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How to solve iqtree crash #233

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kopelol opened this issue Jul 5, 2022 · 1 comment
Open

How to solve iqtree crash #233

kopelol opened this issue Jul 5, 2022 · 1 comment

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@kopelol
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kopelol commented Jul 5, 2022

Hi, I encountered following ERROR.

ERROR: phylokernelnonrev.h:1461: double PhyloTree::computeNonrevLikelihoodBranchSIMD(PhyloNeighbor*, PhyloNode*) [with VectorClass = Vec4d; bool SAFE_NUMERIC = false; int nstates = 4; bool FMA = true]: Assertion `all_prob_const < 1.0 && all_prob_const >= 0.0' failed.
ERROR: STACK TRACE FOR DEBUGGING:
ERROR: 1 funcAbort()
ERROR: 2 ()
ERROR: 3 gsignal()
ERROR: 4 abort()
ERROR: 5 ()
ERROR: 6 double PhyloTree::computeNonrevLikelihoodBranchSIMD<Vec4d, false, 4, true>(PhyloNeighbor*, PhyloNode*)
ERROR: 7 PhyloTree::optimizeAllBranches(int, double, int)
ERROR: 8 PhyloTree::testNumThreads()
ERROR: 9 PhyloTree::ensureNumberOfThreadsIsSet(Params*)
ERROR: 10 CandidateModel::evaluate[abi:cxx11](Params&, ModelCheckpoint&, ModelCheckpoint&, ModelsBlock*, int&, int)
ERROR: 11 CandidateModelSet::test(Params&, PhyloTree*, ModelCheckpoint&, ModelsBlock*, int, int, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, bool)
ERROR: 12 runModelFinder(Params&, IQTree&, ModelCheckpoint&)
ERROR: 13 runPhyloAnalysis(Params&, Checkpoint*, IQTree*&, Alignment*&)
ERROR: 14 runPhyloAnalysis(Params&, Checkpoint*)
ERROR: 15 main()
ERROR: 16 __libc_start_main()
ERROR: 17 ()
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: *** Log file: core.aln2.log
ERROR: *** Alignment files (if possible)

It might be due to my alignment length(It's core gene alignment of bacteria species).
Should I add "-t PARS" option?

Best regards,

@Caiyulu-818
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Hi, have you ever solved this problem?

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