vg giraffe ERROR: Signal 11 occurred. VG has crashed

1. What were you trying to do?

I was trying Mapping pair-end reads to pan-genome with vg giraffe.

2. What did you want to happen? There should be a mapped.gam file output

3. What actually happened? The process was as follows: Guessing that pangenome.xg is XG Preparing Indexes Loading Minimizer Index Loading GBZ Loading Distance Index v2 Initializing MinimizerMapper Loading and initialization: 30.9118 seconds Mapping reads to "-" (GAM) --max-multimaps 1 --hit-cap 10 --hard-hit-cap 500 --score-fraction 0.9 --max-min 500 --num-bp-per-min 1000 --distance-limit 200 --max-extensions 800 --max-alignments 8 --cluster-score 50 --pad-cluster-score 20 --cluster-coverage 0.3 --extension-score 1 --extension-set 20 --rescue-attempts 15 --max-fragment-length 2000 --paired-distance-limit 2 --rescue-subgraph-size 4 --rescue-seed-limit 100 --chaining-cluster-distance 80 --max-lookback-bases 80 --min-lookback-items 1 --max-chain-connection 80 --max-tail-length 100 --rescue-algorithm dozeu ERROR: Signal 11 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_PxvvtI/stacktrace.txt Please include the stack trace file in your bug report!

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:

Crash report for vg v1.45.0 "Alpicella"
Stack trace (most recent call last) in thread 7411:
#11   Object "", at 0xffffffffffffffff, in
#10   Object "/data48t/lizp/software/vg_team/vg", at 0x1f3c532, in __clone
#9    Object "/data48t/lizp/software/vg_team/vg", at 0x14498f8, in start_thread
#8    Object "/data48t/lizp/software/vg_team/vg", at 0x1e70d3d, in gomp_thread_start
#7    Object "/data48t/lizp/software/vg_team/vg", at 0x10412e5, in unsigned long vg::io::paired_for_each_parallel_after_wait<vg::Alignment>(std::function<bool (vg::Alignment&, vg::Alignment&)>, std::function<void (vg::Alignment&, vg::Alignment&)>, std::function<bool ()>, unsigned long) [clone ._omp_fn.0]
#6    Object "/data48t/lizp/software/vg_team/vg", at 0xd371e8, in std::_Function_handler<void (vg::Alignment&, vg::Alignment&), main_giraffe(int, char**)::{lambda()#1}::operator()() const::{lambda(vg::Alignment&, vg::Alignment&)#6}>::_M_invoke(std::_Any_data const&, vg::Alignment&, vg::Alignment&)
#5    Object "/data48t/lizp/software/vg_team/vg", at 0xf9df64, in vg::MinimizerMapper::map_paired(vg::Alignment&, vg::Alignment&, std::vector<std::pair<vg::Alignment, vg::Alignment>, std::allocator<std::pair<vg::Alignment, vg::Alignment> > >&)
#4    Object "/data48t/lizp/software/vg_team/vg", at 0xf98f15, in vg::MinimizerMapper::map_paired(vg::Alignment&, vg::Alignment&)
#3    Object "/data48t/lizp/software/vg_team/vg", at 0xf8cafa, in void vg::MinimizerMapper::process_until_threshold_c<double>(unsigned long, std::function<double (unsigned long)> const&, std::function<bool (unsigned long, unsigned long)> const&, double, unsigned long, unsigned long, vg::LazyRNG&, std::function<bool (unsigned long)> const&, std::function<void (unsigned long)> const&, std::function<void (unsigned long)> const&) const [clone .constprop.0]
#2    Object "/data48t/lizp/software/vg_team/vg", at 0xf86ada, in std::_Function_handler<bool (unsigned long), vg::MinimizerMapper::map_paired(vg::Alignment&, vg::Alignment&)::{lambda(unsigned long)#20}>::_M_invoke(std::_Any_data const&, unsigned long&&)
#1    Object "/data48t/lizp/software/vg_team/vg", at 0x1b43861, in vg::Alignment::Alignment(vg::Alignment const&)
#0    Object "/data48t/lizp/software/vg_team/vg", at 0x1b4eb81, in void google::protobuf::internal::RepeatedPtrFieldBase::MergeFrom<google::protobuf::RepeatedPtrField<vg::Path>::TypeHandler>(google::protobuf::internal::RepeatedPtrFieldBase const&)

5. What data and command can the vg dev team use to make the problem happen? data: pair-end fastq reads, R100_1.fastq.gz, R100_2.fastq.gz command: vg autoindex --workflow giraffe -r $ref -v $vcf -p pangenome -t 40 vg index -x pangenome.xg -g pangenome.gcsa -b tmp/ -k 16 pangenome.vg -t 40 -p vg giraffe -Z pangenome.giraffe.gbz -m pangenome.min -d Bpangenome.dist \

-f R100_2.fastq.gz -f R100_1.fastq.gz -t 40 -p >R100_mapped.gam 6. What does running vg version say?

vg version v1.45.0 "Alpicella"
Compiled with g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 on Linux
Linked against libstd++ 20210601
Built by anovak@octagon

vgteam / vg

vg giraffe ERROR: Signal 11 occurred. VG has crashed #3908