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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 generating genome files #3714

Closed gis-nlsim closed 1 year ago

gis-nlsim commented 1 year ago

I tried generating the genomes using the following command: bcbio_nextgen.py upgrade -u skip --genomes GRCh37 --genomes hg38 --aligners bwa --aligners sta

But encountered a failure. It seems that this file does not exist: https://ftp.ncbi.nih.gov/snp/archive/b154/VCF/GCF_000001405.25.gz

Running GGD recipe: GRCh37 dbsnp 154-20210112 --2023-07-24 09:48:18-- https://ftp.ncbi.nih.gov/snp/archive/b154/VCF/GCF_000001405.25.gz Resolving ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)... 130.14.250.13, 165.112.9.229, 130.14.250.7, ... Connecting to ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)|130.14.250.13|:443... connected. HTTP request sent, awaiting response... 404 Not Found 2023-07-24 09:48:19 ERROR 404: Not Found.

Traceback (most recent call last): File "/apps/bcbio/v129/anaconda/bin/bcbio_nextgen.py", line 228, in install.upgrade_bcbio(kwargs["args"]) File "/apps/bcbio/v129/anaconda/lib/python3.7/site-packages/bcbio/install.py", line 109, in upgrade_bcbio upgrade_bcbio_data(args, REMOTES) File "/apps/bcbio/v129/anaconda/lib/python3.7/site-packages/bcbio/install.py", line 361, in upgrade_bcbio_data args.cores, ["ggd", "s3", "raw"]) File "/install/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 354, in install_data_local _prep_genomes(env, genomes, genome_indexes, ready_approaches, data_filedir) File "/install/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 480, in _prep_genomes retrieve_fn(env, manager, gid, idx) File "/install/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 875, in _install_with_ggd ggd.install_recipe(os.getcwd(), env.system_install, recipe_file, gid) File "/install/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/ggd.py", line 30, in install_recipe recipe["recipe"]["full"]["recipe_type"], system_install) File "/install/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/ggd.py", line 62, in _run_recipe subprocess.check_output(["bash", run_file]) File "/apps/bcbio/v129/anaconda/lib/python3.7/subprocess.py", line 411, in check_output **kwargs).stdout File "/apps/bcbio/v129/anaconda/lib/python3.7/subprocess.py", line 512, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['bash', '/apps/bcbio/v129/genomes/Hsapiens/GRCh37/txtmp/ggd-run.sh']' returned non-zero exit status 8.

gis-nlsim commented 1 year ago

It seems that the gzip file is no longer gzipped in ncbi: https://ftp.ncbi.nih.gov/snp/archive/b154/VCF/GCF_000001405.25