I have created a graph genome using
pggb. Now I want to do SNP calling using this graph genome with
vg. I am trying to achieve:
vg view -F -v sample.gfa > output.vg vg mod -X 256 output.vg > output_1.vg vg index -x output_1.xg -g output_1.gcsa -k 16 output_1.vg vg map -f sample_R1_paired.fastq.gz sample_R2_paired.fastq.gz -x output_1.xg -g output_1.gcsa > aln.gam vg surject -x output_1.xg -b aln.gam > aln.bam vg pack -x output_1.xg -g aln.gam -Q 5 -o aln.pack vg call output_1.xg -k aln.pack > graph_calls.vcf
I was able to run all these commands with a small subset
.gfa file. However, while using the large
.gfa file, I got an error:
/tmp/slurmd/job/slurm_script: line 16: Killed vg index -x output_1.xg -g output_1.gcsa -k 16 output_1.vg terminate called after throwing an instance of 'std::runtime_error' what(): Need XG, GCSA, and LCP to create a Mapper ERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.
I am looking for solutions for this error to create an index and downstream files. Thank you for any help!