vg mpmap ERROR (Signal 11 occurred) #4762
Description
1. What were you trying to do?
Using vg mpmap to align Illumina 150bp paired-end read fastq files to a spliced pantranscriptome graph built from the aligned HLA-E sequences from IMGT.
My mapping command is:
vg mpmap -t 10 -n RNA -N HG00146 -x imgt_E_panEx.spliced.xg -g imgt_E_panEx.spliced.gcsa -d imgt_E_panEx.spliced.dist -f HG00146.HLA-E.R1.fastq -f HG00146.HLA-E.R2.fastq > HG00146.HLA-E.gamp
2. What did you want to happen?
I would have liked a full execution of vg mpmap
3. What actually happened?
vg mpmap crashed with an ERROR: Signal 11 occurred
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 mpmap] elapsed time 0 s: Executing command: vg mpmap -t 10 -n RNA -N HG00146 -x imgt_E_panEx.spliced.xg -g imgt_E_panEx.spliced.gcsa -d imgt_E_panEx.spliced.dist -f HG00146.HLA-E.R1.fastq -f HG00146.HLA-E.R2.fastq
[vg mpmap] elapsed time 0 s: Loading graph from imgt_E_panEx.spliced.xg
[vg mpmap] elapsed time 0 s: Completed loading graph
[vg mpmap] elapsed time 0 s: Graph is in XG format. XG is a good graph format for most mapping use cases. PackedGraph may be selected if memory usage is too high. See `vg convert` if you want to change graph formats.
[vg mpmap] elapsed time 0 s: Identifying reference paths
[vg mpmap] elapsed time 0 s: Loading GCSA2 from imgt_E_panEx.spliced.gcsa
[vg mpmap] elapsed time 0 s: Loading distance index from imgt_E_panEx.spliced.dist (in background)
[vg mpmap] elapsed time 0 s: Completed loading GCSA2
[vg mpmap] elapsed time 0 s: Loading LCP from imgt_E_panEx.spliced.gcsa.lcp
[vg mpmap] elapsed time 0 s: Completed loading LCP
[vg mpmap] elapsed time 0 s: Memoizing GCSA2 queries (in background)
[vg mpmap] elapsed time 0 s: Completed loading distance index
[vg mpmap] elapsed time 0 s: Completed memoizing GCSA2 queries
[vg mpmap] elapsed time 0 s: Building null model to calibrate mismapping detection
[vg mpmap] elapsed time 15 s: Mapping reads from HG00146.HLA-E.R1.fastq and HG00146.HLA-E.R2.fastq using 10 threads
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Crash report for vg v1.69.0 "Bologna"
Caught signal 11 raised at address 0x106048d; tracing with backward-cpp
Stack trace (most recent call last) in thread 809240:
#11 Object "", at 0xffffffffffffffff, in
#10 Object "/mnt/results/twang/software/vg/vg", at 0x2426a3f, in __clone3
#9 Object "/mnt/results/twang/software/vg/vg", at 0x237ff2a, in start_thread
#8 Object "/mnt/results/twang/software/vg/vg", at 0x23227bd, in gomp_thread_start
#7 Object "/mnt/results/twang/software/vg/vg", at 0x2325107, in gomp_team_barrier_wait_end
#6 Object "/mnt/results/twang/software/vg/vg", at 0x231ca0a, in gomp_barrier_handle_tasks
#5 Object "/mnt/results/twang/software/vg/vg", at 0x1086f4a, 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.1]
#4 Object "/mnt/results/twang/software/vg/vg", at 0xf53104, in main_mpmap(int, char**)::{lambda(vg::Alignment&, vg::Alignment&)#7}::operator()(vg::Alignment&, vg::Alignment&) const
#3 Object "/mnt/results/twang/software/vg/vg", at 0x1482e68, in vg::MultipathMapper::multipath_map_paired(vg::Alignment const&, vg::Alignment const&, std::vector<std::pair<vg::multipath_alignment_t, vg::multipath_alignment_t>, std::allocator<std::pair<vg::multipath_alignment_t, vg::multipath_alignment_t> > >&, std::vector<std::pair<vg::Alignment, vg::Alignment>, std::allocator<std::pair<vg::Alignment, vg::Alignment> > >&)
#2 Object "/mnt/results/twang/software/vg/vg", at 0x1480a1d, in vg::MultipathMapper::find_spliced_alignments(vg::Alignment const&, vg::Alignment const&, std::vector<std::pair<vg::multipath_alignment_t, vg::multipath_alignment_t>, std::allocator<std::pair<vg::multipath_alignment_t, vg::multipath_alignment_t> > >&, std::vector<std::pair<std::pair<unsigned long, unsigned long>, long>, std::allocator<std::pair<std::pair<unsigned long, unsigned long>, long> > >&, std::vector<double, std::allocator<double> >&, std::vector<vg::MaximalExactMatch, std::allocator<vg::MaximalExactMatch> > const&, std::vector<vg::MaximalExactMatch, std::allocator<vg::MaximalExactMatch> > const&, std::vector<std::tuple<std::unique_ptr<bdsg::HashGraph, std::default_delete<bdsg::HashGraph> >, std::pair<std::vector<std::pair<vg::MaximalExactMatch