Entering edit mode
23 months ago
Kath__ ▴ 10
I am trying to select samples from a bigger vcf file and write the subset into a new vcf.gz file.
The first part works well, meaning getting the samples out of the initial file.
bcftools view initial_vcf.vcf.gz --force-samples -s samp1,samp2 )
When I try to write the new file though, I end up with a 0 bytes fcf.gz file ("unexpected end of file"). I've tried formats like this:
bcftools view initial_vcf.vcf.gz --force-samples -S selected_samples.txt | bgzip -c > new_vcf.vcf.gz
and versions of
bcftools view initial_vcf.vcf.gz --force-samples -S selected_samples.txt -Oz -o new_vcf.vcf.gz
Any help/suggestion greatly appreciated.
is there any error message ?
Hi Pierre, no error message, it just never finishes.
what is the filesystem ? what is your OS ? "it just never finishes" is contradictory with " I end up with a 0 bytes fcf.gz file" ? what is the size of the initial_vcf.vcf.gz ?
Sorry for the lack of details, I am running it on our Linux server and the original file sizes are around 70GB. And you are right, the claims are a bit contradictory, I can see a file created but nothing is written into it (thus, 0 bytes); the process never terminates though.
70G is high. how long did you wait ?
Several hours, restarted a few hours ago,
ps -u usernameshows me