VG has crashed

[RohitKapila]

1. What were you trying to do?

module load vg-1.44.0
vg construct -r N2_refrence.fna -v N2_1Formal_Manta.vcf > N2_1Formal_graph.vg
vg convert N2_1Formal_graph.vg -a > N2_1Formal_whole-genome.gbz
vg map -x N2_1Formal_whole-genome.gbz -f N2_1Formal_Combined.fq -t 12 > N2_1Formal_whole-genome_aln.gam
vg snarls N2_1Formal_whole-genome.gbz > N2_1Formal_whole-genome.snarls
vg pack -x N2_1Formal_whole-genome.gbz -g N2_1Formal_whole-genome_aln.gam -o N2_1Formal_whole-genome.pack
vg call N2_1Formal_whole-genome.gbz -r N2_1Formal_whole-genome.snarls -k N2_1Formal_whole-genome.pack -s N2_1Formal -z > genotypes.vcf

2. What did you want to happen? generate a genotype.vcf file that is not empty and has SVs 3. What actually happened? it crashed and gave an empty vcf file

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 construct -f -S -I insertions.fa -a -r ref.fasta -v vars.vcf.gz > graph.vg
Since I am getting an empty vcf from the pipeline I mentioned above, I am thinking of running the following vg construct command, but I am not sure how to build an 'insertion.fa' file?
Can you direct me to some example data set for it?

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

vg convert N2_1Formal_graph.vg -a > N2_1Formal_whole-genome.gbz
vg map -x N2_1Formal_whole-genome.gbz -f N2_1Formal_Combined.fq -t 12 > N2_1Formal_whole-genome_aln.gam
vg snarls N2_1Formal_whole-genome.gbz > N2_1Formal_whole-genome.snarls
vg pack -x N2_1Formal_whole-genome.gbz -g N2_1Formal_whole-genome_aln.gam -o N2_1Formal_whole-genome.pack
vg call N2_1Formal_whole-genome.gbz -r N2_1Formal_whole-genome.snarls -k N2_1Formal_whole-genome.pack -s N2_1Formal -z > genotypes.vcf

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