Segfault running snp2h5

[ngcrawford]

Hi,
I'm getting a segfault and a core dump when I run snp2h5. It looks to me like there may be a bug with how the pairs of hap andimpute2 files are associated. The first chromosome that is parsed runs correctly (e.g., chr10), but the second produces an error. I think snp2h5 is not updating to the correct hap file when it cycles to the next chromosome...

Let me know if there is anything I can do to help.

-- Nick

~/data/external_datasets/cbrown_impute2$ ~/source/WASP/snp2h5/bin/./snp2h5 --chrom /home/ngcrawford/data/genomes/chrmInfo.trunc.txt --format impute --geno_prob geno_probs.h5 --snp_index snp_index.h5 --snp_tab snp_tab.h5 --haplotype haps.h5 5M.hg19.RNAseq.d3_unrelated.filtered.o.chr_.impute2.gz 5M.hg19.RNAseq.d3_unrelated.filtered.o.chr_.impute2_haps.gz
writing genotype probabilities to: geno_probs.h5
writing haplotypes to: haps.h5
writing SNP index to: snp_index.h5
writing SNP table to: snp_tab.h5
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr10.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr11.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr12.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr13.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr14.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr15.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr16.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr17.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr18.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr19.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr1.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr20.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr21.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr22.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr2.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr3.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr4.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr5.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr6.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr7.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr8.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr9.impute2.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr10.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr11.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr12.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr13.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr14.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr15.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr16.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr17.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr18.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr19.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr1.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr20.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr21.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr22.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr2.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr3.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr4.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr5.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr6.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr7.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr8.impute2_haps.gz'
'5M.hg19.RNAseq.d3_unrelated.filtered.o.chr9.impute2_haps.gz'
chromosome: chr10, length: 135534747bp
reading from file 5M.hg19.RNAseq.d3_unrelated.filtered.o.chr10.impute2.gz
counting lines in file
total lines: 1461156
number of samples: 162
initializing HDF5 matrix with dimension: (1461156, 486)
parsing file and writing to HDF5 files
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
initializing HDF5 matrix with dimension: (1461156, 324)
reading from file 5M.hg19.RNAseq.d3_unrelated.filtered.o.chr10.impute2_haps.gz
parsing file and writing to HDF5 files
.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
chromosome: chr11, length: 135006516bp
reading from file 5M.hg19.RNAseq.d3_unrelated.filtered.o.chr11.impute2.gz
counting lines in file
total lines: 1640404
number of samples: 162
initializing HDF5 matrix with dimension: (1640404, 486)
parsing file and writing to HDF5 files
........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
initializing HDF5 matrix with dimension: (1640404, 324)
reading from file 5M.hg19.RNAseq.d3_unrelated.filtered.o.chr10.impute2_haps.gz
parsing file and writing to HDF5 files
WARNING: snp2h5.c:775: snp at position 20000105 present in impute2_haps file but not in impute2 file
WARNING: snp2h5.c:775: snp at position 20000144 present in impute2_haps file but not in impute2 file
WARNING: snp2h5.c:775: snp at position 20000279 present in impute2_haps file but not in impute2 file

[... A LARGE NUMBER OF LINES ...]

WARNING: snp2h5.c:775: snp at position 135006472 present in impute2_haps file but not in impute2 file
ERROR: Segmentation fault (core dumped)

[gmcvicker]

Hi Nick. Thanks for letting us know about this problem. Recently I have been testing using just one input file so I didn't notice the problem. I have committed some changes that should fix the issue. Please pull the changes and give it a try again.

[ngcrawford]

Looks like the new code fixed the bug! Thanks. I'll let you know if I find any more. ;)

[ghost]

Hi,
I'm use snp2h5 to convert vcf to h5. I find there is an problem in the latest version.
I use version (v 0.2 & v 0.2.1). The error happened.
...................................................................................................................
long alleles will be truncated to 100bp
writing SNP index to: snp_index.h5
chromosome: C2, length: 52886895bp
reading from file chr_vcf/C2.vcf
counting lines in file
total lines: 0
reading VCF header
ERROR: expected last line in header to start with #CHROM
....................................................................................................................

I check the vcf file, and
....................................................................................................................
grep "#CHR" chr_vcf/C2.vcf
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR3203096
.....................................................................................................................
However, I use the old version (v 01 ), it is fine.

[gmcvicker]

Hi ZhengYaa

I believe that this issue was fixed on the master branch after version 0.2.1. Can you try to checkout the master rather than v0.2.1? (I should make a version 0.2.2 that includes the latest changes).

You might also try adding sample names to your header line if you have more than one sample in the VCF, since it looks like you only have one 'SRR3203096'.

Hope this helps,

Graham