IQ-TREE multicore version 2.2.5 -- CRASHES WITH SIGNAL SEGMENTATION FAULT

[lsjermiin]

Hi,

I am running experimental analysis using the following commands:

iqtree2 -s 488_AA_supermatrix.fst -st AA -m MF --mset NQ.bird -mrate E,I,G,*G,I+G,R,*R,I+R,H,*H -cmax 15 -mfreq FU,FO,F -mtree -T 16 -merit BIC -safe

For some reason it crashes shortly after starting the test of the NQ.bird+H2 model.

I repeated the analysis, and the crash happened again. The last few lines of the log file are included below. The full log and the input file is attached.

Looking forward to a solution to this problem.

All the best,

Lars Jermiin

Total number of iterations: 102
CPU time used for tree search: 118449.299 sec (32h:54m:9s)
Wall-clock time used for tree search: 7570.931 sec (2h:6m:10s)
Total CPU time used: 145746.981 sec (40h:29m:6s)
Total wall-clock time used: 9292.025 sec (2h:34m:52s)
3 finished checkpoint entries erased
38 NQ.bird+I+R6 1239600.621 105 2479411.242 2479411.427 2480429.722

===> Testing model NQ.bird+H2

NOTE: 606 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Initial LogL: -1254961.673, Site proportion and rates: (0.728,0.105) (0.272,3.401)
relative_treelen: 0.153 4.961

1. Initial log-likelihood: -1364807.710
   ERROR: STACK TRACE FOR DEBUGGING:
   ERROR:
   ERROR: *** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT
   ERROR: *** For bug report please send to developers:
   ERROR: *** Log file: 488_AA_supermatrix.fst.log
   ERROR: *** Alignment files (if possible)
   IQTREE2_bug_LSJermiin.zip

[lsjermiin]

Hi,
Just an additional comment relating to the issue I logged earlier on:
The software completes the analysis of the same data when I use the following command:

iqtree2 -s 488_AA_supermatrix.fst -st AA -m MF --mset Q.bird -mrate E,I,G,*G,I+G,R,*R,I+R,H,*H -cmax 15 -m
freq FU,FO,F -mtree -T 16 -merit AIC -safe > timing.txt

The differences between this command and the one that caused the segmentation fault us that this one used AIC and Q.bird while the one that crashed used BIC and NQ.bird.

I suspect this might give you an idea about where the problem lies.
Cheers,
Lars

[corneliusroemer]

A user who ran iqtree 2.2.3 (osx-64 binary) through augur tree recently reported a segmentation fault to us at nextstrain/augur: nextstrain/augur#1338

They ran IQtree on 130 thousand SARS-CoV-2 sequences, which is a lot, probably around 4GB in uncompressed alignment. But probably a segmentation fault shouldn't happen nonetheless.

[bqminh]

This is answered in #198, thus marking this one as duplicate.