gravatar for LilithElina

2 hours ago by


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 | vg mod -M 8 - | vg sort - >
vg index -x graph_mod.xg
vg prune -k 16 -e 3 >
vg index -g graph_mod.gcsa -k 16
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?

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