.java:851)

   at edu.rice.cs.bioinfo.programs.phylonet.algos.network.NetworkLikelihoodFromGTT_SingleTreePerLocus.summarizeData(NetworkLikelihoodFromGTT_SingleTreePerLocus.java:62)

   at edu.rice.cs.bioinfo.programs.phylonet.algos.network.InferNetworkPseudoMLFromGTT.inferNetwork(InferNetworkPseudoMLFromGTT.java:82)

   at edu.rice.cs.bioinfo.programs.phylonet.commands.InferNetwork_MPL.produceResult(InferNetwork_MPL.java:716)

   at edu.rice.cs.bioinfo.programs.phylonet.commands.CommandBaseFileOut.executeCommandHelp(CommandBaseFileOut.java:173)

   at edu.rice.cs.bioinfo.programs.phylonet.commands.InferNetwork_MPL.executeCommandHelp(InferNetwork_MPL.java:53)

   at edu.rice.cs.bioinfo.programs.phylonet.commands.CommandBase.executeCommand(CommandBase.java:306)

   at edu.rice.cs.bioinfo.programs.phylonet.Program.run(Program.java:256)

   at edu.rice.cs.bioinfo.programs.phylonet.Program.main(Program.java:110)

[Cécile Ané]

Hi Sheila,

PhyloNet (in java) and PhyloNetworks (in julia) are different programs. I cannot help with PhyloNet, sorry!

Perhaps someone else on this list may have good pointers for you, though.

Cécile.

On Saturday, February 4, 2023 at 5:20:37 PM UTC-6 Sheila Rodríguez wrote:

Hello Cecile,

Thanks for developing PhyloNet and helping us troubleshoot through this group.

I'm trying to use the software for the first time and I keep getting the same error (see below).

I tried your solution to the problem "Not enough memory" from here https://phylogenomics.rice.edu/html/phylonetTroubleshooting2.html but it didn't work for me. Hope you can help me.

Thanks in advance,

Sheila

From my terminal, I tried the following:

java -jar -Xmx4G PhyloNetv3_8_2.jar MPL/InferNetwork_MPL_pl8_0_393.nex

also, 8G and 12G and still the same error.

...