vg map crashes with signal 11

[cgroza]

1. What were you trying to do?
I am trying to align reads to the hg19 graph.
Here is the command I am using:

vg map -i  -f EU33_NI_ATACSeq_1_2-308169_S12_L001_I.fastq.gz -x hg19.xg -g hg19.gcsa -t 40 -u 1 -m 1 > "control_gam/EU33_NI_ATACSeq_1_2-308169_S12_L001_I_ref.gam"

3. What actually happened?
vg map aligns and outputs reads to a GAM file until it crashes with signal 11 and outputs a stacktrace.

The hg19 graph was built with the latest version of vg.

Here is the stack trace:

cgroza@beluga4[±|master U:131 ?:19 ✗]:.../15/2c7bee92c8ac92c72e71a249f5bf4b $ cat /tmp/vg_crash_oawoZV/stacktrace.txt                                 
Crash report for vg v1.20.0 "Ginestra"
Stack trace (most recent call last):
#21   Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x4d8779, in _start
#20   Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x1ad4b18, in __libc_start_main
#19   Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x40ac62, in main
#18   Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x9a1857, in vg::subcommand::Subcommand::operator()(int, char**) const
#17   Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x8f61e5, in main_map(int, char**)
#16   Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xadf5c7, in vg::fastq_paired_interleaved_for_each_parallel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::function<void (vg::Alignment&, vg::Alignment&)>)
#15   Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xadf390, in vg::fastq_paired_interleaved_for_each_parallel_after_wait(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::function<void (vg::Alignment&, vg::Alignment&)>, std::function<bool ()>)
#14   Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x1abaa2e, in GOMP_parallel
#13   Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xae47f5, in vg::paired_for_each_parallel_after_wait(std::function<bool (vg::Alignment&, vg::Alignment&)>, std::function<void (vg::Alignment&, vg::Alignment&)>, std::function<bool ()>) [clone ._omp_fn.3]
#12   Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x1abf824, in GOMP_task
#11   Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xae44a8, in vg::paired_for_each_parallel_after_wait(std::function<bool (vg::Alignment&, vg::Alignment&)>, std::function<void (vg::Alignment&, vg::Alignment&)>, std::function<bool ()>) [clone ._omp_fn.4]
#10   Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x8f8e71, in main_map(int, char**)::{lambda(vg::Alignment&, vg::Alignment&)#8}::operator()(vg::Alignment&, vg::Alignment&) const
#9    Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xb1a0a7, in vg::Mapper::align_paired_multi(vg::Alignment const&, vg::Alignment const&, bool&, int, bool, bool, bool)
#8    Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xb15f08, in vg::Mapper::pair_rescue(vg::Alignment&, vg::Alignment&, bool&, bool&, int, int, bool, bool)
#7    Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xb15949, in vg::Mapper::align_maybe_flip(vg::Alignment const&, handlegraph::HandleGraph&, bool, bool, bool, bool) [clone .constprop.2186]
#6    Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xb15787, in vg::Mapper::align_maybe_flip(vg::Alignment const&, handlegraph::HandleGraph&, std::vector<vg::MaximalExactMatch, std::allocator<vg::MaximalExactMatch> > const&, bool, bool, bool, bool)
#5    Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xb1533d, in vg::Mapper::align_to_graph(vg::Alignment const&, handlegraph::HandleGraph&, std::vector<vg::MaximalExactMatch, std::allocator<vg::MaximalExactMatch> > const&, bool, bool, bool, bool, bool, int, bool)
#4    Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xb8321a, in vg::Aligner::align(vg::Alignment&, handlegraph::HandleGraph const&, std::vector<handlegraph::handle_t, std::allocator<handlegraph::handle_t> > const&, bool, bool) const
#3    Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xb821df, in vg::Aligner::align_internal(vg::Alignment&, std::vector<vg::Alignment, std::allocator<vg::Alignment> >*, handlegraph::HandleGraph const&, std::vector<handlegraph::handle_t, std::allocator<handlegraph::handle_t> > const*, bool, bool, int, bool, bool) const [clone .constprop.308]
#2    Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xeba95b, in gssw_graph_fill_pinned
#1    Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xeb7545, in gssw_node_fill
#0    Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xeb14dd, in gssw_sw_sse2_byte
cgroza@beluga4[±|master U:131 ?:19 ✗]:.../15/2c7bee92c8ac92c72e71a249f5bf4b $ 

