ekg/freebayes — Issue #26: Error: std::allocator<char> > > >&, AlleleParser*): Assertion `!a->empty()' failed
Author: aeonsim
Created: 2012-01-05 02:20:56+00:00
State: open

Hi Erik

Looks like we've found another bug.
When running the latest commit of freebayes (https://github.com/ekg/freebayes/commit/094879e3e7949d409e451add253c2dbdb3dc9a2d) with our dataset it's aborting with the error below.

A subset bam (35MB) which triggers the bug can be found at: http://dl.dropbox.com/u/21734425/subset-2012-01-05-error.bam

The reference is the same as I've used in the previous reports. If you need any additional information please let me know.

Regards
Chad

Command:

./freebayes/bin/freebayes -v freebayes-output.vcf -f /data/seq/indexed-genomes/bos_taurus/umd31MT/umd31MT.fa -b subset-2012-01-05-error.bam
freebayes: ResultData.cpp:161: 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->empty()' failed.
Aborted

With freebayes -d output:
position: Chr1:571963 coverage: 1076
insufficient alternate observations
position: Chr1:571964 coverage: 1069
insufficient alternate observations
position: Chr1:571965 coverage: 1058
insufficient alternate observations
position: Chr1:571966 coverage: 1065
insufficient alternate observations
position: Chr1:571967 coverage: 1068
allele group A
allele group C:571966:4X1M1X1M5X:GCTATTTAGGGT
reference:1:A has support of 48 in individual 10841297 and fraction 1
complex:12:GCTATTTAGGGT has support of 1 in individual 363 and fraction 0.0188679
building haplotype alleles, currently there are 2 genotype alleles
reference:1:A|complex:12:GCTATTTAGGGT
allele group A
allele group C:571966:4X1M1X1M5X:GCTATTTAGGGT
allele group C:571977:2X2I1M1X3M3X:TGAGGCCTCGAC
allele group S:571971:1X:A
allele group S:571974:1X:T
reference:1:A has support of 1 in individual 17108826 and fraction 1
complex:12:GCTATTTAGGGT has support of 1 in individual 363 and fraction 0.5
complex:12:TGAGGCCTCGAC has support of 1 in individual 96329 and fraction 0.333333
snp:1:A has support of 1 in individual 501038 and fraction 0.5
snp:1:T has support of 1 in individual 346 and fraction 0.5
allele group A
allele group C:571977:2X2I1M1X3M3X:TGAGGCCTCGAC
allele group C:571981:1X3M2X:TTCCAT
allele group S:571971:1X:A
allele group S:571974:1X:T
reference:1:A has support of 1 in individual 17108826 and fraction 1
complex:12:TGAGGCCTCGAC has support of 1 in individual 96329 and fraction 0.333333
complex:6:TTCCAT has support of 1 in individual 346 and fraction 0.333333
snp:1:A has support of 1 in individual 501038 and fraction 0.5
snp:1:T has support of 1 in individual 346 and fraction 0.333333
allele group A
allele group C:571966:11M2X2I1M1X3M3X:AAAGTCTGACATGAGGCCTCGAC
allele group C:571966:4X1M1X1M5X9M:GCTATTTAGGGTTGTCTCCCA
allele group C:571966:8M1X6M1X3M2X:AAAGTCTGTCACTGTTTCCAT
allele group S:571966:5M1X15M:AAAGTATGACACTGTCTCCCA
reference:1:A has support of 37 in individual 10841297 and fraction 1
complex:23:AAAGTCTGACATGAGGCCTCGAC has support of 1 in individual 96329 and fraction 0.0212766
complex:21:GCTATTTAGGGTTGTCTCCCA has support of 1 in individual 363 and fraction 0.025641
complex:21:AAAGTCTGTCACTGTTTCCAT has support of 1 in individual 346 and fraction 0.00877193
snp:1:AAAGTATGACACTGTCTCCCA has support of 1 in individual 501038 and fraction 0.0212766
built haplotype alleles, now there are 5 genotype alleles
reference:1:A|complex:23:AAAGTCTGACATGAGGCCTCGAC|complex:21:GCTATTTAGGGTTGTCTCCCA|complex:21:AAAGTCTGTCACTGTTTCCAT|snp:1:AAAGTATGACACTGTCTCCCA
reference:1:A|complex:23:AAAGTCTGACATGAGGCCTCGAC|complex:21:GCTATTTAGGGTTGTCTCCCA|complex:21:AAAGTCTGTCACTGTTTCCAT|snp:1:AAAGTATGACACTGTCTCCCA
genotype alleles: reference:1:A|complex:23:AAAGTCTGACATGAGGCCTCGAC|complex:21:GCTATTTAGGGTTGTCTCCCA|complex:21:AAAGTCTGTCACTGTTTCCAT|snp:1:AAAGTATGACACTGTCTCCCA
pVar = 1.03827e-05 0.0001 pHom = 0.99999 1 - pHom = 1.03827e-05
position: Chr1:571988 coverage: 1055
insufficient alternate observations
position: Chr1:571989 coverage: 1050
allele group A
allele group M:571988:2X:GT
reference:1:A has support of 46 in individual 10841297 and fraction 1
mnp:2:GT has support of 1 in individual 346 and fraction 0.0075188
building haplotype alleles, currently there are 2 genotype alleles
reference:1:A|mnp:2:GT
allele group A
allele group M:571988:2X:GT
reference:1:A has support of 1 in individual 346 and fraction 0.5
mnp:2:GT has support of 1 in individual 346 and fraction 0.5
allele group A
allele group D:571988:1D1M
allele group M:571988:2X:GT
reference:1:A has support of 45 in individual 10841297 and fraction 1
deletion:1:G has support of 1 in individual 18093560 and fraction 0.0714286
mnp:2:GT has support of 1 in individual 346 and fraction 0.00763359
built haplotype alleles, now there are 3 genotype alleles
reference:1:A|deletion:1:G|mnp:2:GT
reference:1:A|deletion:1:G|mnp:2:GT
genotype alleles: reference:1:A|deletion:1:G|mnp:2:GT
pVar = 0.00055255 0.0001 pHom = 0.999447 1 - pHom = 0.00055255
calculating marginal likelihoods
freebayes: ResultData.cpp:161: 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->empty()' failed.