Segmentation fault (core dumped)

[dabao1990]

1、spack install --overwrite --keep-stage --no-checksum -y trimal@1.5.0
2、cd trimal@1.5.0/dataset

cat /etc/os-release
NAME="openEuler"
VERSION="22.03 (LTS-SP3)"
ID="openEuler"
VERSION_ID="22.03"
PRETTY_NAME="openEuler 22.03 (LTS-SP3)"
ANSI_COLOR="0;31"

I had 2 problems during use. I don't understand why core dumped is reported.

=======================
[root@localhost dataset]#trimal -in example.001.AA.clw -out trimal_gappyout.clw -gappyout
Segmentation fault (core dumped)

[root@localhost dataset]#trimal -in example.094.DNADeg.sequential_phy -out trimal_selectcols.phy -selectcols { 0,2,3,10,45-60,68,70-78 }
WARNING: Removing column '506' composed only by gaps
Segmentation fault (core dumped)

However, it is normal for me to use version 1.5.0.

[nicodr97]

I am not familiar with spack, but I understand the only available version there is v1.4.1 https://github.com/spack/spack-packages/blob/develop/repos/spack_repo/builtin/packages/trimal/package.py. Also, I don't know if spack is supposed to both download the repository, compile the binaries and include them in your $PATH. Otherwise, the binaries should be inside the source folder because it's where they are compiled and running just trimal inside the dataset directory should either fail or use another installed version. Could you check the version you are running with the command trimal --version? Does this error appear with just trimal -in example.004.fasta for instance?

[dabao1990]

I am not familiar with spack, but I understand the only available version there is v1.4.1 https://github.com/spack/spack-packages/blob/develop/repos/spack_repo/builtin/packages/trimal/package.py. Also, I don't know if spack is supposed to both download the repository, compile the binaries and include them in your $PATH. Otherwise, the binaries should be inside the source folder because it's where they are compiled and running just trimal inside the dataset directory should either fail or use another installed version. Could you check the version you are running with the command trimal --version? Does this error appear with just trimal -in example.004.fasta for instance?

=====1.5.0 version
I use version 1.5.0 and use example.001.AA.clw of 1.5.1 dataset.
[root@localhost dataset]#trimal -in example.001.AA.clw -out trimal_gappyout.clw -gappyout
[root@localhost dataset]#sha256sum trimal_gappyout.clw
a17a2eebfa3fa6fceeada4e09e73245358f1eab04673b29875102038cc39f22e trimal_gappyout.clw
[root@localhost dataset]#pwd
/home/stage/root/spack-stage-trimal-1.5.0-tt77vk7tg76u6vy7r4fqh6zjw5bmsgs2/spack-src/trimal-1.5.1/dataset
[root@localhost dataset]#trimal --version
trimAl v1.5.rev0 build[2024-05-27]

=====1.5.1 version
[root@localhost dataset]#trimal -in example.001.AA.clw -out trimal_gappyout.clw -gappyout
Segmentation fault (core dumped)
[root@localhost dataset]#trimal --version
trimAl v1.5.rev1 build[2025-11-25]
[root@localhost dataset]#pwd
/home/stage/root/spack-stage-trimal-1.5.1-t447wtqlvo6kiappeuw3x5i5ru53gwgz/spack-src/trimal-1.5.1/dataset

However, the same operation fails in 1.5.1.Environment variables are not involved. The dataset is not referenced during compilation. The verification is performed after compilation.

[nicodr97]

I think I found the bug. The linked PR in this issue should fix it. Thank you for notifying the problem!