vgteam
vg pack error
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!
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.
