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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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failed in downloading gnomad sites #3654

Open lmanchon opened 2 years ago

lmanchon commented 2 years ago

subprocess.CalledProcessError: Command '['/BCBIO/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/media/data/SeaDB/BCBIO', '--genomes', 'hg38', '--aligners', 'bwa', '--datatarget', 'gemini', '--data']' returned non-zero exit status 1.

https://storage.googleapis.com/gnomad-public/release/2.1.1/liftover_grch38/vcf/exomes/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz

404 not found.

it seems https://storage.googleapis.com repository moved

naumenko-sa commented 2 years ago

Thanks for reporting! I am switching to gsutil download and removing gnomad exome dataset (lifted over in hg38) in favour of genomes https://gnomad.broadinstitute.org/help/whats-the-difference-between-gnomad-v2-and-v3

naumenko-sa commented 2 years ago

HI @lmanchon ! I've fixed the gnomad exome recipe to download from gcloud: https://github.com/chapmanb/cloudbiolinux/blob/master/ggd-recipes/hg38/gnomad_exome.yaml it works in a fresh 1.2.9 install. Let me know if it works for you as well. SN

kokyriakidis commented 2 years ago

@naumenko-sa

Can you please fix link for hg19 too?