vg index generates Message Node::encode(): Offset 69398 too large

[jjfarrell]

Any suggestions for this error message while vg indexing?

Node::encode(): Offset 69398 too large error

The vg file was constructed using this command line:
vg construct -r chr11.fasta >chr11.vg
WARNING: Lower case letters found during construction
Sequences may not map to this reference.

The chr11.fasta contains just the beginning of the chromosome just beyond the gamma globin genes (11:1-5280000).

vg index -x chr11.xg -g chr11.gcsa -k 11 -T -t 4 -p chr11.vg
loading graph [===================================================]100.0%
Node::encode(): Offset 69398 too large============= ] 33.3%
Node::encode(): Offset 69409 too large
Node::encode(): Offset 69399 too large
Node::encode(): Offset 69410 too large
Node::encode(): Offset 97528 too large
Node::encode(): Offset 97539 too large
Node::encode(): Offset 97529 too large
Node::encode(): Offset 97540 too large
Node::encode(): Offset 97530 too large
Node::encode(): Offset 97541 too large
Node::encode(): Offset 97531 too large
Node::encode(): Offset 97542 too large
Node::encode(): Offset 97532 too large
Node::encode(): Offset 97543 too large
Node::encode(): Offset 97533 too large
Node::encode(): Offset 97544 too large

[adamnovak]

The GCSA2 index packs kmer offsets into (I believe) 10 bits, so you can't GCSA2-index a graph with nodes larger than 1024 bases.

You can use vg mod -X 1000 graph.vg > chopped.vg to chop up your graph nodes, or use the -m option in vg construct to make sure that they are small enough to begin with.

This really needs to be the default in vg construct.