.gamp file can not convert to .gam file

[Sourirewang]

Hi,
I used vg mpmap to produce multipath alignments with RNA-seq data. But vg crashed when I want to convert the .gamp file to .gam file, so I could not do the Variant Calling analysis. Are there any resolutions to fix this error? Thanks a lot!

1. What were you trying to do?
I try to convert GAMP to a GAM, and my code is "vg view -K -G DLS01_mapped_reads.gamp > DLS01_mapped_reads.gam"

2. What did you want to happen?
DLS01_mapped_reads.gam is generated.

3. What actually happened?
vg crashed.

4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:
vg view -K -G DLS01_mapped_reads.gamp > DLS01_mapped_reads.gam
terminate called after throwing an instance of 'std::runtime_error'
what(): [io::ProtobufIterator] could not parse message
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.50.1 "Monopoli"
Stack trace (most recent call last):
#15 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x6163d4, in _start
#14 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x205e5f6, in __libc_start_main
#13 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x205cd99, in __libc_start_call_main
#12 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0xdf5fab, in vg::subcommand::Subcommand::operator()(int, char**) const
#11 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0xe6fc9e, in main_view(int, char**)
#10 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x1429487, in vg::get_input_file(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::function<void (std::istream&)>)
#9 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0xe6b908, in std::_Function_handler<void (std::istream&), main_view(int, char**)::{lambda(std::istream&)#20}>::_M_invoke(std::_Any_data const&, std::istream&)
#8 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0xe734c2, in void vg::io::for_eachvg::MultipathAlignment(std::istream&, std::function<void (long, vg::MultipathAlignment&)> const&)
#7 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0xd7c487, in vg::io::ProtobufIteratorvg::MultipathAlignment::fill_value()
#6 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x1f96b58, in __cxa_throw
#5 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x1f969f6, in std::terminate()
#4 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x1f9698b, in __cxxabiv1::__terminate(void (*)())
#3 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x5e29e3, in __gnu_cxx::__verbose_terminate_handler() [clone .cold]
#2 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x5e512b, in abort
#1 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x20757d5, in raise
#0 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x20a21dc, in __pthread_kill
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Please include this entire error log in your bug report!

Place stacktrace here.

**5. What data and command can the vg dev team use to make the problem happen?**


**6. What does running `vg version` say?**

``` vg v1.50.1
Place vg version output here

[jeizenga]

Can you verify that the GAMP file is not empty? If not, what gets printed out if you try vg view -K -j DLS01_mapped_reads.gamp | head?

[Sourirewang]

Can you verify that the GAMP file is not empty? If not, what gets printed out if you try vg view -K -j DLS01_mapped_reads.gamp | head?

It seems not empty because the file size is 11G. But when I try "vg view -K -j DLS01_mapped_reads.gamp | head", the vg crashed. Here is the print:
vg view -K -j DLS01_mapped_reads.gamp | head
terminate called after throwing an instance of 'std::runtime_error'
what(): [io::ProtobufIterator] could not parse message
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.50.1 "Monopoli"
Stack trace (most recent call last):
#15 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x6163d4, in _start
#14 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x205e5f6, in __libc_start_main
#13 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x205cd99, in __libc_start_call_main
#12 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0xdf5fab, in vg::subcommand::Subcommand::operator()(int, char**) const
#11 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0xe6fbbc, in main_view(int, char**)
#10 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x1429487, in vg::get_input_file(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::function<void (std::istream&)>)
#9 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0xe6b9a8, in std::_Function_handler<void (std::istream&), main_view(int, char**)::{lambda(std::istream&)#22}>::_M_invoke(std::_Any_data const&, std::istream&)
#8 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0xe734c2, in void vg::io::for_eachvg::MultipathAlignment(std::istream&, std::function<void (long, vg::MultipathAlignment&)> const&)
#7 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0xd7c487, in vg::io::ProtobufIteratorvg::MultipathAlignment::fill_value()
#6 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x1f96b58, in __cxa_throw
#5 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x1f969f6, in std::terminate()
#4 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x1f9698b, in __cxxabiv1::__terminate(void (*)())
#3 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x5e29e3, in __gnu_cxx::__verbose_terminate_handler() [clone .cold]
#2 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x5e512b, in abort
#1 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x20757d5, in raise
#0 Object "/data/Wangmeizhen/.conda/envs/vg/bin/vg", at 0x20a21dc, in __pthread_kill
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Please include this entire error log in your bug report!

[jeizenga]

Most likely it's not actually saved in GAMP format. What command did you use to generate the file? You can try vg view -aj DLS01_mapped_reads.gamp to see if it's already in GAM format.

[Sourirewang]

Most likely it's not actually saved in GAMP format. What command did you use to generate the file? You can try vg view -aj DLS01_mapped_reads.gamp to see if it's already in GAM format.

Yes, I found the problem. I was using vg mpmap directly with the nohup command, but it resulted in a mixing of the log file and gamp file. This might be the reason why the .gamp file couldn't be converted to a .gam file. To resolve this issue, I started the mapping step again using the vg mpmap code within a bash file, and the log file and gamp file were correctly separated.

[jeizenga]

Great. Glad you got it worked out.