gravatar for kingcohn

2 hours ago by

I'm attempting to call variants using a reference graph I've generated first with minigraph ./minigraph -xggs -t16 f1.fa f2.fa f3.fa f4.fa f5.fa > PG_1.gfa and then vg./vg convert -g -a PG_1.gfa >

When I try to index, I'm prompted to modify the length of the nodes to 256 ./vg mod -X 256 > but it stalls out when I use this to index ./vg index -x -p PG_3.xg -g PG_3.gcsa

exiting at

Building XG index Saving XG index to Ldec_vg.xg
Generating kmer files...
Building the GCSA2 index...
InputGraph::InputGraph(): 2193921420 kmers in 1 file(s)


The input is 1.3G in size, how much memory and CPUs should I be using to generate an index and call variants using fastq reads approximately 1.5-2GB in size?


modified 2 hours ago

2 hours ago


Source link