Unexpected token 'I', "Internal S"... is not valid JSON

[guo23e]

Hello. I encountered an error.
Unexpected token 'I', "Internal S"... is not valid JSON When I only add the .xg file, it can be output. However, adding the .gbwt file causes the following error. This is the command I used to generate the .gbwt file. vg index -g c244_HA_Chr8A.gbwt c244_HA_Chr8A.vg Could you help me take a look when you have time? Thank you very much.

[adamnovak]

I think that vg index -g builds a GCSA2 index, not a GBWT. If you need a GBWT, you would use the vg gbwt subcommand, which is documented at https://github.com/vgteam/vg/wiki/VG-GBWT-Subcommand

To make the GBWT, you probably need a VCF, and a .vg file that was made with the -a option to vg construct.

To fix this bug, we need to add some machinery to detect when what was submitted as a GBWT file isn't actually a GBWT file, and produce a useful error message instead of this kind of internal error.