Version
# Name Version
bcftools 1.21
Command
echo -e "chr8:128700-128900", "chr9:128900-129000" | bcftools consensus -s 'GTEX-1117F' -c gs://my-bucket/GTEX-1117F_h1.chain -H '1pIu' -f 'gs://my-bucket/genome_hg38.fa' 'gs://my-bucket/file.vcf.gz'
I would expect the chain file to be uploaded to the bucket but instead I am getting Failed to create gs://my-bucjet/GTEX-1117F_h1.chain: No such file or directory.
The communication with GCP works (after setting the GCS_OAUTH_TOKEN path) and this can be seen by doing something simple as bcftools query -l 'gs://my-bucket/file.vcf.gz'.
Is bcftools consensous supposed to be able to write to GCP? (I can't find any information in the documentation https://samtools.github.io/bcftools/bcftools.html#consensus).
The temporary solution is to write locally and then push the result.
Version
Command
I would expect the chain file to be uploaded to the bucket but instead I am getting
Failed to create gs://my-bucjet/GTEX-1117F_h1.chain: No such file or directory.The communication with GCP works (after setting the
GCS_OAUTH_TOKENpath) and this can be seen by doing something simple asbcftools query -l 'gs://my-bucket/file.vcf.gz'.Is
bcftools consensoussupposed to be able to write to GCP? (I can't find any information in the documentation https://samtools.github.io/bcftools/bcftools.html#consensus).The temporary solution is to write locally and then push the result.