ERROR: Signal 6 occurred. VG has crashed.

[shin0727]

1. What were you trying to do?
I'm trying to create a coverage index with "vg pack" from my gaf.gz input file

vg giraffe -t 40 -Z ${REF}.d2.gbz -m ${REF}.d2.min -d ${REF}.d2.dist -f ${R1} -f ${R2} -p -o gaf | bgzip > ${SAMPLE}.gaf.gz
vg pack -x ${REF}.gbz -Q5 -a ${SAMPLE}.gaf.gz -o ${PREFIX}.pack

2. What did you want to happen?
get vcf file

3. What actually happened?
Stopped with some errors

vg: /public/home/anovak/build/vg/deps/libvgio/src/alignment_io.cpp:691: vg::io::gaf_to_alignment(std::function<long unsigned int(long long int)>, std::function<std::__cxx11::basic_string(long long int, bool)>, const gafkluge::GafRecord&, vg::Alignment&)::<lambda(const char&, const size_t&, const string&, const string&)>: Assertion cur_offset < cur_len || ((cigar_cat == '+' || cigar_cat == 'I' || cigar_cat == 'S') && cur_offset <= cur_len)' failed. ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.57.0 "Franchini" vg: /public/home/anovak/build/vg/deps/libvgio/src/alignment_io.cpp:691: vg::io::gaf_to_alignment(std::function<long unsigned int(long long int)>, std::function<std::__cxx11::basic_string<char>(long long int, bool)>, const gafkluge::GafRecord&, vg::Alignment&)::<lambda(const char&, const size_t&, const string&, const string&)>: Assertion cur_offset < cur_len || ((cigar_cat == '+' || cigar_cat == 'I' || cigar_cat == 'S') && cur_offset <= cur_len)' failed.
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Crash report for vg v1.57.0 "Franchini"
vg: /public/home/anovak/build/vg/deps/libvgio/src/alignment_io.cpp:691: vg::io::gaf_to_alignment(std::function<long unsigned int(long long int)>, std::function<std::__cxx11::basic_string(long long int, bool)>, const gafkluge::GafRecord&, vg::Alignment&)::<lambda(const char&, const size_t&, const string&, const string&)>: Assertion cur_offset < cur_len || ((cigar_cat == '+' || cigar_cat == 'I' || cigar_cat == 'S') && cur_offset <= cur_len)' failed. ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.57.0 "Franchini" vg: /public/home/anovak/build/vg/deps/libvgio/src/alignment_io.cpp:691: vg::io::gaf_to_alignment(std::function<long unsigned int(long long int)>, std::function<std::__cxx11::basic_string<char>(long long int, bool)>, const gafkluge::GafRecord&, vg::Alignment&)::<lambda(const char&, const size_t&, const string&, const string&)>: Assertion cur_offset < cur_len || ((cigar_cat == '+' || cigar_cat == 'I' || cigar_cat == 'S') && cur_offset <= cur_len)' failed.
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.57.0 "Franchini"
vg: /public/home/anovak/build/vg/deps/libvgio/src/alignment_io.cpp:691: vg::io::gaf_to_alignment(std::function<long unsigned int(long long int)>, std::function<std::__cxx11::basic_string(long long int, bool)>, const gafkluge::GafRecord&, vg::Alignment&)::<lambda(const char&, const size_t&, const string&, const string&)>: Assertion cur_offset < cur_len || ((cigar_cat == '+' || cigar_cat == 'I' || cigar_cat == 'S') && cur_offset <= cur_len)' failed. ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.57.0 "Franchini" vg: /public/home/anovak/build/vg/deps/libvgio/src/alignment_io.cpp:691: vg::io::gaf_to_alignment(std::function<long unsigned int(long long int)>, std::function<std::__cxx11::basic_string<char>(long long int, bool)>, const gafkluge::GafRecord&, vg::Alignment&)::<lambda(const char&, const size_t&, const string&, const string&)>: Assertion cur_offset < cur_len || ((cigar_cat == '+' || cigar_cat == 'I' || cigar_cat == 'S') && cur_offset <= cur_len)' failed.
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.57.0 "Franchini"
vg: /public/home/anovak/build/vg/deps/libvgio/src/alignment_io.cpp:691: vg::io::gaf_to_alignment(std::function<long unsigned int(long long int)>, std::function<std::__cxx11::basic_string(long long int, bool)>, const gafkluge::GafRecord&, vg::Alignment&)::<lambda(const char&, const size_t&, const string&, const string&)>: Assertion cur_offset < cur_len || ((cigar_cat == '+' || cigar_cat == 'I' || cigar_cat == 'S') && cur_offset <= cur_len)' failed. ━━━━━━━━━━━━━━━━━━vg: /public/home/anovak/build/vg/deps/libvgio/src/alignment_io.cpp:691: vg::io::gaf_to_alignment(std::function<long unsigned int(long long int)>, std::function<std::__cxx11::basic_string<char>(long long int, bool)>, const gafkluge::GafRecord&, vg::Alignment&)::<lambda(const char&, const size_t&, const string&, const string&)>: Assertion cur_offset < cur_len || ((cigar_cat == '+' || cigar_cat == 'I' || cigar_cat == 'S') && cur_offset <= cur_len)' failed.
━━
Crash report for vg v1.57.0 "Franchini"
━━━━━━━━━━━━━━━━━━━━
Crash report for vg vg: /public/home/anovak/build/vg/deps/libvgio/src/alignment_io.cpp:691: vg::io::gaf_to_alignment(std::function<long unsigned int(long long int)>, std::function<std::__cxx11::basic_string(long long int, bool)>, const gafkluge::GafRecord&, vg::Alignment&)::<lambda(const char&, const size_t&, const string&, const string&)>: Assertion cur_offset < cur_len || ((cigar_cat == '+' || cigar_cat == 'I' || cigar_cat == 'S') && cur_offset <= cur_len)' failed. v1.57.0 "Franchini" ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.57.0 "Franchini" vg: /public/home/anovak/build/vg/deps/libvgio/src/alignment_io.cpp:691: vg::io::gaf_to_alignment(std::function<long unsigned int(long long int)>, std::function<std::__cxx11::basic_string<char>(long long int, bool)>, const gafkluge::GafRecord&, vg::Alignment&)::<lambda(const char&, const size_t&, const string&, const string&)>: Assertion cur_offset < cur_len || ((cigar_cat == '+' || cigar_cat == 'I' || cigar_cat == 'S') && cur_offset <= cur_len)' failed.
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.57.0 "Franchini"
vg: /public/home/anovak/build/vg/deps/libvgio/src/alignment_io.cpp:691: vg::io::gaf_to_alignment(std::function<long unsigned int(long long int)>, std::function<std::__cxx11::basic_string(long long int, bool)>, const gafkluge::GafRecord&, vg::Alignment&)::<lambda(const char&, const size_t&, const string&, const string&)>: Assertion cur_offset < cur_len || ((cigar_cat == '+' || cigar_cat == 'I' || cigar_cat == 'S') && cur_offset <= cur_len)' failed. ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.57.0 "Franchini" vg: /public/home/anovak/build/vg/deps/libvgio/src/alignment_io.cpp:691: vg::io::gaf_to_alignment(std::function<long unsigned int(long long int)>, std::function<std::__cxx11::basic_string<char>(long long int, bool)>, const gafkluge::GafRecord&, vg::Alignment&)::<lambda(const char&, const size_t&, const string&, const string&)>: Assertion cur_offset < cur_len || ((cigar_cat == '+' || cigar_cat == 'I' || cigar_cat == 'S') && cur_offset <= cur_len)' failed.
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.57.0 "Franchini"
vg: /public/home/anovak/build/vg/deps/libvgio/src/alignment_io.cpp:691: vg::io::gaf_to_alignment(std::function<long unsigned int(long long int)>, std::function<std::__cxx11::basic_string(long long int, bool)>, const gafkluge::GafRecord&, vg::Alignment&)::<lambda(const char&, const size_t&, const string&, const string&)>: Assertion `cur_offset < cur_len || ((cigar_cat == '+' || cigar_cat == 'I' || cigar_cat == 'S') && cur_offset <= cur_len)' failed.
━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.57.0 "Franchini"
Stack trace (most recent call last) in thread 4086348:
Stack trace (most recent call last) in thread 4086300:
#16 Object "", at 0xffffffffffffffff, in
#15 Object "", at 0x21cb33f, in
#14 Object "", at 0x212481a, in
#13 Object "", at 0x20c70ad, in
#12 Object "", at 0x20c99f7, in
#11 Object "", at 0x20c12fa, in
#10 Object "", at 0x1d5b53e, in
#9 Object "", at 0x1d64fa6, in
#8 Object "", at 0x1d6303b, in
#7 Object "", at 0x1d66250, in
#6 Object "", at 0x1d658e8, in
#5 Object "", at 0x1d5d91d, in
#4 Object "", at 0x20f3015, in
#3 Object "", at 0x5eb273, in
#2 Object "", at 0x5eb34b, in
#1 Object "", at 0x20f9625, in
#0 Object "", at 0x212617c, in
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!
━━━━━━━━━━━━━━━━━━━━
#16 Object "", at 0xffffffffffffffff, in
Stack trace (most recent call last) in thread 4086300:
#16 Object "", at 0xffffffffffffffff, in
Stack trace (most recent call last) in thread 4086300:
#16 Object "", at 0xffffffffffffffff, in

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:

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

6. What does running vg version say?

vg: variation graph tool, version v1.57.0 "Franchini"

[glennhickey]

The commands look okay. One idea is to use vg convert to convert your GAF to GAM. Then vg validate -a to make sure the GAM is valid.