vg dist on (large) graph runtime?

Question

[kingcohn]

hello, I'm looking to map short, paired-end Illumina reads to my PGGB graph (chromosome level) using vg. I've generated a gbz, combined from GBWT and GBWTgraph files, but the program is hung up on [IndexRegistry]: Constructing distance index for Giraffe.

Here are the steps I used after generating the gfa:

$ ./vg gbwt -G ../LowerPI_Cglan_pggb/Curculio_Chrom1_revisedPanSN.fasta.2afcd0e.11fba48.33b105f.smooth.final.gfa --num-threads 64 -p -d $(pwd) -L -o Cg1CcCn2.gbwt -g Cg1CcCn2.gg
Building input GBWTs
Input type: GFA
Opening GFA file ../LowerPI_Cglan_pggb/Curculio_Chrom1_revisedPanSN.fasta.2afcd0e.11fba48.33b105f.smooth.final.gfa
Validating GFA file ../LowerPI_Cglan_pggb/Curculio_Chrom1_revisedPanSN.fasta.2afcd0e.11fba48.33b105f.smooth.final.gfa
Found 5369317 segments, 7286546 links, 3 paths, and 0 walks in 570.024 seconds
Storing generic named paths as sample _gbwt_ref
GBWT insertion batch size: 101953820 nodes
Parsing segments
Breaking segments into 1024 bp nodes
Parsed 5881329 nodes in 6.71451 seconds
Parsing links
Parsed 7798558 edges in 4.67029 seconds
Creating jobs
Created 1 jobs for 1 components in 2.3017 seconds
Parsing metadata
Metadata: 3 paths with names, 3 samples with names, 3 haplotypes, 2 contigs with names
Parsed metadata in 0.000147939 seconds
Indexing paths/walks
Starting job 0 (5881329 nodes, 3 paths, 0 walks)
Finished job 0 in 17.5745 seconds
Merging partial indexes
Indexed 3 paths and 0 walks in 20.5536 seconds
Parsing GFA header tags
Parsed header tags in 1.01738e-05 seconds
GBWTs built in 604.867 seconds, 4.86007 GiB

Saving compressed GBWT to Cg1CcCn2.gbwt
GBWT serialized in 19.4852 seconds, 4.86007 GiB

Building GBWTGraph
Saving GBWTGraph to Cg1CcCn2.gg
GBWTGraph built in 295.132 seconds, 4.86007 GiB

& current command...

$ ./vg giraffe -p -g Cg1CcCn2.gg -f trimmed/S471.R1.trim.fq.gz -f trimmed/S471.R2.trim.fq.gz --read-group "@RG\tID:S471\tSM:S471\tPL:ILLUMINA"  -H Cg1CcCn2.gbwt >> Cg_C1/S471_index.gam
Preparing Indexes
[IndexRegistry]: Combining Giraffe GBWT and GBWTGraph into GBZ.
[IndexRegistry]: Constructing distance index for Giraffe.

any insight into runtime, resources or ways of expediting this step would be great! Thank you.

[Kevin Blighe]

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