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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 > PG_2.vg.

When I try to index, I'm prompted to modify the length of the nodes to 256 ./vg mod -X 256 PG_2.vg > PG_3.vg but it stalls out when I use this to index ./vg index -x -p PG_3.xg -g PG_3.gcsa PG_3.vg

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 PG_3.vg 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?

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kingcohn20



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