mm10 Genome Installation Error

[daisysdan]

Hi,

Thanks for developing and maintaining the bcbio package! Could you help me look into the error below? Thank you so much!

Version info

• bcbio version (bcbio_nextgen.py --version): 1.2.9
• OS name and version (lsb_release -ds): "Springdale Linux release 7.9 (Verona)"

To Reproduce
Exact bcbio command you have used:

~/bcbio/bin/bcbio_nextgen.py upgrade -u skip --genomes mm10 --aligners bwa

Error

Upgrading bcbio
Upgrading bcbio-nextgen data files
List of genomes to get (from the config file at '{'genomes': [{'dbkey': 'mm10', 'name': 'Mouse (mm10)', 'indexes': ['seq', 'twobit'], 'annotations': ['problem_regions', 'prioritize', 'dbsnp', 'vcfanno', 'transcripts', 'rmsk', 'mirbase']}], 'genome_indexes': ['bwa', 'rtg'], 'install_liftover': False, 'install_uniref': False}'): Mouse (mm10)
Running GGD recipe: mm10 srnaseq 20211203
Traceback (most recent call last):
  File "/usr/people/sd5675/bcbio/bin/bcbio_nextgen.py", line 228, in <module>
    install.upgrade_bcbio(kwargs["args"])
  File "/usr/people/sd5675/bcbio/anaconda/lib/python3.7/site-packages/bcbio/install.py", line 109, in upgrade_bcbio
    upgrade_bcbio_data(args, REMOTES)
  File "/usr/people/sd5675/bcbio/anaconda/lib/python3.7/site-packages/bcbio/install.py", line 361, in upgrade_bcbio_data
    args.cores, ["ggd", "s3", "raw"])
  File "/mnt/cup/people/sd5675/bcbio/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 354, in install_data_local
    _prep_genomes(env, genomes, genome_indexes, ready_approaches, data_filedir)
  File "/mnt/cup/people/sd5675/bcbio/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 480, in _prep_genomes
    retrieve_fn(env, manager, gid, idx)
  File "/mnt/cup/people/sd5675/bcbio/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 "/mnt/cup/people/sd5675/bcbio/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/ggd.py", line 30, in install_recipe
    recipe["recipe"]["full"]["recipe_type"], system_install)
  File "/mnt/cup/people/sd5675/bcbio/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/ggd.py", line 62, in _run_recipe
    subprocess.check_output(["bash", run_file])
  File "/usr/people/sd5675/bcbio/anaconda/lib/python3.7/subprocess.py", line 411, in check_output
    **kwargs).stdout
  File "/usr/people/sd5675/bcbio/anaconda/lib/python3.7/subprocess.py", line 512, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['bash', '/mnt/cup/people/sd5675/bcbio/genomes/Mmusculus/mm10/txtmp/ggd-run.sh']' returned non-zero exit status 5.