Unable to complete tree drawing and software crashes due to memory usage

[AJW31]

Hi,

I am trying to use SplitsTee to visualise my .splits.nex output from IQTREE2. These files are around ~2kb - 3kb in size and are built from 254 BUSCO genes. However, when drawing the network, SplitsTree seems to crash and never finishes producing the visualisation of the tree.

I am running the software on a Mac with 30GB of RAM, but when looking at how much memory SplitsTree is using, it appears to always be using more memory than it has been allocated which could be leading to the software crashing. I therefore changed the amount of memory SplitsTree could use to 20GB so that there would be excess available if it went over the allocated amount, however it still appears to crash before completing the network drawing.

I have also tried to run this on another dataset from a colleague, who has done an phylogenetic analysis on bacteria, but the same issue seems to occur.

Any help would be greatly appreciated!
Thanks,
Amy

[husonlab]

Dear Any, sorry to here that, could you please send me the file (using my Univ of Tuebingen email address) and I will look into the problem Best wishes Daniel

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On Apr 9, 2025, at 15:21, AJW31 ***@***.***> wrote: AJW31 created an issue (husonlab/splitstree6#49) Hi, I am trying to use SplitsTee to visualise my .splits.nex output from IQTREE2. These files are around ~2kb - 3kb in size and are built from 254 BUSCO genes. However, when drawing the network, SplitsTree seems to crash and never finishes producing the visualisation of the tree. I am running the software on a Mac with 30GB of RAM, but when looking at how much memory SplitsTree is using, it appears to always be using more memory than it has been allocated which could be leading to the software crashing. I therefore changed the amount of memory SplitsTree could use to 20GB so that there would be excess available if it went over the allocated amount, however it still appears to crash before completing the network drawing. I have also tried to run this on another dataset from a colleague, who has done an phylogenetic analysis on bacteria, but the same issue seems to occur. Any help would be greatly appreciated! Thanks, Amy — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread. <#49> <https://github.com/notifications/unsubscribe-auth/ABTNU4TFN2IDKSVW2UPNWO32YUNEXAVCNFSM6AAAAAB2Y7KDAWVHI2DSMVQWIX3LMV43ASLTON2WKOZSHE4DEOBRGI4TQNY> AJW31 created an issue (husonlab/splitstree6#49) <#49> Hi, I am trying to use SplitsTee to visualise my .splits.nex output from IQTREE2. These files are around ~2kb - 3kb in size and are built from 254 BUSCO genes. However, when drawing the network, SplitsTree seems to crash and never finishes producing the visualisation of the tree. I am running the software on a Mac with 30GB of RAM, but when looking at how much memory SplitsTree is using, it appears to always be using more memory than it has been allocated which could be leading to the software crashing. I therefore changed the amount of memory SplitsTree could use to 20GB so that there would be excess available if it went over the allocated amount, however it still appears to crash before completing the network drawing. I have also tried to run this on another dataset from a colleague, who has done an phylogenetic analysis on bacteria, but the same issue seems to occur. Any help would be greatly appreciated! Thanks, Amy — Reply to this email directly, view it on GitHub <#49>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABTNU4TFN2IDKSVW2UPNWO32YUNEXAVCNFSM6AAAAAB2Y7KDAWVHI2DSMVQWIX3LMV43ASLTON2WKOZSHE4DEOBRGI4TQNY>. You are receiving this because you are subscribed to this thread.

[AJW31]

That would be great! Thanks so much. I have sent the files to you now.

Best,
Amy

[husonlab]

easy fix: when splits tree starts computing the network, cancel that. Then right click on the Working Splits item in the sidebar and select Dimension Filter. (I will look into having this part of the pipeline by default). This will push the splits through a dimension filter before attempting to create the network. This removes tiny splits in the visualization that you can’t really see, but that contribute a huge number of nodes and edges to the network

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On Apr 9, 2025, at 15:21, AJW31 ***@***.***> wrote: AJW31 created an issue (husonlab/splitstree6#49) Hi, I am trying to use SplitsTee to visualise my .splits.nex output from IQTREE2. These files are around ~2kb - 3kb in size and are built from 254 BUSCO genes. However, when drawing the network, SplitsTree seems to crash and never finishes producing the visualisation of the tree. I am running the software on a Mac with 30GB of RAM, but when looking at how much memory SplitsTree is using, it appears to always be using more memory than it has been allocated which could be leading to the software crashing. I therefore changed the amount of memory SplitsTree could use to 20GB so that there would be excess available if it went over the allocated amount, however it still appears to crash before completing the network drawing. I have also tried to run this on another dataset from a colleague, who has done an phylogenetic analysis on bacteria, but the same issue seems to occur. Any help would be greatly appreciated! Thanks, Amy — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread. <#49> <https://github.com/notifications/unsubscribe-auth/ABTNU4TFN2IDKSVW2UPNWO32YUNEXAVCNFSM6AAAAAB2Y7KDAWVHI2DSMVQWIX3LMV43ASLTON2WKOZSHE4DEOBRGI4TQNY> AJW31 created an issue (husonlab/splitstree6#49) <#49> Hi, I am trying to use SplitsTee to visualise my .splits.nex output from IQTREE2. These files are around ~2kb - 3kb in size and are built from 254 BUSCO genes. However, when drawing the network, SplitsTree seems to crash and never finishes producing the visualisation of the tree. I am running the software on a Mac with 30GB of RAM, but when looking at how much memory SplitsTree is using, it appears to always be using more memory than it has been allocated which could be leading to the software crashing. I therefore changed the amount of memory SplitsTree could use to 20GB so that there would be excess available if it went over the allocated amount, however it still appears to crash before completing the network drawing. I have also tried to run this on another dataset from a colleague, who has done an phylogenetic analysis on bacteria, but the same issue seems to occur. Any help would be greatly appreciated! Thanks, Amy — Reply to this email directly, view it on GitHub <#49>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABTNU4TFN2IDKSVW2UPNWO32YUNEXAVCNFSM6AAAAAB2Y7KDAWVHI2DSMVQWIX3LMV43ASLTON2WKOZSHE4DEOBRGI4TQNY>. You are receiving this because you are subscribed to this thread.