ekg/freebayes — Issue #28: Assertion `*a != var.ref' failed.
Author: aeonsim
Created: 2012-01-10 07:44:53+00:00
State: open

Hi Erik

Looks like I've found another one. This appears to be very rare, I've only observed it occurring on 1 of our 31 Chromosomes (the rest ran to completion :-) ).

When running:
freebayes -v freebayes-pop-Chr26c.vcf -f /data/seq/indexed-genomes/bos_taurus/umd31MT/umd31MT.fa -b Chr26-issue.bam 2> Attempt-3-Chr26-error

We get the following error:

freebayes: ResultData.cpp:162: vcf::Variant& Results::vcf(vcf::Variant&, long double, long double, Samples&, std::string, std::vector >&, std::map, std::allocator >, int, std::less, std::allocator > >, std::allocator, std::allocator >, int> > >, std::vector, std::allocator >, std::allocator, std::allocator > > >&, int, GenotypeCombo&, bool, std::map, std::allocator >, std::vector >, std::less, std::allocator > >, std::allocator, std::allocator >, std::vector > > > >&, std::map >, std::less, std::allocator > > > >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, AlleleParser*): Assertion `*a != var.ref' failed.

An example BAM file can be found here: http://dl.dropbox.com/u/163580/Chr26-issue.bam

As usual it's the same reference as before.
Using the latest build of freebayes: https://github.com/ekg/freebayes/commit/31cffd89e22923e13f56e047974a5163880a0bd9

--------------------------------------
tail of freebayes -d output

allele group S:7163650:1X:G
complex:4:TAGA has support of 2 in individual 10841297 and fraction 1
reference:1:G has support of 1 in individual 17108826 and fraction 1
snp:1:G has support of 1 in individual 17144784 and fraction 1
allele group C:7163649:1X2M1I:TAGA
allele group G
allele group S:7163649:1M1X1M:GGG
allele group S:7163649:1X2M:AAG
complex:4:TAGA has support of 2 in individual 10841297 and fraction 0.0606061
reference:1:G has support of 30 in individual 10841297 and fraction 0.909091
snp:1:GGG has support of 1 in individual 17144784 and fraction 0.0344828
snp:1:AAG has support of 1 in individual 10841297 and fraction 0.030303
built haplotype alleles, now there are 4 genotype alleles
complex:4:TAGA|reference:1:G|snp:1:GGG|snp:1:AAG
complex:4:TAGA|reference:1:G|snp:1:GGG|snp:1:AAG
genotype alleles: complex:4:TAGA|reference:1:G|snp:1:GGG|snp:1:AAG
pVar = 1 0.0001 pHom = 1.67445e-12 1 - pHom = 1
calculating marginal likelihoods
position: Chr26:7163653 coverage: 805
allele group A
allele group I:7163652:1I3M:AAAA
reference:1:A has support of 35 in individual 10841297 and fraction 1
insertion:1:AAAA has support of 1 in individual 17144784 and fraction 0.0384615
building haplotype alleles, currently there are 2 genotype alleles
reference:1:A|insertion:1:AAAA
allele group A
allele group I:7163652:1I3M:AAAA
reference:1:A has support of 5 in individual 10841297 and fraction 1
insertion:1:AAAA has support of 1 in individual 17144784 and fraction 0.5
allele group A
allele group I:7163652:1I3M:AAAA
reference:1:A has support of 35 in individual 10841297 and fraction 1
insertion:1:AAAA has support of 1 in individual 17144784 and fraction 0.0384615
built haplotype alleles, now there are 2 genotype alleles
reference:1:A|insertion:1:AAAA
reference:1:A|insertion:1:AAAA
genotype alleles: reference:1:A|insertion:1:AAAA
pVar = 0.000175625 0.0001 pHom = 0.999824 1 - pHom = 0.000175625
calculating marginal likelihoods
freebayes: ResultData.cpp:162: vcf::Variant& Results::vcf(vcf::Variant&, long double, long double, Samples&, std::string, std::vector >&, std::map, std::allocator >, int, std::less, std::allocator > >, std::allocator, std::allocator >, int> > >, std::vector, std::allocator >, std::allocator, std::allocator > > >&, int, GenotypeCombo&, bool, std::map, std::allocator >, std::vector >, std::less, std::allocator > >, std::allocator, std::allocator >, std::vector > > > >&, std::map >, std::less, std::allocator > > > >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, AlleleParser*): Assertion `*a != var.ref' failed.