ERROR: ratefree.cpp:199: virtual void RateFree::initFromCatMinusOne(Checkpoint&, double): Assertion `fabs(sum_prop + getPInvar() - 1.0) < 0.01' failed.

[yeeus]

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]

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: [email protected] if it is convenient. Thank you!

[yeeus]

Thanks, I have emailed to you.

[kevinbretscher]

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.