const*, std::tuple<long long, bool, unsigned long> >, std::allocator<std::pair<vg::MaximalExactMatch const*, std::tuple<long long, bool, unsigned long> > > >, double>, unsigned long>, std::allocator<std::tuple<std::unique_ptr<bdsg::HashGraph, std::default_delete<bdsg::HashGraph> >, std::pair<std::vector<std::pair<vg::MaximalExactMatch const*, std::tuple<long long, bool, unsigned long> >, std::allocator<std::pair<vg::MaximalExactMatch const*, std::tuple<long long, bool, unsigned long> > > >, double>, unsigned long> > >&, std::vector<std::tuple<std::unique_ptr<bdsg::HashGraph, std::default_delete<bdsg::HashGraph> >, std::pair<std::vector<std::pair<vg::MaximalExactMatch const*, std::tuple<long long, bool, unsigned long> >, std::allocator<std::pair<vg::MaximalExactMatch const*, std::tuple<long long, bool, unsigned long> > > >, double>, unsigned long>, std::allocator<std::tuple<std::unique_ptr<bdsg::HashGraph, std::default_delete<bdsg::HashGraph> >, std::pair<std::vector<std::pair<vg::MaximalExactMatch const*, std::tuple<long long, bool, unsigned long> >, std::allocator<std::pair<vg::MaximalExactMatch const*, std::tuple<long long, bool, unsigned long> > > >, double>, unsigned long> > >&, std::unordered_map<vg::MaximalExactMatch const*, std::deque<std::pair<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, char>, std::allocator<std::pair<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, char> > >, std::hash<vg::MaximalExactMatch const*>, std::equal_to<vg::MaximalExactMatch const*>, std::allocator<std::pair<vg::MaximalExactMatch const* const, std::deque<std::pair<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, char>, std::allocator<std::pair<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, char> > > > > > const*)
#1 Object "/mnt/results/twang/software/vg/vg", at 0x14798e5, in vg::MultipathMapper::test_splice_candidates(vg::Alignment const&, bool, vg::multipath_alignment_t&, double*, vg::MultipathMapper::SpliceStrand&, long, std::function<vg::multipath_alignment_t const& (long)> const&, std::function<double (long)> const&, std::function<vg::multipath_alignment_t&& (long)> const&) const
#0 Object "/mnt/results/twang/software/vg/vg", at 0x106048d, in vg::QualAdjAligner::score_exact_match(vg::Alignment const&, unsigned long, unsigned long) const
Library locations:
ERROR: Signal 11 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
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Context dump:
Thread 0: Starting 'mpmap' subcommand
Found 1 threads with context.
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Please include this entire error log in your bug report!
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5. What data and command can the vg dev team use to make the problem happen?
I can provide my data through Email. It's a testing data set, so it's not big at all.
I used the MSA of HLA-E from IMGT, and a simple HLA-E gene annotation gtf file (read headers and chromosome name in gtf file were manually edited to make vg autoindex work) to build a spliced pantranscriptome graph using these commands, and it was successful.
vg construct -p -t 10 -M msa_E.fasta > imgt_E.vg
vg view imgt_E.vg > imgt_E.gfa
sed -i '1s/$/\tRS:Z:Consensus_E/' imgt_E.gfa
vg autoindex -w mpmap -w rpvg -p imgt_E_panEx -g imgt_E.gfa -x annotation_E.gtf
I could use this command to view the graph; it looked good, although the nodes were not topologically re-sorted
vg viz -x imgt_E_panEx.spliced.xg -o imgt_E_panEx.spliced.svg
Then I used vg mpmap to map reads, but got the Error and Signal 11
vg mpmap -t 10 -n RNA -N HG00146 -x imgt_E_panEx.spliced.xg -g imgt_E_panEx.spliced.gcsa -d imgt_E_panEx.spliced.dist -f HG00146.HLA-E.R1.fastq.gz -f HG00146.HLA-E.R2.fastq.gz > HG00146.HLA-E.gamp
6. What does running vg version say?
vg version v1.69.0 "Bologna"
Compiled with g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 on Linux
Linked against libstd++ 20230528
Using HTSlib headers 101990, library 1.19.1-29-g3cfe8769
Built by [email protected]