IQtree 1.6.5 crash - "Assertion `freq_type != FREQ_UNKNOWN' failed"

[Andrew Swafford]

Hi, I'm running IQtree on a very large alignment of ~17,000 genes. I just got this error:

ERROR: modelmarkov.cpp:274: void ModelMarkov::init_state_freq(StateFreqType): Assertion `freq_type != FREQ_UNKNOWN' 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: twilight_extended.log

ERROR: ***    Alignment files (if possible)

/var/spool/torque/mom_priv/jobs/2259626.node96.SC: line 8:  5841 Aborted 

This is running on linux with the following command with 500GB of RAM available: 

iqtree -s long_aln.aln -nt 12 -m LG4X -bb 10000 -nm 10000 -abayes -alrt 1000 -pre twilight_extended

The tail end of the log file reads:

Create initial parsimony tree by phylogenetic likelihood library (PLL)... 25323.288 seconds

Generating 10000 samples for ultrafast bootstrap (seed: 407400)...

Model LG4X is alias for MIX{LG4X1,LG4X2,LG4X3,LG4X4}*R4

ERROR: modelmarkov.cpp:274: void ModelMarkov::init_state_freq(StateFreqType): Assertion `freq_type != FREQ_UNKNOWN' 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: twilight_extended.log

ERROR: ***    Alignment files (if possible)

Any help/insight would be greatly appreciated. Thank you!

-Andrew

[Andrew Swafford]

I noticed this is a possible bug when using LG4M and LG4X in 1.6.5, see thread here: https://groups.google.com/forum/#!topic/iqtree/Wgob9pyABtM