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Cibiv / IQ-TREE

Efficient phylogenomic software by maximum likelihood
http://www.iqtree.org
GNU General Public License v2.0
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EDCluster - memory allocation #171

Open hermeseduardo opened 3 years ago

hermeseduardo commented 3 years ago

Hi there, I am trying EDCluster with iqtree, following https://github.com/dschrempf/EDCluster. Iqtree runs OK with udm under 128 (eg. udm_hogenom_0128_none_iqtree.nex, udm_hogenom_0128_lclr_iqtree.nex ) but anything larger than that (udm_hogenom_0256_lclr_iqtree.nex) gaves an error like the one below (bug??). I tried subsampling the alignment (>10,000sites) and the error persist. Any help will be appreciated.

LOG FILE: Q-TREE multicore version 1.6.12 for Linux 64-bit built Sep 4 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: r001 (AVX2, FMA3, 3023 GB RAM) Command: iqtree -s aligment.fasta -mdef udm_hogenom_0256_lclr_iqtree.nex -m Poisson+UDM0256LCLR -mwopt -nt 10 Seed: 417946 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Thu Sep 24 10:36:26 2020 Kernel: AVX+FMA - 10 threads (48 CPU cores detected) Reading alignment file aligment.fasta.fasta ... Fasta format detected Alignment most likely contains protein sequences Alignment has 49 sequences with 1415 columns, 1293 distinct patterns 855 parsimony-informative, 213 singleton sites, 347 constant sites

ERROR: STACK TRACE FOR DEBUGGING: ERROR: 2 ModelMixture::initMem() ERROR: 3 ModelMixture::initMixture(std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::cxx11::basic_string<char, std::char_traits, std::allocator >, ModelsBlock*, StateFreqType, std::cxx11::basic_string<char, std::char_traits, std::allocator >, PhyloTree, bool) ERROR: 4 ModelMixture::ModelMixture(std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, ModelsBlock, StateFreqType, std::cxx11::basic_string<char, std::char_traits, std::allocator >, PhyloTree*, bool) ERROR: 5 ModelFactory::ModelFactory(Params&, std::cxx11::basic_string<char, std::char_traits, std::allocator >&, PhyloTree, ModelsBlock) ERROR: 6 IQTree::initializeModel(Params&, std::cxx11::basic_string<char, std::char_traits, std::allocator >&, ModelsBlock) ERROR: 7 runTreeReconstruction(Params&, IQTree&) ERROR: 8 runPhyloAnalysis(Params&, Checkpoint*) ERROR: 9 main() ERROR: 10 libc_start_main() ERROR: 11 _start() ERROR: Not enough memory, allocation of -15032385536 bytes failed (bad_alloc)

dschrempf commented 3 years ago

Please see https://github.com/dschrempf/EDCluster/issues/1.

Sorry for the late reply. Development moved to https://github.com/iqtree/iqtree2.