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On bcbio-nextgen v1.2.9, the command
bcbio_nextgen.py upgrade -u skip --genomes hg38 --aligners bwa
results in the following error:
Running GGD recipe: hg38 dbsnp 156-20230320 --2023-05-10 01:03:20-- http://ftp.ncbi.nih.gov/snp/archive/b156/VCF/GCF_000001405.38.gz Resolving ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)... 130.14.250.12, 130.14.250.10, 2607:f220:41f:250::228, ... Connecting to ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)|130.14.250.12|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://ftp.ncbi.nih.gov/snp/archive/b156/VCF/GCF_000001405.38.gz [following] --2023-05-10 01:03:21-- https://ftp.ncbi.nih.gov/snp/archive/b156/VCF/GCF_000001405.38.gz Connecting to ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)|130.14.250.12|:443... connected. HTTP request sent, awaiting response... 404 Not Found 2023-05-10 01:03:21 ERROR 404: Not Found. Traceback (most recent call last): File "/data/share/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py", line 228, in <module> install.upgrade_bcbio(kwargs["args"]) File "/data/share/bcbio-nextgen/anaconda/lib/python3.7/site-packages/bcbio/install.py", line 109, in upgrade_bcbio upgrade_bcbio_data(args, REMOTES) File "/data/share/bcbio-nextgen/anaconda/lib/python3.7/site-packages/bcbio/install.py", line 361, in upgrade_bcbio_data args.cores, ["ggd", "s3", "raw"]) File "/home/ubuntu/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 354, in install_data_local _prep_genomes(env, genomes, genome_indexes, ready_approaches, data_filedir) File "/home/ubuntu/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 480, in _prep_genomes retrieve_fn(env, manager, gid, idx) File "/home/ubuntu/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 "/home/ubuntu/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/ggd.py", line 30, in install_recipe recipe["recipe"]["full"]["recipe_type"], system_install) File "/home/ubuntu/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/ggd.py", line 62, in _run_recipe subprocess.check_output(["bash", run_file]) File "/data/share/bcbio-nextgen/anaconda/lib/python3.7/subprocess.py", line 411, in check_output **kwargs).stdout File "/data/share/bcbio-nextgen/anaconda/lib/python3.7/subprocess.py", line 512, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['bash', '/data/share/bcbio-nextgen/genomes/Hsapiens/hg38/txtmp/ggd-run.sh']' returned non-zero exit status 8.
The text was updated successfully, but these errors were encountered:
Not sure if this is right but I see that .38 is gone and .40 is now available https://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/
Sorry, something went wrong.
Met this problem too. Is there fixation now?
Presumably this has been closed by chapmanb/cloudbiolinux#412
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On bcbio-nextgen v1.2.9, the command
results in the following error:
The text was updated successfully, but these errors were encountered: