<div dir="ltr"><div><br></div><div>A stacktrace from the segmentation fault looks like follows.</div><div><br></div><div>It triggers consistently for me with the following steps in a source-tree<br></div><div><br></div><div></div><div><span style="font-family:monospace"><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">fakeroot debian/rules binary</span></span></div><div><span style="font-family:monospace"><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">cd sample_data/</span></span></div><div><span style="font-family:monospace"><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"><span style="font-family:monospace"><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">/tmp/salmon-1.9.0+ds1/obj-x86_64-linux-gnu/src/salmon index -t transcripts.fasta -i sample_salmon_quasi_index</span><br></span></span></span></div><div><br></div><div><span style="font-family:monospace"><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">
</span><br>#0  <span style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x00007ffff7495993</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">__GI__IO_fwrite</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> (</span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">buf</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x7fffffffc978, </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">size</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=1, </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">count</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=82, </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">fp</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x7ffff6060400) at </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">./libio/iofwrite.c</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">:37
</span><br>#1  <span style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x000055555560f55d</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">spdlog::details::file_helper::write</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> (</span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">this</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x7ffff607f980, </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">msg</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=...) at </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">./include/spdlog/details/../sinks/../details/file_helper.h</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">:90
</span><br>#2  <span style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x00005555556299dd</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">spdlog::sinks::simple_file_sink<spdlog::details::null_mutex>::_sink_it</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> (</span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">msg</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=..., </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">this</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x7ffff607f970) at </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">./include/spdlog/details/../sinks/file_sinks.h</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">:45
</span><br>#3  <span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">spdlog::sinks::base_sink<spdlog::details::null_mutex>::log</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> (</span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">this</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x7ffff607f970, </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">msg</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=...) at </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">./include/spdlog/sinks/base_sink.h</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">:37
</span><br>#4  <span style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x0000555555618aa3</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">spdlog::logger::_sink_it</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> (</span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">this</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x7ffff6025810, </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">msg</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=...) at </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">/usr/include/c++/12/bits/shared_ptr_base.h</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">:1665
</span><br>#5  <span style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x0000555555a8ae19</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">spdlog::logger::log<double></span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> (</span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">fmt</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x555555cd7f0b "mphf size = {} MB", </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">lvl</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=spdlog::level::info, </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">this</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x7ffff6025810) at </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">./external/pufferfish/include/spdlog/details/logger_impl.h</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">:74
</span><br>#6  <span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">spdlog::logger::info<double></span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> (</span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">arg1</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=<optimized out>, </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">fmt</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x555555cd7f0b "mphf size = {} MB", </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">this</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x7ffff6025810) at </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">./external/pufferfish/include/spdlog/details/logger_impl.h</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">:145
</span><br>#7  <span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">pufferfishIndex</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> (</span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">indexOpts</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=...) at </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">./external/pufferfish/src/PufferfishIndexer.cpp</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">:660
</span><br>#8  <span style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x00005555556636ae</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">SalmonIndex::buildPuffIndex_</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> (</span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">idxOpt</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=..., </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">indexDir</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=..., </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">this</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x7ffff603e280) at </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">./include/SalmonIndex.hpp</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">:111
</span><br>#9  <span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">SalmonIndex::build</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> (</span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">idxOpt</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=..., </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">indexDir</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=..., </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">this</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x7ffff603e280) at </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">./include/SalmonIndex.hpp</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">:76
</span><br>#10 <span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">salmonIndex</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> (</span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">argc</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=<optimized out>, </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">argv</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=<optimized out>) at </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">./src/BuildSalmonIndex.cpp</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">:247
</span><br>#11 <span style="color:rgb(24,24,178);background-color:rgb(255,255,255)">0x00005555555fe510</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> in </span><span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">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</span><br>almonIndex> >&) const<span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> (</span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">__args#2</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=std::unique_ptr<SalmonIndex> = {...}, </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">__args#1</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=<optimized out>, </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">__args#0</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=<optimized out>, </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">this</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x7ffff604e1a8) at </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">/usr/include/c++/12/bits/std_function.h</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">:591
</span><br>#12 <span style="color:rgb(178,104,24);background-color:rgb(255,255,255)">main</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"> (</span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">argc</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=<optimized out>, </span><span style="color:rgb(24,178,178);background-color:rgb(255,255,255)">argv</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">=0x7fffffffe028) at </span><span style="color:rgb(24,178,24);background-color:rgb(255,255,255)">./src/Salmon.cpp</span><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">:267</span></span></div><div><span style="font-family:monospace"><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)"><br></span></span></div></div>