BUG: terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >'

[sriramgarg121]

This has been posted in the Google groups. re-posting it here since it was recommended.

I am trying to estimate a new Q matrix from a folder of alignments (~6K alignments) with a custom starting substitution matrix.

I first run Step 1 with the following command:

/iqtree-2.2.0.7.mix-Linux/bin/iqtree2 -seed 1 -S ALN_DIR -nt 144 -m MFP -mset gtr20etf -cmax 4 --prefix train.1

This command runs to completion and generates a train1.best_model.nex file and train.1.treefile with ~6K partition and trees.

Then I try to estimate a joint model in step 2 with the command

/iqtree-2.2.0.7.mix-Linux/bin/iqtree2 -v -seed 1 -T AUTO -S train_plant.best_model.nex -te train.1.treefile --model-joint GTR20+FO --init-model gtr20etf -pre train_pfam.GTR20

I get the following error "terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits, std::allocator >'"

I have checked the nexus file and not sure what is causing this error.
I have tried with iqtree version 2.2.2.6 and 2.2.5 as well

Example of the ERROR output, with the -v Option

Reading partition model file /u/gargs/ptmp_link/Databases/qmaker_pfam_datasets/qmaker_etfgtr20/train.1.best_model.nex ... Reading "SETS" block... terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >' ERROR: STACK TRACE FOR DEBUGGING: ERROR: ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED ERROR: *** For bug report please send to developers: ERROR: *** Log file: train_pfam.GTR20_test.log ERROR: *** Alignment files (if possible)

These are the contents of the Log file
`IQ-TREE multicore version 2.2.5 COVID-edition for Linux 64-bit built Sep 11 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host: raven03 (AVX512, FMA3, 503 GB RAM)
Command: /u/gargs/Scripts/iqtree-2.2.5-Linux/bin/iqtree2 -v -seed 1 -T AUTO -S /u/gargs/ptmp_link/Databases/qmaker_pfam_datasets/qmaker_etfgtr20/train.1.best_model.nex -te /u/gargs/ptmp_link/Databases/qmaker_pfam_datasets/qmaker_etfgtr20/train.1.treefile --model-joint GTR20+FO --init-model gtr20etf -pre train_pfam.GTR20_test
Seed: 1 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Oct 12 09:59:44 2023
Kernel: AVX+FMA - auto-detect threads (144 CPU cores detected)

Reading partition model file /u/gargs/ptmp_link/Databases/qmaker_pfam_datasets/qmaker_etfgtr20/train.1.best_model.nex ...
Reading "SETS" block...
ERROR: STACK TRACE FOR DEBUGGING:
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: *** Log file: train_pfam.GTR20_test.log
ERROR: *** Alignment files (if possible)`

If I reduce the number of partitions to 350 then the command runs and generates the Q matrix as expected. Any help will be much appreciated.

Thank you

Regards

Sriram