Crash due to std::bad_alloc when analyzing 5k sequences with ~15k informative sites #41
Description
When running mpboot (from master) on 5k sequences with ~15k informative sites I get:
libc++abi: terminating due to uncaught exception of type std::bad_alloc: std::bad_alloc
Here are files for replication (remove .txt before unzstd, the txt is necessary for upload to Github to work):
And full logs:
../../mpboot/mpboot -s prealigned.fa
MPBoot version 1.1.1 for Mac OS X 64-bit built Mar 28 2025
Copyright (c) 2016 Diep Thi Hoang, Le Sy Vinh, Tomas Flouri, Alexandros Stamatakis, Arndt von Haeseler and Bui Quang Minh.
Host: Corneliuss-MBP.asus.router (SSE4.2, 64 GB RAM)
Command: ../../mpboot/mpboot -s prealigned.fa
Seed: 541278 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Apr 17 21:11:07 2025
Kernel: SSE3
Reading alignment file prealigned.fa ... Fasta format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 5173 sequences with 197209 columns and 170138 patterns
ID Sequence #Gap/Ambiguity
1 NC_063383 0 (0.000%) 4
2 PP_000SPS7 14348 (7.276%) 10
3 PP_000SPMH 4761 (2.414%) 10
... SNIP ...
172 PP_0014F18 3320 (1.683%) 4
5173 PP_0014F26 13676 (6.935%) 4
WARNING: 4 sequences contain more than 50% gaps/ambiguity
**** TOTAL 35220516 (3.452%)
Computing random stepwise addition parsimony tree for evaluating patterns...
Time for random stepwise addition parsimony tree construction: 190.182 seconds
libc++abi: terminating due to uncaught exception of type std::bad_alloc: std::bad_alloc
*** MPBoot CRASHES WITH SIGNAL ABORTED
*** For bug report please send developers:
*** Log file: prealigned.fa.log
*** Alignment files (if possible)
zsh: abort ../../mpboot/mpboot -s prealigned.fa