ERROR: Signal 6 occurred. VG has crashed. Terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc

[RohitKapila]

1. What were you trying to do? Trying to call Structural variants. Have Illumina reads and SVs called from Manta.

2. What did you want to happen? the vcf it is generating is empty. It is working well until it generates .gam file (around 8gb in size) but it fails at last step of generating vcf. I am expecting a vcf with structural variant information.

3. What actually happened? the vcf it is generating is empty. It is working well until it generates .gam file (around 8gb in size) but it fails at last step of generating vcf. I am expecting a vcf with structural variant information.

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:

Stack trace path: /tmp/vg_crash_xIZ3xM/stacktrace.txt

5. What data and command can the vg dev team use to make the problem happen? ile.modules module load vg-1.44.0 vg construct -r N2_refrence.fna -v N2_1Formal_Manta.vcf > N2_1Formal_graph.vg vg index -x N2_1Formal_graph.xg -g N2_1Formal_graph.gcsa -k 16 N2_1Formal_graph.vg vg map -x N2_1Formal_graph.xg -g N2_1Formal_graph.gcsa -f N2_1Formal_Combined.fq > N2_1Formal_aln.gam vg call N2_1Formal_graph.vg -k N2_1Formal_aln.gam > N2_1Formal_calls.vcf

N2_1Formal_calls.vcf file is empty.

6. What does running vg version say?

vg version v1.44.0 "Solara"
Compiled with g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 on Linux
Linked against libstd++ 20210601
Built by anovak@octagon

[glennhickey]

There's some examples and documentation about using vg call here and here, take note that it does not take a GAM file as input....