Hello, I'm trying to run iqtree with two partitions, one nucleotide alignment and one binary data. I created the nexus file as following:

nexus

begin sets; charset part1 = novo_dataset.unique.noRef.fasta: ; charset part2 = indel.novo_dataset.unique.noRef.fasta: ; charpartition mine = UNREST+FO+I+G4:part1, JC2+FQ+ASC+G4:part2; end;

Then I tried to run with the following line: iqtree2.1.3 -p iqtree_multiPart_models.nexus -alrt 1000 -ninit 1000 -nstop 200 -czb -nt AUTO

And it crashes giving me this error message: NOTE: 1908 MB RAM (1 GB) is required! Measuring multi-threading efficiency up to 6 CPU cores ERROR: STACK TRACE FOR DEBUGGING: ERROR: 2 _sigtramp() ERROR: 4 kmp_invoke_microtask() ERROR: 5 kmp_fork_call() ERROR: 6 __kmpc_fork_call() ERROR: 7 double PhyloTree::computeLikelihoodBranchGenericSIMD<Vec4d, true, true, false>(PhyloNeighbor, PhyloNode) ERROR: 9 PhyloSuperTreePlen::computeFunction(double) ERROR: 10 PhyloSuperTreePlen::computeLikelihoodBranch(PhyloNeighbor, PhyloNode) ERROR: 11 PhyloTree::optimizeAllBranches(int, double, int) ERROR: 12 PhyloTree::testNumThreads() ERROR: 13 runTreeReconstruction(Params&, IQTree&) ERROR: 14 runPhyloAnalysis(Params&, Checkpoint) ERROR: ERROR: IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT ERROR: For bug report please send to developers: ERROR: Log file: iqtree_multiPart_models.nexus.log ERROR: Alignment files (if possible) zsh: segmentation fault iqtree2.1.3 -p iqtree_multiPart_models.nexus -alrt 1000 -ninit 1000 -nstop 20

This is the size of my files: Subset Type Seqs Sites Infor Invar Model Name 1 2058 29903 709 27767 UNREST+FO+I+G4 part1 2 BIN 2058 3 3 0 JC2+FQ+ASC+G4 part2

What is interesting is that I was able to run similar analysis with a shorter dataset (below): Subset Type Seqs Sites Infor Invar Model Name 1 DNA 837 29403 334 28179 TIM+F+R4 part1 2 BIN 837 3 3 0 JC2+FQ+ASC part2

Could you help me?

Does it run if you specify the number of threads, instead of AUTO? For example, -nt 2.

Minh

On 1 Mar 2023, at 12:34 am, Tiago Gräf @.***> wrote:

Hello, I'm trying to run iqtree with two partitions, one nucleotide alignment and one binary data. I created the nexus file as following:

nexus

begin sets; charset part1 = novo_dataset.unique.noRef.fasta: ; charset part2 = indel.novo_dataset.unique.noRef.fasta: ; charpartition mine = UNREST+FO+I+G4:part1, JC2+FQ+ASC+G4:part2; end;

Then I tried to run with the following line: iqtree2.1.3 -p iqtree_multiPart_models.nexus -alrt 1000 -ninit 1000 -nstop 200 -czb -nt AUTO

This is the size of my files: Subset Type Seqs Sites Infor Invar Model Name 1 2058 29903 709 27767 UNREST+FO+I+G4 part1 2 BIN 2058 3 3 0 JC2+FQ+ASC+G4 part2

Could you help me?

— Reply to this email directly, view it on GitHubhttps://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FCibiv%2FIQ-TREE%2Fissues%2F244&data=05%7C01%7Cm.bui%40anu.edu.au%7C92acc949aa744f42218d08db19909812%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C638131881039078889%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=P9O1h%2Bsbm7%2FnxzW6tTNkU6bOtEcX%2BfPAIktDLafsoNo%3D&reserved=0, or unsubscribehttps://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADRTPU43D73BVDWPMMPVY5DWZX5IHANCNFSM6AAAAAAVKXOXTM&data=05%7C01%7Cm.bui%40anu.edu.au%7C92acc949aa744f42218d08db19909812%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C638131881039078889%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Wp90rwrk2JK5Ty8t246SzLc2JH9cXza8ATdZ7y2G%2BZo%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>

Cibiv / IQ-TREE

IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT - partitioned analyses #244

nexus

nexus