search

vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
Other
1.07k stars 191 forks source link

ERROR: Signal 6 occurred. VG has crashed. #4238

Closed mariarecuerda6 closed 3 months ago

mariarecuerda6 commented 3 months ago

1. What were you trying to do? I was running vg call in a machine where I have previously run it succesfully, using the following command: vg call spp-pg.d2.xg -k B009636.pack -a > B009636.vcf

2. What did you want to happen? I want to obtain the vcf file

3. What actually happened? ERROR: Signal 6 occurred. VG has 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: /public/home/anovak/build/vg/include/sdsl/vlc_vector.hpp:172: sdsl::vlc_vector<t_coder, t_dens, t_width>::value_type sdsl::vlc_vector<t_coder, t_dens, t_width>::operator[](sdsl::vlc_vector<t_coder, t_dens, t_width>::size_type) const [with t_coder = sdsl::coder::elias_delta; unsigned int t_dens = 128; unsigned char t_width = 0; sdsl::vlc_vector<t_coder, t_dens, t_width>::value_type = long unsigned int; sdsl::vlc_vector<t_coder, t_dens, t_width>::size_type = long unsigned int]: Assertion `i < m_size' failed.
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.53.0 "Valmontone"
Stack trace (most recent call last):
#17   Object "/programs/vg-1.53.0/vg", at 0x617214, in _start
#16   Object "/programs/vg-1.53.0/vg", at 0x206e796, in __libc_start_main
#15   Object "/programs/vg-1.53.0/vg", at 0x206cf39, in __libc_start_call_main
#14   Object "/programs/vg-1.53.0/vg", at 0xdfa8ab, in vg::subcommand::Subcommand::operator()(int, char**) const
#13   Object "/programs/vg-1.53.0/vg", at 0xc7781e, in main_call(int, char**)
#12   Object "/programs/vg-1.53.0/vg", at 0x14d9d89, in vg::algorithms::binned_packed_depth_index(vg::Packer const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned long, unsigned long, double, unsigned long, bool, bool)
#11   Object "/programs/vg-1.53.0/vg", at 0x14d8379, in vg::algorithms::binned_packed_depth(vg::Packer const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, unsigned long, bool)
#10   Object "/programs/vg-1.53.0/vg", at 0x204a6f5, in GOMP_parallel
#9    Object "/programs/vg-1.53.0/vg", at 0x14db5f5, in vg::algorithms::binned_packed_depth(vg::Packer const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long, unsigned long, bool) [clone ._omp_fn.0]
#8    Object "/programs/vg-1.53.0/vg", at 0x14db3e2, in vg::algorithms::packed_depth_of_bin(vg::Packer const&, handlegraph::step_handle_t, handlegraph::step_handle_t, unsigned long, bool)
#7    Object "/programs/vg-1.53.0/vg", at 0x187d3d5, in xg::XG::follow_edges_impl(handlegraph::handle_t const&, bool, std::function<bool (handlegraph::handle_t const&)> const&) const
#6    Object "/programs/vg-1.53.0/vg", at 0x14d888e, in _ZNSt17_Function_handlerIFbRKN11handlegraph8handle_tEEZNS0_20BoolReturningWrapperIZN2vg10algorithms19packed_depth_of_binERKNS6_6PackerENS0_13step_handle_tESB_mbEUlS1_E_Lb0EE4wrapERKSC_EUlDpOT_E_E9_M_invokeERKSt9_Any_dataS3_
#5    Object "/programs/vg-1.53.0/vg", at 0x126dbb7, in sdsl::vlc_vector<sdsl::coder::elias_delta, 128u, (unsigned char)0>::operator[](unsigned long) const
#4    Object "/programs/vg-1.53.0/vg", at 0x207f365, in __assert_fail
#3    Object "/programs/vg-1.53.0/vg", at 0x5e5eb3, in __assert_fail_base.cold
#2    Object "/programs/vg-1.53.0/vg", at 0x5e5f8b, in abort
#1    Object "/programs/vg-1.53.0/vg", at 0x2085975, in raise
#0    Object "/programs/vg-1.53.0/vg", at 0x20b237c, 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!

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

6. What does running vg version say?

vg version v1.53.0 "Valmontone"
Compiled with g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 on Linux
Linked against libstd++ 20230528
Built by anovak@courtyard.gi.ucsc.edu
jeizenga commented 3 months ago

Can you also share the commands you used to make the graph, map reads, and make the pack file? Often these errors result from some mismatch between the graphs used at different stages in the analysis.

mariarecuerda6 commented 3 months ago

Hello,

The weird thing is that I've been running in the same machine with the same graphs using the same commands for all of them and now they are giving me this error.

To generate the graph I used cactus minigraph Then I run:

vg gbwt -o spp-pg.d2.gbwt -Z spp-pg.d2.gbz

Then I mapped the reads with vg giraffe

vg giraffe -Z spp-pg.d2.gbz -m spp-pg.d2.min -d spp-pg.d2.dist -f /min_O5.pair1.fa -f min_O5.pair2.fa > min_O5.gam

vg convert -Hx spp-pg.d2.gbz > spp-pg.d2.xg vg convert -Hp spp-pg.d2.gbz > spp-pg.d2.vg

Then make the pack file

vg pack -x spp-pg.xg -g min_O5_p12.gam -Q 5 -o min_O5.pack

Then vg call

vg call spp-pg.d2.xg -k min_O5.pack -a > min_O5.vcf

I've been running these commands in 3 different machines and they work (some of them are running right now) but I don't know why it is not working anymore.