6. What does running vg version say?

vg version v1.20.0 "Ginestra"
Compiled with g++ (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0 on Linux
Linked against libstd++ 20181206
Built by anovak@hex

Here is the first few lines of the output GAM:

ls -lh
-rw-r----- 1 cgroza 245M Nov 19 17:41 EU33_NI_ATACSeq_1_2-308169_S12_L001_I_ref.gam

cgroza@beluga4[±|master U:131 ?:19 ✗]:...ol_game92c8ac92c72e71a249f5bf4b/control_gam $ vg view -aj EU33_NI_ATACSeq_1_2-308169_S12_L001_I_ref.gam | head -2
{"fragment": [{"name": "chr4"}], "fragment_length_distribution": "0:0:0:0:1", "fragment_next": {"name": "A00266:108:HHJHGDMXX:1:1101:31250:14403 "}, "identity": 1.0, "mapping_quality": 60, "name": "A00266:108:HHJHGDMXX:1:1101:31250:14403 ", "path": {"mapping": [{"edit": [{"from_length": 7, "to_length": 7}], "position": {"is_reverse": true, "node_id": "24208706", "offset": "25"}, "rank": "1"}, {"edit": [{"from_length": 32, "to_length": 32}], "position": {"is_reverse": true, "node_id": "24208705"}, "rank": "2"}, {"edit": [{"from_length": 32, "to_length": 32}], "position": {"is_reverse": true, "node_id": "24208704"}, "rank": "3"}, {"edit": [{"from_length": 17, "to_length": 17}], "position": {"is_reverse": true, "node_id": "24208703"}, "rank": "4"}]}, "quality": "JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ==", "refpos": [{"is_reverse": true, "name": "chr4", "offset": "84205999"}], "score": 98, "sequence": "CCCTAGAGTAAGCGACCACGATGACCCCAATTTCACAAGTAAGGATGAGGAAAGGTTCTGCCCACACCGCCGCCCAGCCTGGCAGACT", "time_used": 6219.0}
{"fragment": [{"name": "chr4"}], "fragment_length_distribution": "0:0:0:0:1", "fragment_prev": {"name": "A00266:108:HHJHGDMXX:1:1101:31250:14403 "}, "identity": 1.0, "mapping_quality": 60, "name": "A00266:108:HHJHGDMXX:1:1101:31250:14403 ", "path": {"mapping": [{"edit": [{"from_length": 17, "to_length": 17}], "position": {"node_id": "24208703", "offset": "15"}, "rank": "1"}, {"edit": [{"from_length": 32, "to_length": 32}], "position": {"node_id": "24208704"}, "rank": "2"}, {"edit": [{"from_length": 32, "to_length": 32}], "position": {"node_id": "24208705"}, "rank": "3"}, {"edit": [{"from_length": 7, "to_length": 7}], "position": {"node_id": "24208706"}, "rank": "4"}]}, "quality": "JSUlJSUlJSUlJSUlGSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUZJSUlJSUlJSUlJSUlJQ==", "refpos": [{"name": "chr4", "offset": "84205999"}], "score": 98, "sequence": "AGTCTGCCAGGCTGGGCGGCGGTGTGGGCAGAACCTTTCCTCATCCTTACTTGTGAAATTGGGGTCATCGTGGTCGCTTACTCTAGGG", "time_used": 6219.0}

So it seems it can align just fine but eventually just crashes.
Do you know what could be causing this issue?

[ekg]

Would you be able to provide a reproducible example? How did you build the graph? What is the sequence of the read that's crashes?

