A stacktrace from the segmentation fault looks like follows.
It triggers consistently for me with the following steps in a source-tree
fakeroot debian/rules binary
cd sample_data/
/tmp/salmon-1.9.0+ds1/obj-x86_64-linux-gnu/src/salmon index -t
transcripts.fasta -i sample_salmon_quasi_index
#0 0x00007ffff7495993 in __GI__IO_fwrite (buf=0x7fffffffc978, size=1,
count=82,
fp=0x7ffff6060400) at ./libio/iofwrite.c:37
#1 0x000055555560f55d in spdlog::details::file_helper::write
(this=0x7ffff607f980,
msg=...) at ./include/spdlog/details/../sinks/../details/file_helper.h:90
#2 0x00005555556299dd in
spdlog::sinks::simple_file_sink<spdlog::details::null_mutex>::_sink_it
(msg=...,
this=0x7ffff607f970) at ./include/spdlog/details/../sinks/file_sinks.h:45
#3 spdlog::sinks::base_sink<spdlog::details::null_mutex>::log
(this=0x7ffff607f970,
msg=...) at ./include/spdlog/sinks/base_sink.h:37
#4 0x0000555555618aa3 in spdlog::logger::_sink_it
(this=0x7ffff6025810, msg=...)
at /usr/include/c++/12/bits/shared_ptr_base.h:1665
#5 0x0000555555a8ae19 in spdlog::logger::log<double> (fmt=0x555555cd7f0b
"mphf size = {} MB", lvl=spdlog::level::info, this=0x7ffff6025810) at
./external/pufferfish/include/spdlog/details/logger_impl.h:74
#6 spdlog::logger::info<double> (arg1=<optimized out>, fmt=0x555555cd7f0b
"mphf size = {} MB", this=0x7ffff6025810) at
./external/pufferfish/include/spdlog/details/logger_impl.h:145
#7 pufferfishIndex (indexOpts=...) at
./external/pufferfish/src/PufferfishIndexer.cpp:660
#8 0x00005555556636ae in SalmonIndex::buildPuffIndex_ (idxOpt=...,
indexDir=...,
this=0x7ffff603e280) at ./include/SalmonIndex.hpp:111
#9 SalmonIndex::build (idxOpt=..., indexDir=..., this=0x7ffff603e280) at
./include/SalmonIndex.hpp:76
#10 salmonIndex (argc=<optimized out>, argv=<optimized out>) at
./src/BuildSalmonIndex.cpp:247
#11 0x00005555555fe510 in std::function<int (int, char const**,
std::unique_ptr<SalmonIndex, std::default_delete<SalmonIndex>
>&)>::operator()(int, char const**, std::unique_ptr<SalmonIndex,
std::default_delete<S
almonIndex> >&) const (__args#2=std::unique_ptr<SalmonIndex> = {...},
__args#1=<optimized out>, __args#0=<optimized out>, this=0x7ffff604e1a8) at
/usr/include/c++/12/bits/std_function.h:591
#12 main (argc=<optimized out>, argv=0x7fffffffe028) at ./src/Salmon.cpp:267
