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