Launcher unable to close index

DcornishUCL commented 2 years ago

Verify

if you cannot compile/install , read https://github.com/lindenb/jvarkit/wiki/Compilation before submitting a new issue
the version of java

Subject of the issue

Hi, I am having a slight problem using your tool vcfancestralalleles.jar to fill ancestral alleles into a VCF file. My script is erroring with the message:

[SEVERE][Launcher]Unable to close index for file://files/ALL.chr21.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes_fillAA.vcf.gz

Your environment

I am using jvarkit commit 3f7bba5f9
I am using Java version openjdk version "1.8.0_212"

Steps to reproduce

The script I tried to obtain this error was: N.B. I have already removed the ancestral alleles from the input with BCFtools and validated this myself.

java -jar /.../jvarkit/dist/vcfancestralalleles.jar \ -m /.../human_ancestor_GRCh37_e59/manifest.mf \ -o /.../ALL.chr21.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes_fillAA.vcf.gz \ /.../ALL.chr21.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes_rmAA.vcf.gz

I wondered if this means I am required to index the input VCF: ..._rmAA.vcf.gz any help to rectify this issue would be much appreciated. Thank you.

lindenb commented 2 years ago

yes ALL.chr21.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes_rmAA.vcf.gz should be indexed using bcftools index -t ALL.chr21.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes_rmAA.vcf.gz

lindenb commented 2 years ago

also, can you please try without specifying the output file but redirect into bcftools

java -jar /.../jvarkit/dist/vcfancestralalleles.jar \
-m /.../human_ancestor_GRCh37_e59/manifest.mf \
/.../ALL.chr21.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes_rmAA.vcf.gz |\
   bcftools view -O z -o  ALL.chr21.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes_fillAA.vcf.gz

DcornishUCL commented 2 years ago

This works perfectly, thank you!

lindenb / jvarkit