Thank you for your help, Maria

El mar, 5 mar 2024 a las 15:05, Jordan Eizenga @.***>) escribió:

Can you also share the commands you used to make the graph, map reads, and make the pack file? Often these errors result from some mismatch between the graphs used at different stages in the analysis.

— Reply to this email directly, view it on GitHub https://github.com/vgteam/vg/issues/4238#issuecomment-1979539800, or unsubscribe https://github.com/notifications/unsubscribe-auth/A7AU2SYD6CSC2V23Z5JBQP3YWYQQ3AVCNFSM6AAAAABEHXR6TGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZZGUZTSOBQGA . You are receiving this because you authored the thread.Message ID: @.***>

-- María Recuerda, PhD

Postdoctoral Research Associate Department of Ecology and Evolutionary Biology Fuller Evolutionary Biology Program Cornell Lab of Ornithology Cornell University @.** https://mariarecuerda.weebly.com/ https://mariarecuerda.weebly.com/*

jeizenga commented 3 months ago

Presumably this is new sequencing data, despite using the same graphs, correct?

In any case, nothing jumps out to me as incorrect in the pipeline, although you don't seem to be actually using all of the indexes/graphs that you create. Are you able to share the data?

mariarecuerda6 commented 3 months ago

I manage to run the pipeline previously with all the samples, but I have to repeat it because I mapped the wrong files and I lost a lot of information.. I thought that the vg graph was used when you call in the command the xg index, but you don't have to specify the graph directly.

What files do you need? the graph (vg), the index (xg) and a pack file? the graph and the index are 6.1 and 8.7 GB

El mar, 5 mar 2024 a las 15:25, Jordan Eizenga @.***>) escribió:

Presumably this is new sequencing data, despite using the same graphs, correct?

In any case, nothing jumps out to me as incorrect in the pipeline, although you don't seem to be actually using all of the indexes/graphs that you create. Are you able to share the data?

— Reply to this email directly, view it on GitHub https://github.com/vgteam/vg/issues/4238#issuecomment-1979579074, or unsubscribe https://github.com/notifications/unsubscribe-auth/A7AU2S7SZN5GZ2UNHMP5ZVLYWYS3JAVCNFSM6AAAAABEHXR6TGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZZGU3TSMBXGQ . You are receiving this because you authored the thread.Message ID: @.***>

-- María Recuerda, PhD

Postdoctoral Research Associate Department of Ecology and Evolutionary Biology Fuller Evolutionary Biology Program Cornell Lab of Ornithology Cornell University @.** https://mariarecuerda.weebly.com/ https://mariarecuerda.weebly.com/*

jeizenga commented 3 months ago

Ideally, the d2 GBZ file, the full GBZ, and the sequences you're mapping.

Before that though, can you check what happens if you use spp-pg.xg instead of spp-pg.d2.xg in vg call?

mariarecuerda6 commented 3 months ago

I have tried with the spp-pg.xg file and I got the same error (ERROR: Signal 6 occurred. VG has crashed. )

El mar, 5 mar 2024 a las 17:21, Jordan Eizenga @.***>) escribió:

Ideally, the d2 GBZ file, the full GBZ, and the sequences you're mapping.

Before that though, can you check what happens if you use spp-pg.xg instead of spp-pg.d2.xg in vg call?

— Reply to this email directly, view it on GitHub https://github.com/vgteam/vg/issues/4238#issuecomment-1979736033, or unsubscribe https://github.com/notifications/unsubscribe-auth/A7AU2SZN532EIV5N6LVHXY3YWZAP3AVCNFSM6AAAAABEHXR6TGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZZG4ZTMMBTGM . You are receiving this because you authored the thread.Message ID: @.***>

-- María Recuerda, PhD

Postdoctoral Research Associate Department of Ecology and Evolutionary Biology Fuller Evolutionary Biology Program Cornell Lab of Ornithology Cornell University @.** https://mariarecuerda.weebly.com/ https://mariarecuerda.weebly.com/*

mariarecuerda6 commented 3 months ago

Hi Jordan,

I have solved the problem, It seems that the pack files were somehow corrupted. I just repeated the pack step and now vg call it's working fine. Thank you for your time and suggestions.

Best, Maria

El mié, 6 mar 2024 a las 0:08, Maria Recuerda Carrasco (< @.***>) escribió:

I have tried with the spp-pg.xg file and I got the same error (ERROR: Signal 6 occurred. VG has crashed. )

El mar, 5 mar 2024 a las 17:21, Jordan Eizenga @.***>) escribió:

Ideally, the d2 GBZ file, the full GBZ, and the sequences you're mapping.

Before that though, can you check what happens if you use spp-pg.xg instead of spp-pg.d2.xg in vg call?

— Reply to this email directly, view it on GitHub https://github.com/vgteam/vg/issues/4238#issuecomment-1979736033, or unsubscribe https://github.com/notifications/unsubscribe-auth/A7AU2SZN532EIV5N6LVHXY3YWZAP3AVCNFSM6AAAAABEHXR6TGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZZG4ZTMMBTGM . You are receiving this because you authored the thread.Message ID: @.***>

-- María Recuerda, PhD

Postdoctoral Research Associate Department of Ecology and Evolutionary Biology Fuller Evolutionary Biology Program Cornell Lab of Ornithology Cornell University @.** https://mariarecuerda.weebly.com/ https://mariarecuerda.weebly.com/*

-- María Recuerda, PhD

Postdoctoral Research Associate Department of Ecology and Evolutionary Biology Fuller Evolutionary Biology Program Cornell Lab of Ornithology Cornell University @.** https://mariarecuerda.weebly.com/ https://mariarecuerda.weebly.com/*

jeizenga commented 3 months ago

Glad it worked out!