vcftools - errors running vcf-merge

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vcftools - errors running vcf-merge

richjp

Hi all,

I am trying to run the vcf-merge tool, which depends on the vcftools 0.1.11 package. I have this vcftools package and also the required tabix 0.2.6 both installed via the toolshed (tabix is set in the PATH of the Galaxy startup script). However, I keep getting gunzip error messages such as the following:

Log: tool progress
gunzip: error writing to output: Broken pipe
gunzip: 0.vcf.sorted.gz: uncompress failed
Using column name 'mutant' for 0.vcf.sorted.gz:mutant
Using column name 'sibling' for 0.vcf.sorted.gz:sibling
gunzip: error writing to output: Broken pipe
gunzip: 1.vcf.sorted.gz: uncompress failed
Using column name '1.vcf.sorted_mutant' for 1.vcf.sorted.gz:mutant
Using column name '1.vcf.sorted_sibling' for 1.vcf.sorted.gz:sibling
Does anyone have any idea how to solve this?

The command that the wrapper is generating is:

vcf-sort /Volumes/ngs/database/files/058/dataset_58073.dat > 0.vcf.sorted ; bgzip 0.vcf.sorted ; tabix -p vcf 0.vcf.sorted.gz ; vcf-sort /Volumes/ngs/database/files/058/dataset_58078.dat > 1.vcf.sorted ; bgzip 1.vcf.sorted ; tabix -p vcf 1.vcf.sorted.gz ; vcf-merge 0.vcf.sorted.gz 1.vcf.sorted.gz > /Volumes/ngs/database/files/058/dataset_58489.dat

Thanks,
Richard

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