Error in generating index file using vg index
Entering edit mode
5 months ago
evafinegan • 0


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 >
vg mod -X 256 >  
vg index -x output_1.xg -g output_1.gcsa -k 16
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
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!

vg pggb • 226 views

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