Aborted (core dumped) during mike sketch process

[guosongjia]

Dear developers:\ Thanks for developing such a fashion tool to simplify the phylogenetic tree estimation using sketched K-mers!\ I'm now trying to use this tool to estimate a tree for my yeast isolates (all belonging to the same species) instead of calling SNP. I met with the following error during mike sketch process:

$ ~/softwares/mike/src/mike sketch -l /data/c/jiaguosong/large_species_tree_mash-distance/2404_testing_MIKE/1_toy_trail_on_Sversatilis/list -d /data/c/jiaguosong/large_species_tree_mash-distance/2404_testing_MIKE/1_toy_trail_on_Sversatilis
*************************************************************
/data/c/jiaguosong/large_species_tree_mash-distance/2404_testing_MIKE/1_toy_trail_on_Sversatilis/DY47854.0.txt
/data/c/jiaguosong/large_species_tree_mash-distance/2404_testing_MIKE/1_toy_trail_on_Sversatilis/DY47854.1.txt
/data/c/jiaguosong/large_species_tree_mash-distance/2404_testing_MIKE/1_toy_trail_on_Sversatilis/DY47854.2.txt
/data/c/jiaguosong/large_species_tree_mash-distance/2404_testing_MIKE/1_toy_trail_on_Sversatilis/DY47854.3.txt
/data/c/jiaguosong/large_species_tree_mash-distance/2404_testing_MIKE/1_toy_trail_on_Sversatilis/DY47854.4.txt
/data/c/jiaguosong/large_species_tree_mash-distance/2404_testing_MIKE/1_toy_trail_on_Sversatilis/DY47854.5.txt
/data/c/jiaguosong/large_species_tree_mash-distance/2404_testing_MIKE/1_toy_trail_on_Sversatilis/DY47854.6.txt
/data/c/jiaguosong/large_species_tree_mash-distance/2404_testing_MIKE/1_toy_trail_on_Sversatilis/DY47854.7.txt
/data/c/jiaguosong/large_species_tree_mash-distance/2404_testing_MIKE/1_toy_trail_on_Sversatilis/DY47854.8.txt
/data/c/jiaguosong/large_species_tree_mash-distance/2404_testing_MIKE/1_toy_trail_on_Sversatilis/DY47854.9.txt
<<<<<<<<<<<<<<<<<<<<<<<< thread 2 has finished， quit。>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<< thread 1 has finished， quit。>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<< thread 5 has finished， quit。>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<< thread 3 has finished， quit。>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<< thread 7 has finished， quit。>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<< thread 0 has finished， quit。>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<< thread 4 has finished， quit。>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<< thread 6 has finished， quit。>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<< thread 8 has finished， quit。>>>>>>>>>>>>>>>>>>>>>>>>>
<<<<<<<<<<<<<<<<<<<<<<<< thread 9 has finished， quit。>>>>>>>>>>>>>>>>>>>>>>>>>
/builddir/build/BUILD/gcc-8.5.0-20210514/obj-x86_64-redhat-linux/x86_64-redhat-linux/libstdc++-v3/include/bits/basic_string.h:1071: std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::reference std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator[](std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::reference = char&; std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type = long unsigned int]: Assertion '__pos <= size()' failed.
Aborted (core dumped)

It seems the mike sketch process is finished and I obtained the file ending with 'jac'. However, all the processing files named DY47854.0.txt to DY47854.9.txt were not removed and I'm not sure whether the resulting .jac file can be used or not because of the errors.\ Can you help me to solve this error?\ Best regards,\ Guo-Song

[mgaynor1]

I also received the same error:

/builddir/build/BUILD/gcc-8.5.0-20210514/obj-x86_64-redhat-linux/x86_64-redhat-linux/libstdc++-v3/include/bits/basic_string.h:1071: std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::reference std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator[](std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>; std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::reference = char&; std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type = long unsigned int]: Assertion '__pos <= size()' failed.
Aborted

Though I would love to use your software, I cannot debug past this step.

[mgaynor1]

I was running this on a cluster and found that module load gcc/11.4.0 was all I needed to bypass this error.