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

Hello,

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!

vg pggb • 226 views
ADD COMMENT

Login before adding your answer.

Traffic: 2033 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6