vg view

[erivals]

1. What you were trying to do
   getting the graph in GFA format with vg view on the "tiny" example with simple tiny.vcf files from your test directory

2. What you wanted to happen
   see above

3. What actually happened
   vg view crashed

4. What data and command line to use to make the problem recur, if applicable

vg construct -r tiny.fa -v tiny.vcf.gz > t.vg
vg view t.vg > t.gfa
ERROR: Signal 4 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_z18o2M/stacktrace.txt

here is the stacktrace

cat /tmp/vg_crash_z18o2M/stacktrace.txt
Crash report for vg v1.18.0 "Zungoli"
Stack trace (most recent call last):
#6    Object "/home/rivals/local/bin/vg", at 0x4d5819, in _start
#5    Object "/home/rivals/local/bin/vg", at 0x1a5d498, in __libc_start_main
#4    Object "/home/rivals/local/bin/vg", at 0x4098a2, in main
#3    Object "/home/rivals/local/bin/vg", at 0x9ac137, in vg::subcommand::Subcommand::operator()(int, char**) const
#2    Object "/home/rivals/local/bin/vg", at 0x9b2cf4, in main_view(int, char**)
#1    Object "/home/rivals/local/bin/vg", at 0xb2e9c5, in vg::graph_to_gfa(vg::VG const*, std::ostream&)
#0    Object "/home/rivals/local/bin/vg", at 0x11d187c, in gfak::GFAKluge::GFAKluge()

[ekg]

Did you build this vg executable? We have discovered problems with the binary releases going back some time.

…

On Sat, Sep 14, 2019, 08:14 erivals ***@***.***> wrote: 1. What you were trying to do getting the graph in GFA format with vg view on the "tiny" example with simple tiny.vcf files from your test directory 2. What you wanted to happen see above 3. What actually happened vg view crashed 4. What data and command line to use to make the problem recur, if applicable vg construct -r tiny.fa -v tiny.vcf.gz > t.vg vg view t.vg > t.gfa ERROR: Signal 4 occurred. VG has crashed. Run 'vg bugs --new' to report a bug. Stack trace path: /tmp/vg_crash_z18o2M/stacktrace.txt here is the stacktrace cat /tmp/vg_crash_z18o2M/stacktrace.txt Crash report for vg v1.18.0 "Zungoli" Stack trace (most recent call last): #6 Object "/home/rivals/local/bin/vg", at 0x4d5819, in _start #5 Object "/home/rivals/local/bin/vg", at 0x1a5d498, in __libc_start_main #4 Object "/home/rivals/local/bin/vg", at 0x4098a2, in main #3 Object "/home/rivals/local/bin/vg", at 0x9ac137, in vg::subcommand::Subcommand::operator()(int, char**) const #2 Object "/home/rivals/local/bin/vg", at 0x9b2cf4, in main_view(int, char**) #1 Object "/home/rivals/local/bin/vg", at 0xb2e9c5, in vg::graph_to_gfa(vg::VG const*, std::ostream&) #0 Object "/home/rivals/local/bin/vg", at 0x11d187c, in gfak::GFAKluge::GFAKluge() — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2457?email_source=notifications&email_token=AABDQEN55TWMS5QJTFZ45ITQJSFOBA5CNFSM4IWWGIJ2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HLLUPHA>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABDQEJBVD2OWMHYMLEF6A3QJSFOBANCNFSM4IWWGIJQ> .

[erivals]

Hi
no i installed the conda package.

[hd00ljy]

Hi,
I experienced the same issue.

Commands

vg view  test.vg

Error message

Crash report for vg v1.18.0 "Zungoli"
Stack trace (most recent call last):
#6    Object "/root/bin/vg", at 0x4d5819, in _start
#5    Object "/root/bin/vg", at 0x1a5d498, in __libc_start_main
#4    Object "/root/bin/vg", at 0x4098a2, in main
#3    Object "/root/bin/vg", at 0x9ac137, in vg::subcommand::Subcommand::operator()(int, char**) const
#2    Object "/root/bin/vg", at 0x9b2cf4, in main_view(int, char**)
#1    Object "/root/bin/vg", at 0xb2e9c5, in vg::graph_to_gfa(vg::VG const*, std::ostream&)
#0    Object "/root/bin/vg", at 0x11d187c, in gfak::GFAKluge::GFAKluge()

I used binary release and the version is

vg version v1.18.0 "Zungoli"
Compiled with g++ (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0 on Linux
Built by ubuntu@ip-172-31-45-169

[ekg]

I suspect the problem is with the binary package. Can you reproduce this crash with a binary that you compile on this system?

…

On Mon, Sep 23, 2019, 02:21 hd00ljy ***@***.***> wrote: Hi, I experienced the same issue. Crash report for vg v1.18.0 "Zungoli" Stack trace (most recent call last): #6 Object "/root/bin/vg", at 0x4d5819, in _start #5 Object "/root/bin/vg", at 0x1a5d498, in __libc_start_main #4 Object "/root/bin/vg", at 0x4098a2, in main #3 Object "/root/bin/vg", at 0x9ac137, in vg::subcommand::Subcommand::operator()(int, char**) const #2 Object "/root/bin/vg", at 0x9b2cf4, in main_view(int, char**) #1 Object "/root/bin/vg", at 0xb2e9c5, in vg::graph_to_gfa(vg::VG const*, std::ostream&) #0 Object "/root/bin/vg", at 0x11d187c, in gfak::GFAKluge::GFAKluge() I used binary release and the version is vg version v1.18.0 "Zungoli" Compiled with g++ (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0 on Linux Built by ***@***.*** — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2457?email_source=notifications&email_token=AABDQEKTXIOVYTSS6RQNNDTQLAD2BA5CNFSM4IWWGIJ2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7JSSBA#issuecomment-533932292>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AABDQEPGZAMZBC2ESIFBOBDQLAD2BANCNFSM4IWWGIJQ> .