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bcftools consensous fails to write to GCP #2316

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Ieremie opened this issue Nov 11, 2024 · 0 comments
Open

bcftools consensous fails to write to GCP #2316

Ieremie opened this issue Nov 11, 2024 · 0 comments

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@Ieremie
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Ieremie commented Nov 11, 2024

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.

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