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segmentation fault #39

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chrishah opened this Issue · 0 comments

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chrishah
chrishah

Hello freebayes developers and users,

I am new to SNP calling and freebayes. I am trying to call SNPs for different geographical strains (pooled samples). The datasets vary in coverage between 70x to some 7x. Freebayes (v 0.9.6) works nicely on the big dataset. But for the low coverage datasets freebayes stops with segmentation fault. I am running for example:
freebayes --pooled --min-coverage 5 --min-alternate-fraction 0.2 --no-complex --ploidy 10 --vcf SNPs-let-freebayes.vcf --debug --fasta-reference reference.fasta sorted.bam

See the last lines of debug below.
I was trying to create a test dataset to post here for debugging, but I cant identify any particular contig or so that seems to cause the problem. If I run freebayes twice on the exact same dataset with the same parameters the segmentation fault occurs at the same point (at the same contig), but if I take just the last contig that was analysed when the segmentation fault happened, map reads onto that one and redo freebayes with the exact same parameters it works without error. I am stuck..

I would highly appreciate any ideas and/or assistance!

much obliged,
Christoph

position: 1032053_len_1505_COV_52.328_gc_37.17_r:618 coverage: 5
allele group D:617:1M3D
allele group S:617:1X:G
allele group S:617:1X:T
deletion:3:A has support of 1 in individual unknown and fraction 0.2
snp:1:G has support of 2 in individual unknown and fraction 0.4
snp:1:T has support of 2 in individual unknown and fraction 0.4
building haplotype alleles, currently there are 4 genotype alleles
reference:1:A|deletion:3:A|snp:1:G|snp:1:T
allele group D:617:1M3D
allele group D:618:1M4D
allele group S:618:1X:C
allele group S:619:1X:G
deletion:3:A has support of 1 in individual unknown and fraction 0.25
deletion:4:T has support of 1 in individual unknown and fraction 0.25
snp:1:C has support of 1 in individual unknown and fraction 0.25
snp:1:G has support of 1 in individual unknown and fraction 0.25
allele group D:618:1M4D
allele group I:622:1M1I:CG
allele group S:618:1X:C
allele group S:619:1X:G
allele group S:622:1X:G
snp:1:G has support of 3 in individual unknown and fraction 0.428571
built haplotype alleles, now there are 0 genotype alleles
/var/spool/slurmd/job10677564/slurm_script: line 24: 2052 Segmentation fault

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