I am trying to generate indexes for giraffe of a GFA file generated using PGGB but I am unable to do so. The process is getting killed before finishing.
Command for generating the graph: pggb -i ./Chr1_combined.fasta.gz -n 7 -D temp/ -t 16 -o ./Chr1_pggb_default
Command used : vg autoindex -w giraffe --prefix pggb_real --gfa pggb.gfa -T ../../temp/
Error:
vg autoindex -w giraffe --prefix pggb_real --gfa pggb.gfa -T ../../temp/
[IndexRegistry]: Checking for haplotype lines in GFA.
[IndexRegistry]: Constructing VG graph from GFA input.
[IndexRegistry]: Constructing XG graph from VG graph.
[IndexRegistry]: Constructing a greedy path cover GBWT
[IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation.
[IndexRegistry]: Constructing distance index for Giraffe.
Killed
GBZ file is being generated but distance and minimizer indexes are not being generated.
Can somebody guide me if I am doing something wrong here.?
I am trying to generate indexes for giraffe of a GFA file generated using PGGB but I am unable to do so. The process is getting killed before finishing.
Command for generating the graph: pggb -i ./Chr1_combined.fasta.gz -n 7 -D temp/ -t 16 -o ./Chr1_pggb_default Command used : vg autoindex -w giraffe --prefix pggb_real --gfa pggb.gfa -T ../../temp/
Error: vg autoindex -w giraffe --prefix pggb_real --gfa pggb.gfa -T ../../temp/ [IndexRegistry]: Checking for haplotype lines in GFA. [IndexRegistry]: Constructing VG graph from GFA input. [IndexRegistry]: Constructing XG graph from VG graph. [IndexRegistry]: Constructing a greedy path cover GBWT [IndexRegistry]: Constructing GBZ using NamedNodeBackTranslation. [IndexRegistry]: Constructing distance index for Giraffe. Killed
GBZ file is being generated but distance and minimizer indexes are not being generated. Can somebody guide me if I am doing something wrong here.?
Vg version: v1.57.0-21-gdb574a520 "Franchini"