…

On Tue, Nov 19, 2019, 23:34 Groza Cristian ***@***.***> wrote: *1. What were you trying to do?* I am trying to align reads to the hg19 graph. *3. What actually happened?* vg map aligns and outputs reads to a GAM file until it crashes with signal 11 and outputs a stacktrace. The hg19 graph was built with the latest version of vg. Here is the stack trace: ***@***.***[±|master U:131 ?:19 ✗]:.../15/2c7bee92c8ac92c72e71a249f5bf4b $ cat /tmp/vg_crash_oawoZV/stacktrace.txt Crash report for vg v1.20.0 "Ginestra" Stack trace (most recent call last): #21 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x4d8779, in _start #20 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x1ad4b18, in __libc_start_main #19 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x40ac62, in main #18 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x9a1857, in vg::subcommand::Subcommand::operator()(int, char**) const #17 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x8f61e5, in main_map(int, char**) #16 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xadf5c7, in vg::fastq_paired_interleaved_for_each_parallel(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::function<void (vg::Alignment&, vg::Alignment&)>) #15 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xadf390, in vg::fastq_paired_interleaved_for_each_parallel_after_wait(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::function<void (vg::Alignment&, vg::Alignment&)>, std::function<bool ()>) #14 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x1abaa2e, in GOMP_parallel #13 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xae47f5, in vg::paired_for_each_parallel_after_wait(std::function<bool (vg::Alignment&, vg::Alignment&)>, std::function<void (vg::Alignment&, vg::Alignment&)>, std::function<bool ()>) [clone ._omp_fn.3] #12 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x1abf824, in GOMP_task #11 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xae44a8, in vg::paired_for_each_parallel_after_wait(std::function<bool (vg::Alignment&, vg::Alignment&)>, std::function<void (vg::Alignment&, vg::Alignment&)>, std::function<bool ()>) [clone ._omp_fn.4] #10 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0x8f8e71, in main_map(int, char**)::{lambda(vg::Alignment&, vg::Alignment&)#8}::operator()(vg::Alignment&, vg::Alignment&) const #9 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xb1a0a7, in vg::Mapper::align_paired_multi(vg::Alignment const&, vg::Alignment const&, bool&, int, bool, bool, bool) #8 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xb15f08, in vg::Mapper::pair_rescue(vg::Alignment&, vg::Alignment&, bool&, bool&, int, int, bool, bool) #7 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xb15949, in vg::Mapper::align_maybe_flip(vg::Alignment const&, handlegraph::HandleGraph&, bool, bool, bool, bool) [clone .constprop.2186] #6 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xb15787, in vg::Mapper::align_maybe_flip(vg::Alignment const&, handlegraph::HandleGraph&, std::vector<vg::MaximalExactMatch, std::allocator<vg::MaximalExactMatch> > const&, bool, bool, bool, bool) #5 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xb1533d, in vg::Mapper::align_to_graph(vg::Alignment const&, handlegraph::HandleGraph&, std::vector<vg::MaximalExactMatch, std::allocator<vg::MaximalExactMatch> > const&, bool, bool, bool, bool, bool, int, bool) #4 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xb8321a, in vg::Aligner::align(vg::Alignment&, handlegraph::HandleGraph const&, std::vector<handlegraph::handle_t, std::allocator<handlegraph::handle_t> > const&, bool, bool) const #3 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xb821df, in vg::Aligner::align_internal(vg::Alignment&, std::vector<vg::Alignment, std::allocator<vg::Alignment> >*, handlegraph::HandleGraph const&, std::vector<handlegraph::handle_t, std::allocator<handlegraph::handle_t> > const*, bool, bool, int, bool, bool) const [clone .constprop.308] #2 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xeba95b, in gssw_graph_fill_pinned #1 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xeb7545, in gssw_node_fill #0 Object "/lustre04/scratch/cgroza/Epi_10X/work/15/2c7bee92c8ac92c72e71a249f5bf4b/vg", at 0xeb14dd, in gssw_sw_sse2_byte ***@***.***[±|master U:131 ?:19 ✗]:.../15/2c7bee92c8ac92c72e71a249f5bf4b $ *6. What does running vg version say?* Place vg vg version v1.20.0 "Ginestra" Compiled with g++ (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0 on Linux Linked against libstd++ 20181206 Built by ***@***.*** Do you know what could be causing this issue? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2541?email_source=notifications&email_token=AABDQEKWLG2MG4SMBW3CFXDQURSVXA5CNFSM4JPKLEE2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4H2PR46Q>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDQELI2C2JM5THP225APTQURSVXANCNFSM4JPKLEEQ> .