vg pack error

[jinshangkun]

Hello!
I am trying to use giraffe to genotype structural variants. The commands I used for the constructions:
vg autoindex --workflow giraffe --prefix Gh -R XG --ref-fasta $ref --vcf $vcf -t 10 -T ./
vg giraffe -x $output/Gh.xg -H $output/Gh.giraffe.gbwt -g $output/Gh.gg -m $output/Gh.min -d $output/Gh.dist -f $input/D1_1.fq.gz -f $input/D1_2.fq.gz -t 30 -p 2>$output/log.txt >$output/D1.gam
vg pack -t 30 -Q 5 -x $output/Gh.xg -g $output/D1.gam -o $output/D1.pack
vg call -t 30 -k $output/D1.pack $output/Gh.xg > $output/D1.vcf
But I got an error when running vg call.
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Stack trace path: /tmp/vg_crash_6Mbioy/stacktrace.txt

The content of the stacktrace.txt is as follows：
Crash report for vg v1.32.0 "Sedlo"
Stack trace (most recent call last):
#11 Object "", at 0x59fe8d, in
#10 Object "", at 0x1d6d9df, in
#9 Object "", at 0x578414, in
#8 Object "", at 0xb7b91b, in
#7 Object "", at 0xaf9362, in
#6 Object "", at 0x4f1517, in
#5 Object "", at 0x1ca983c, in
#4 Object "", at 0x1ca9686, in
#3 Object "", at 0x1ca961b, in
#2 Object "", at 0x574ec2, in
#1 Object "", at 0x577953, in
#0 Object "", at 0x127feeb, in

Many thanks for any solutions!

[glennhickey]

I suspect it's running out of memory when computing snarls. Can you try

vg snarls $output/Gh.xg > $output/Gh.snarls

then add -r $output/Gh.snarls to the vg call command line?

As an aside @jeizenga is there a way for autoindex to return the snarls index too -- presumably it made one while making the giraffe indexes. It would be handy to have the option to keep around for people who want to use pack/call to genotype SVs after.

[jinshangkun]

@glennhickey Thanks! I will try it.