ERROR in inferring locus trees

[Shiling Han]

Hi,

I'd like to calculate gene concordance factors (gCF) and sites concordance factors (sCF) to illustrate disagreement among gene trees and sites. My datasets include 5103 alignment files, each file including 81 strains.

My problems are as follows: when I run the loci tree using the 5103 files, the command can not operate properly, but when I run the loci tree using any 500 files of the 5103 files, the command runs successfully.  Why this happens, and what should I do to solve it?

Version: 

IQ-TREE multicore version 2.2.0.3 COVID-edition for Linux 64-bit built Aug  2 2022

Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    dell (AVX512, FMA3, 2014 GB RAM)
Command: iqtree -S ../ALN/ --prefix loci -T AUTO
Seed:    834501 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Mon Nov 14 11:19:40 2022
Kernel:  AVX+FMA - auto-detect threads (160 CPU cores detected)

Reading 5103 alignment files in directory ../ALN/
Reading alignment file ../ALN/OG0002042.fasta ... Fasta format detected
Reading fasta file: done in 0.000383367 secs using 33.13% CPU
Alignment most likely contains protein sequences

Error in the log file:

Optimizing NNI: done in 2.43783 secs using 7267% CPU
Estimate model parameters (epsilon = 1.000)
Estimate model parameters (epsilon = 1.000)
ERROR: STACK TRACE FOR DEBUGGING:
Optimizing NNI: done in 0.956813 secs using 7566% CPU
Optimizing NNI: done in 1.76619 secs using 7425% CPU
Estimate model parameters (epsilon = 1.000)
ERROR: 1   funcAbort()
ERROR: 2   ()
ERROR: 3   ()
ERROR: 4   std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >::_M_get_insert_hint_unique_pos(std::_Rb_tree_const_iterator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)
ERROR: 5   ()
ERROR: 6   ()
ERROR: 7   RateInvar::saveCheckpoint()
ERROR: 8   virtual thunk to RateGammaInvar::saveCheckpoint()
ERROR: 9   ModelFactory::saveCheckpoint()
ERROR: 10   IQTree::doNNISearch(bool)
ERROR: 11   ()
ERROR: 12   GOMP_parallel()
ERROR: 13   PhyloSuperTreeUnlinked::doNNISearch(bool)
ERROR: 14   computeFastMLTree(Params&, Alignment*, ModelCheckpoint&, ModelsBlock*, int&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
ERROR: 15   runModelFinder(Params&, IQTree&, ModelCheckpoint&)
ERROR: 16   runPhyloAnalysis(Params&, Checkpoint*, IQTree*&, Alignment*&)
ERROR: 17   runPhyloAnalysis(Params&, Checkpoint*)
ERROR: 18   main()
ERROR: 19   __libc_start_main()
ERROR: 20   ()
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT
ERROR: *** For bug report please send to developers:
ERROR: ***    Log file: loci.log
ERROR: ***    Alignment files (if possible)

The log file is attached, and I could send the alignments if necessary.

Thanks!

Shiling Han