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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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vg map crashed #2537

Open AEDWIP opened 4 years ago

AEDWIP commented 4 years ago

I found the following error in my pipeline log file. Please see attached stack trace.

could very well have to do with something else in my pipeline or data

Kind regards

Andy

+ vg index -p -t 2 -b ./tmp/ -g graph.gcsa graph.pruned.vg
Generating kmer files...
 loading graph                  [=====================================================]100.0%
Building the GCSA2 index...
InputGraph::InputGraph(): 0 kmers in 1 file(s)
GCSA2 index built in 0.0 seconds, 0.0 GB
I/O volume: 0.0 GB read, 0.0 GB write
Saving the index to disk...
ERROR: Signal 11 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
Stack trace path: /tmp/vg_crash_XCooDN/stacktrace.txt
[stacktrace.txt](https://github.com/vgteam/vg/files/3826434/stacktrace.txt)

+ rm graph.pruned.vg
+ vg map -t 2 -i -x graph.xg -g graph.gcsa -f reads.fq
libc++abi.dylib: terminating with uncaught exception of type std::bad_alloc: std::bad_alloc
ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.

version info

(HLA_haplotype) $ vg -v
error:[vg] command -v not found
vg: variation graph tool, version v1.19.0-44-gc08bc8569 "Tramutola"
jltsiren commented 4 years ago

The graph you are trying to index is empty. When GCSA2 construction detects that the input graph is empty, it leaves the index in an invalid state. Serialization then crashes.

jltsiren commented 4 years ago

The GCSA2 construction issue has now been fixed in the master branch of GCSA2.