Crashes during different processes/ modules

[shesanIsland]

Hello,

Thank you for developing one of the few tools that computes strain abundance, this has been very helpful!

Is there any way to force the script, more specifically StrainFLAIR.sh query to continue if it has already been started for specific samples.

I unfortunately keep running into at least one issues for each module ie...

• StrainFLAIR.sh: line 613: json2csv: command not found there was a problem with the gene-level table generation
• obj, end = self.scan_once(s, idx) json.decoder.JSONDecodeError: Unterminated string starting at: line 1 column 581 (char 580) there was a problem with the gene-level table generation

...which means I must start re-mapping from scratch which takes ~ 1 day per sample to run.

Sadly I have tried running the module (ie json2csv.py) alone but this does not create any new files, there is no output at all. EDIT: json2csv module seems to work for now

Many thanks

[shesanIsland]

Main error message:

[E::bgzf_uncompress] Inflate operation failed: 3
terminate called after throwing an instance of 'std::runtime_error'
  what():  [vg::io::MessageIterator] obsolete, invalid, or corrupt input at message 63427734666876 group 63424750402179
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_SKQV5D/stacktrace.txt
Please include the stack trace file in your bug report!

Contents of stack trace file:

Crash report for vg v1.28.0 "Acquafredda"
Stack trace (most recent call last):
#15   Object "/home/USER/.conda/envs/strain/bin/vg", at 0x661d0d, in _start
#14   Object "/home/USER/.conda/envs/strain/bin/vg", at 0x1f49d1f, in __libc_start_main
#13   Object "/home/USER/.conda/envs/strain/bin/vg", at 0x57f838, in main
#12   Object "/home/USER/.conda/envs/strain/bin/vg", at 0xc3523b, in vg::subcommand::Subcommand::operator()(int, char**) const
#11   Object "/home/USER/.conda/envs/strain/bin/vg", at 0xc45da1, in main_view(int, char**)
#10   Object "/home/USER/.conda/envs/strain/bin/vg", at 0xddba80, in vg::get_input_file(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::function<void (std::istream&)>)
#9    Object "/home/USER/.conda/envs/strain/bin/vg", at 0xc439a1, in std::_Function_handler<void (std::istream&), main_view(int, char**)::{lambda(std::istream&)#23}>::_M_invoke(std::_Any_data const&, std::istream&)
#8    Object "/home/USER/.conda/envs/strain/bin/vg", at 0xc4a0db, in void vg::io::for_each<vg::MultipathAlignment>(std::istream&, std::function<void (long, vg::MultipathAlignment&)> const&)
#7    Object "/home/USER/.conda/envs/strain/bin/vg", at 0x12675aa, in vg::io::MessageIterator::operator++()
#6    Object "/home/USER/.conda/envs/strain/bin/vg", at 0x519847, in vg::io::MessageIterator::handle(bool, long, long) [clone .cold]
#5    Object "/home/USER/.conda/envs/strain/bin/vg", at 0x1e85b78, in __cxa_throw
#4    Object "/home/USER/.conda/envs/strain/bin/vg", at 0x1e85a16, in std::terminate()
#3    Object "/home/USER/.conda/envs/strain/bin/vg", at 0x1e859ab, in __cxxabiv1::__terminate(void (*)())
#2    Object "/home/USER/.conda/envs/strain/bin/vg", at 0x57c302, in __gnu_cxx::__verbose_terminate_handler() [clone .cold]
#1    Object "/home/USER/.conda/envs/strain/bin/vg", at 0x57ed93, in abort
#0    Object "/home/USER/.conda/envs/strain/bin/vg", at 0x12e27bb, in raise