Segmentation fault with vg call on cactus graph chunk

[eldariont]

Hi,

my toil-vg call pipeline crashes for short reads aligned to a cactus-derived graph. Quite similar to #2041, the pipeline crashes at the following step:

RuntimeError: Docker container for command vg call chunk_S288C.chrXV_0_aug.vg -t 4 -S SRR4074256.recall.cactus.four -z chunk_S288C.chrXV_0.trans -s chunk_S288C.chrXV_0.support -b chunk_S288C.chrXV_0.vg -u -n 0 -r S288C.chrXV -c S288C.chrXV -l 1091343 -o 0 failed with code 139

This time, the error code is 139, not 134, indicating a segmentation fault. I could reproduce the error on courtyard with the most recent vg version v1.14.0-72-g0538d699 "Quadrelle":

>vg call chunk_S288C.chrXV_0_aug.vg -t 4 -S SRR4074256.recall.cactus.four -z chunk_S288C.chrXV_0.trans -s chunk_S288C.chrXV_0.
support -b chunk_S288C.chrXV_0.vg -u -n 0 -r S288C.chrXV -c S288C.chrXV -l 1091343 -o 0
##fileformat=VCFv4.2
##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">
##INFO=<ID=XREF,Number=0,Type=Flag,Description="Present in original graph">
##INFO=<ID=XSEE,Number=.,Type=String,Description="Original graph node:offset cross-references">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##FILTER=<ID=lowad,Description="Variant does not meet minimum allele read support threshold of 5">
##FILTER=<ID=highabsdp,Description="Variant has total depth greater than 0">
##FILTER=<ID=highreldp,Description="Variant has total depth greater than 0 times global baseline">
##FILTER=<ID=highlocaldp,Description="Variant has total depth greater than 0 times local baseline">
##FILTER=<ID=lowxadl,Description="Variant has AD log likelihood less than -9">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=XDP,Number=2,Type=Integer,Description="Expected Local and Global Depth">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=XADL,Number=1,Type=Float,Description="Likelihood of allelic depths for called alleles">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Forward and reverse support for ref and alt alleles.">
##FORMAT=<ID=XAAD,Number=1,Type=Integer,Description="Alt allele read count.">
##FORMAT=<ID=AL,Number=.,Type=Float,Description="Allelic likelihoods for the ref and alt alleles in the order listed">
##contig=<ID=S288C.chrXV,length=1091343>
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SRR4074256.recall.cactus.four
Segmentation fault

The file from the command can be found here: /public/groups/cgl/users/daheller/reproduce_error.

David

[glennhickey]

This looks like #2066. Best to verify with latest toil-vg/vg to be sure.

[eldariont]

Thanks, running it with latest version now.

[eldariont]

Hi, with the lastest versions of toil-vg and vg, the error did not occur anymore. However, the run took 62 hours which is much slower than we would expect for yeast. I created vgteam/toil-vg#737 for that reason and will close this issue.