I ran autoindex giraffe of vg tools , Step : Constructing a greedy path cover GBWT was killed

Question

[dragon940401]

Hi, everyone. Recently, I use vg tool and had problem.

My code is below

vg autoindex --workflow giraffe --prefix ./output/ -r ./fasta/ref.fasta -v ./vcf/test.vcf.gz -T ./log/ --threads 2 --target-mem 3G

And I got message

[IndexRegistry]: Checking for phasing in VCF(s).

[IndexRegistry]: Chunking inputs for parallelism.

[IndexRegistry]: Chunking FASTA(s).

[IndexRegistry]: Chunking VCF(s).

warning:[IndexRegistry] Skipping contig chr1, which is found in VCF(s) but not reference.

[IndexRegistry]: Constructing VG graph from FASTA and VCF input.

[IndexRegistry]: Constructing XG graph from VG graph.

[IndexRegistry]: Constructing a greedy path cover GBWT

Killed

And I got "chunked fasta file, vg file, xg file, maxid.txt file" in temp directory (log)

So my question is how do i restart step3 "Constructing a greedy path cover GBWT" Can i rerun that?

Thanks to your help!

Answer 1

[Jouni Sirén]

Restarting vg autoindex from an intermediate step is not really supported. You could try adding option --provide "XG:graph.xg" to use the existing XG graph, which may work. You may also want to use --verbosity 2 to get some information on why the path cover GBWT construction fails.

[dragon940401]

@Jouni Sirén Thanks to your help. But Can i ask one more? Is it "--provide" options in "autoindex"? I couldn't find that

[dragon940401]

Oh! I got it! Thank you!