vcftools - errors running vcf-merge

classic Classic list List threaded Threaded
1 message Options
| Threaded
Open this post in threaded view
Report Content as Inappropriate

vcftools - errors running vcf-merge


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


Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

To search Galaxy mailing lists use the unified search at: