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iqtree / iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
GNU General Public License v2.0
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ERROR: ratefree.cpp:199: virtual void RateFree::initFromCatMinusOne(Checkpoint&, double): Assertion `fabs(sum_prop + getPInvar() - 1.0) < 0.01' failed. #291

Open yeeus opened 3 months ago

yeeus commented 3 months ago

I was running iqtree when I got this error:

ERROR: ratefree.cpp:199: virtual void RateFree::initFromCatMinusOne(Checkpoint&, double): Assertion `fabs(sum_prop + getPInvar() - 1.0) < 0.01' failed.
ERROR: STACK TRACE FOR DEBUGGING:
ERROR: 1   funcAbort()
ERROR: 2   ()
ERROR: 3   gsignal()
ERROR: 4   abort()
ERROR: 5   ()
ERROR: 6   RateFree::initFromCatMinusOne(Checkpoint&, double)
ERROR: 7   CandidateModel::evaluate[abi:cxx11](Params&, ModelCheckpoint&, ModelCheckpoint&, ModelsBlock*, int&, int)
ERROR: 8   CandidateModelSet::test(Params&, PhyloTree*, ModelCheckpoint&, ModelsBlock*, int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, bool, bool)
ERROR: 9   runModelFinder(Params&, IQTree&, ModelCheckpoint&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)
ERROR: 10   startTreeReconstruction(Params&, IQTree*&, ModelCheckpoint&)
ERROR: 11   runPhyloAnalysis(Params&, Checkpoint*, IQTree*&, Alignment*&)
ERROR: 12   runPhyloAnalysis(Params&, Checkpoint*)
ERROR: 13   main()
ERROR: 14   __libc_start_main()
ERROR: 15   ()
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: ***    Log file: SLC35F3.log
ERROR: ***    Alignment files (if possible)

This is my log file: SLC35F3.log

Best wishes!

thomaskf commented 3 months ago

Thank you very much @yeeus for reporting the issue. In order to understand the issue, is it possible for us to have the alignment file? You may email the compressed file to my email address: thomaskf@gmail.com if it is convenient. Thank you!

yeeus commented 3 months ago

Thanks, I have emailed to you.

kevinbretscher commented 3 weeks ago

Hi, I am running into the same issue with IQtree 2.3.6 and cannot quite figure out how to solve this. Any update on this?

iqtree2 -s flavo_aligned.afa -B 1000 -alrt 1000 flavo_aligned.afa.log

Let me know if you would like my alligment file.