BUG - constraint tree ERROR

[edmu...@gmail.com]

I'm trying to run an analysis with a constrained topology, at first I was getting a message saying certain sequences will be dropped due to being identical, when I removed these (from both the tree and alignment) I still get the same error which leads me to believe it is a different problem:

IQ-TREE multicore version 1.6.2 for Linux 64-bit built Mar 28 2018

Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,

Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host:   -- (AVX2, FMA3, 62 GB RAM)

Command: iqtree -s reducedtestalignmentbac.faa -m GTR+F -g constraintree.tre

Seed:    295241 (Using SPRNG - Scalable Parallel Random Number Generator)

Time:    Thu Apr 11 09:38:34 2019

Kernel:  AVX+FMA - 1 threads (40 CPU cores detected)

WARNING: 61 sequences contain more than 50% gaps/ambiguity

****  TOTAL                                       5.33%  24 sequences failed composition chi2 test (p-value<5%; df=3)

Reading constraint tree constraintree.tre...

Creating fast initial parsimony tree by random order stepwise addition...

ERROR: phylotreepars.cpp:382: int PhyloTree::computeParsimonyTree(const char*, Alignment*): Assertion `taxon_order.size() == constraintTree.leafNum' failed.

ERROR: STACK TRACE FOR DEBUGGING:

ERROR: 1   funcAbort()

ERROR: 2   ()

ERROR: 3   gsignal()

ERROR: 4   abort()

ERROR: 6   PhyloTree::computeParsimonyTree(char const*, Alignment*)

ERROR: 7   IQTree::computeInitialTree(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, LikelihoodKernel)

ERROR: 8   initializeParams(Params&, IQTree&, ModelCheckpoint&, ModelsBlock*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)

ERROR: 9   runTreeReconstruction(Params&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, IQTree*&, ModelCheckpoint&)

ERROR: 10   runPhyloAnalysis(Params&, Checkpoint*)

ERROR: 11   main()

ERROR: 12   __libc_start_main()

ERROR: 13   _start()

ERROR: 

ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED

ERROR: *** For bug report please send to developers:

ERROR: ***    Log file: reducedtestalignmentbac.faa.log

ERROR: ***    Alignment files (if possible)

Aborted (core dumped)

On a different version:

IQ-TREE multicore version 1.6.5 for Linux 64-bit built May  8 2018

Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,

Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host:    -- (AVX2, FMA3, 251 GB RAM)

Command: iqtree -s reducedtestalignmentbac.faa -m GTR+F -g constraintree.tre

Seed:    742718 (Using SPRNG - Scalable Parallel Random Number Generator)

Time:    Thu Apr 11 09:39:41 2019

Kernel:  AVX+FMA - 1 threads (40 CPU cores detected)

ERROR: phylotreepars.cpp:382: int PhyloTree::computeParsimonyTree(const char *, Alignment *): Assertion `taxon_order.size() == constraintTree.leafNum' failed.

ERROR: STACK TRACE FOR DEBUGGING:

ERROR: 

ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED

ERROR: *** For bug report please send to developers:

ERROR: ***    Log file: reducedtestalignmentbac.faa.log

ERROR: ***    Alignment files (if possible)

[Minh Bui]

Hi there,

It looks like some issue with the input constraint file, e.g. some taxa might not appear in the alignment or vice versa. Can you check that? If not, please send me the input files and I’ll have further look.

Cheers,

Minh

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[Conrad van den Ende]

Hi Minh,

Thanks yes it was a problem with the nexus file. Some characters were ambiguous (one species with multiple character states) and some characters had more than 9 states once I removed those it worked!

Thanks again!