vg repeatedly crashes during the graph construction phase

[jdwinkler-lanzatech]

Hi,

I am trying out StrainFLAIR at the moment, and noticed a huge, repeating stream of errors during the graph construction phase:

Stack trace path: /tmp/vg_crash_1XXwg5/stacktrace.txt
Please include the stack trace file in your bug report!
error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph
error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_IkwoiT/stacktrace.txt
Please include the stack trace file in your bug report!
error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph
error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph
seqwish: error while loading shared libraries: libatomic.so.1: cannot open shared object file: No such file or directory
seqwish: error while loading shared libraries: libatomic.so.1: cannot open shared object file: No such file or directory
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_XPeI58/stacktrace.txt
Please include the stack trace file in your bug report!
vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed. error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_jSkxpb/stacktrace.txt Please include the stack trace file in your bug report! vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed.
error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph
vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed. error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_eE7vxo/stacktrace.txt Please include the stack trace file in your bug report! vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed.
error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph
error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph
vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed. ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_WtvH71/stacktrace.txt Please include the stack trace file in your bug report! ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_SBiDqw/stacktrace.txt Please include the stack trace file in your bug report! seqwish: error while loading shared libraries: libatomic.so.1: cannot open shared object file: No such file or directory error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found while loading handlegraph::MutablePathDeletableHandleGraph error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed.
vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed. error[VPKG::load_one]: Correct input type not found in standard input while loading handlegraph::MutablePathMutableHandleGraph seqwish: error while loading shared libraries: libatomic.so.1: cannot open shared object file: No such file or directory vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed.
vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed. vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion false' failed.
vg: /home/erik/vg-release/vg/include/gfakluge.hpp:569: size_t gfak::mmap_open(const string&, char*&, int&): Assertion `false' failed.
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_sDZ3Kf/stacktrace.txt
Please include the stack trace file in your bug report!
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_GRUTMm/stacktrace.txt

I assume I need to install the missing shared libraries, but any help beyond that would be appreciated!

[kevsilva]

Hi,

Sorry for the late reply.
Maybe first try to update vg and seqwish.
Also, more information about the graph intended to construct would be useful.

Regards