I tried to run
vg surject on a GAM file I generated with
vg map, but the call ended with "Segmentation fault (core dumped)" and the BAM file that was generated is truncated. I generated my graph from whole bacterial genomes and then did the following to index the graph and map my reads to it:
vg mod -X 32 graph.vg | vg mod -M 8 - | vg sort - > graph_mod.vg vg index -x graph_mod.xg graph_mod.vg vg prune -k 16 -e 3 graph_mod.vg > graph_prune.vg vg index -g graph_mod.gcsa -k 16 graph_prune.vg vg map -d graph_mod -f reads.fastq.gz > graph_reads.gam
This is the call that failed:
vg surject -x graph_mod.xg -b graph_reads.gam > graph_reads.bam
Should I use a different index for this?