dw.p...@gmail.com
Dear IQ-Tree developers,
IQ-Tree crashed while inferring a tree . . . interesting looking bits of log file are below (thanks!):
IQ-TREE multicore version 1.5.2 for Linux 64-bit built Dec 30 2016
Copyright (c) 2011-2016 Nguyen Lam Tung, Olga Chernomor, Arndt von Haeseler and Bui Quang Minh.
Host: _ (AVX, 15 GB RAM)
Command: _/iqtree-omp -spp sequences/WGS_alnd_partitioned.nex -bb 1000 -nt 3 -redo -safe
Seed: 266582 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Fri Dec 30 11:59:48 2016
Kernel: Safe AVX - 3 threads(4 CPU cores detected)
Reading partition model file sequences/WGS_alnd_partitioned.nex ...
Reading partition CR (model=MGK+F3X4+G4, aln=sequences/WGS_alnd_concat_CR.fna, seq=CODON, pos= 1-14160) ...
Reading alignment file sequences/WGS_alnd_concat_CR.fna ... Fasta format detected
Alignment most likely contains DNA/RNA sequences
Converting to codon sequences with genetic code ...
WARNING: Sequence MVs/Taunton.GBR/15.13 has ambiguous character GMA at site 4378
WARNING: Sequence MVs/London.GBR/28.12 has ambiguous character RGT at site 4510
WARNING: Sequence MVi/BritishColumbia.CAN/12.10/1 has ambiguous character CAR at site 8443
Alignment has 77 sequences with 4720 columns and 2137 patterns (1749 informative sites)
WARNING: Some sequence names are changed as follows:
...
**** TOTAL 0.07% 0 sequences failed composition chi2 test (p-value<5%; df=63)
77 sequences and 4720 sites extracted
Reading partition NCR (model=TIM+G4, aln=sequences/WGS_alnd_concat_NCR.fna, seq=DNA, pos= 1-1548) ...
Reading alignment file sequences/WGS_alnd_concat_NCR.fna ... Fasta format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 77 sequences with 1548 columns and 485 patterns (492 informative sites)
...
**** TOTAL 0.59% 0 sequences failed composition chi2 test (p-value<5%; df=3)
77 sequences and 1548 sites extracted
NOTE: Mixed codon and other data, branch lengths of codon partitions are rescaled by 3!
Degree of missing data: 0.000
Info: multi-threading strategy over alignment sites
...
NOTE: 334 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Initial log-likelihood: -55341.422
Current log-likelihood at step 1: -53563.312
Current log-likelihood at step 2: -53445.415
Current log-likelihood at step 3: -53445.315
Current log-likelihood at step 4: -53445.315
Partition-specific rates: 2.519 2.467
Parameters optimization took 3 rounds (111.987 sec)
WARNING: Estimated model parameters are at boundary that can cause numerical instability!
...
Iteration 100 / LogL: -53427.373 / Time: 2h:34m:36s (0h:1m:33s left)
Log-likelihood cutoff on original alignment: -53498.585
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.980
NOTE: UFBoot does not converge, continue at least 100 more iterations
WARNING: Numerical underflow for lh-derivative
...
Iteration 170 / LogL: -53530.469 / Time: 4h:16m:0s (0h:45m:26s left)
WARNING: Numerical underflow for lh-derivative
WARNING: Numerical underflow for lh-derivative
STACK TRACE FOR DEBUGGING:
1 funcAbort()
2 ()
3 gsignal()
4 abort()
5 ()
6 ()
7 double PhyloTree::computeLikelihoodFromBufferGenericSIMD<Vec4d, true, false, false>()
9 GOMP_parallel()
11 PhyloSuperTreePlen::swapNNIBranch(double, PhyloNode*, PhyloNode*, SwapNNIParam*, NNIMove*)
12 PhyloSuperTreePlen::getBestNNIForBran(PhyloNode*, PhyloNode*, NNIMove*)
13 IQTree::evaluateNNIs(std::map<int, std::pair<Node*, Node*>, std::less<int>, std::allocator<std::pair<int const, std::pair<Node*, Node*> > > >&, std::vector<NNIMove, std::allocator<NNIMove> >&)
14 IQTree::optimizeNNI(bool)
15 IQTree::doNNISearch()
16 IQTree::doTreeSearch()
17 runTreeReconstruction(Params&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, IQTree&, std::vector<ModelInfo, std::allocator<ModelInfo> >&)
18 runPhyloAnalysis(Params&, Checkpoint*)
19 main()
20 __libc_start_main()
21 _start()
*** IQ-TREE CRASHES WITH SIGNAL ABORTED
Bui Quang Minh
Thanks for the report. This sounds like a bug. Can you please send me the alignments, partition file and the log file via my personal email?
Cheers, Minh
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--
Bui Quang Minh
Center for Integrative Bioinformatics Vienna (CIBIV)
Campus Vienna Biocenter 5, VBC5, Ebene 1
A-1030 Vienna, Austria
Phone: ++43 1 4277 74326
Email: minh.bui (AT) univie.ac.at