bcftools consensous fails to write to GCP

[Ieremie]

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.

[daviesrob]

This is an HTSlib issue, so I'll move it there. GCP support looks like it intended to support writes, but it doesn't seem to match the REST APIs as currently defined, and should probably use multipart anyway (see #1814). I'll take a look.