ekg/freebayes — Issue #21: Segfault with recent releases
Author: aeonsim
Created: 2011-11-15 03:07:30+00:00
State: open

Hi

We've been attempting to run freebayes (have tried 0.9.2., 0.9.3, 0.9.4 (ubuntu 10.04.2 LTS x64b)) on a small population of of medium to high coverage animals, and are getting a segfault after a number of hours.

We've tried a variety of different versions and settings, none of which seem to have any effect. The group consists of 25 animals (cows), with coverage varying between 16x and 170x (total is ~1200x) the data is supplied to freebayes as BAM files (one for each animal) and is paired end Illumina data that's been mapped with RTG.

The run starts fine and we get a decent proportion of the way through chromosome 1 (between 14m and 30m bp) before the segfault occurs. I've run freebayes with -d and -dd but can't spot anything specific in the output (717GB output for -dd :-)) I've stuck the last ~40 lines of the -dd option below.

Previously we've had success running freebayes (date: 2011-07-20, version: 0.8.7, on ubuntu 10.04.2 LTS) on a much smaller subset of the data (~180x coverage).

Any idea what might be causing this? Is it an issue with the dataset size (~1200x a 2.95Gb Genome), Though I've tried with a smaller (900x coverage) set and still got the segfault. Anything you can think of that we should test or any other additional information we can provide?

Thanks
CH

./freebayes/bin/freebayes -j -dd --min-coverage 6 --left-align-indels -P 1 -v freebayes-output.vcf -f /data/seq/indexed-genomes/bos_taurus/umd31MT/umd31MT.fa -b /data/seq/processed-genomes/RTG/F1_Sires/664221/sequence/664221_mated.bam -b /data/seq/processed-genomes/RTG/F1_Sires/664195/sequence/664195_mated.bam -b /data/seq/processed-genomes/RTG/F1_Sires/99592/sequence/99592_mated.bam -b /data/seq/processed-genomes/RTG/F1_Sires/99593/sequence/99593_mated.bam -b /data/seq/processed-genomes/RTG/F1_Sires/99594/sequence/99594_mated.bam -b /data/seq/processed-genomes/RTG/FJXB_Trio/F1-Sire-99591/aligned_sequence/99591_mated.bam -b /data/seq/processed-genomes/RTG/FJXB_Trio/F1-Dam-10841297/aligned_sequence/10841297_mated_v2.bam -b /data/seq/processed-genomes/RTG/FJXB_Trio/F2-Daughter-17144784/aligned_sequence/17144784_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_17074197/sequence/17074197_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_17108826/sequence/17108826_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_17144783/sequence/17144783_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_17145716/sequence/17145716_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_18033109/sequence/18033109_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_18093560/sequence/18093560_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_18143602/sequence/18143602_mated.bam -b /data/seq/processed-genomes/RTG/F2_Daughters/F2_18186561/sequence/18186561_mated.bam 2> freebayes.debug
Segmentation fault
--------------------------

freebayes.debug:
----------------------------
read: CGCGAACCCATGAACTGCAGCACTCCAGGCCTCTCTGTCCATCACCAACTCCCGGAGTCCACCCAAACCCAAGTCCATAGAGTCGGTGATGACATCAAAC
aligned bases: CGCGAACCCATGAACTGCAGCACTCCAGGCCTCTCTGTCCATCACCAACTCCCGGAGTCCACCCAAACCCAAGTCCATAGAGTCGGTGATGACATCAAAC
reference seq: NNCGAACCCATGAACTGCAGCACTCCAGGCCTCTCTGTCCATCACCAACTCCCGGAGTCCACCCAAACCCAAGTCCATAGAGTCGGTGATGACATCAAAC
cigar item: M100
18093560:91899485:mnp:2:2:17092806:+:CG:2X:30.0
18093560:91899485:reference:98:98:17092808:+:CGAACCCATGAACTGCAGCACTCCAGGCCTCTCTGTCCATCACCAACTCCCGGAGTCCACCCAAACCCAAGTCCATAGAGTCGGTGATGACATCAAAC:98M:55.0
... finished pushing new alignments
updating variants
updating registered alleles
erasing old registered alignments
erasing old input variant alleles
erasing old genotype likelihoods
updating reference sequence cache
getting alleles
done getting alleles
at start of main loop
current reference base is N
processing position 17092808 in sequence Chr1
updating alignment queue
currentPosition = 17092807; currentSequenceStart = 0; currentSequence end = 17092906
currentAlignment.Position == 17092807, currentAlignment.AlignedBases.size() == 100, currentPosition == 17092807, currentSequenceStart == 0 .. + currentSequen
currentAlignment.Name == 92632067
registering alignment 0 17092807 17092807
alignment readName 92632067
alignment isPaired 1
alignment isMateMapped 1
alignment isProperPair 1
alignment mapQual 55
alignment sampleID 363
alignment position 17092807
alignment length 100
alignment AlignedBases.size() 100
alignment GetEndPosition() 17092906
alignment end position 17092907
alignment cigar M100
current sequence pointer: 17092807
read: NCGAACCCATGAACTGCAGCACTCCAGGCCTCTCTGTCCATCACCAACTCCCGGAGTCCACCCAAACCCAAGTCCATAGAGTCGGTGATGACATCAAACC
aligned bases: NCGAACCCATGAACTGCAGCACTCCAGGCCTCTCTGTCCATCACCAACTCCCGGAGTCCACCCAAACCCAAGTCCATAGAGTCGGTGATGACATCAAACC
reference seq: NCGAACCCATGAACTGCAGCACTCCAGGCCTCTCTGTCCATCACCAACTCCCGGAGTCCACCCAAACCCAAGTCCATAGAGTCGGTGATGACATCAAACC
cigar item: M100