bcbio-nextgen: Problem installing genome data

Version info

• bcbio version (bcbio_nextgen.py --version): 1.2.3
• OS name and version (lsb_release -ds): "CentOS Linux release 7.6.1810 (Core) "

To Reproduce Exact bcbio command you have used:

PIPEDIR="/SAN/colcc/lab-software/bcbio-pipeline"

python ${PIPEDIR}/bcbio_nextgen_install.py $PIPEDIR --tooldir ${PIPEDIR}/tools \
--datatarget vep \
--datatarget battenberg \
--datatarget gnomad \
--genomes hg38 \
--genomes hg19 \
--genomes GRCh37 \
--genomes mm9 \
--genomes mm10 \
--genomes phix \
--aligners bwa \

Observed behavior Error message or bcbio output:

Traceback (most recent call last):
  File "/SAN/colcc/pillaylab-software/bcbio-pipeline/anaconda/bin/bcbio_nextgen.py", line 228, in <module>
    install.upgrade_bcbio(kwargs["args"])
  File "/SAN/colcc/pillaylab-software/bcbio-pipeline/anaconda/lib/python3.7/site-packages/bcbio/install.py", line 107, in upgrade_bcbio
  File "/SAN/colcc/pillaylab-software/bcbio-pipeline/anaconda/lib/python3.7/site-packages/bcbio/install.py", line 377, in upgrade_bcbio_data
  File "/home/dajayi/general_output/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/dajayi/general_output/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 480, in _prep_genomes
    retrieve_fn(env, manager, gid, idx)
  File "/home/dajayi/general_output/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/dajayi/general_output/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/ggd.py", line 30, in install_recipe
    recipe["recipe"]["full"]["recipe_type"], system_install)
  File "/home/dajayi/general_output/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/ggd.py", line 62, in _run_recipe
    subprocess.check_output(["bash", run_file])
  File "/SAN/colcc/pillaylab-software/bcbio-pipeline/anaconda/lib/python3.7/subprocess.py", line 411, in check_output
  File "/SAN/colcc/pillaylab-software/bcbio-pipeline/anaconda/lib/python3.7/subprocess.py", line 512, in run
subprocess.CalledProcessError: Command '['bash', '/SAN/colcc/pillaylab-software/bcbio-pipeline/genomes/Hsapiens/hg19/txtmp/ggd-run.sh']' returned non-zero exit status 4.
Checking required dependencies
Installing isolated base python installation
Installing mamba
Installing conda-build
Installing bcbio-nextgen
Installing data and third party dependencies
Traceback (most recent call last):
  File "/SAN/colcc/pillaylab-software/bcbio-pipeline/bcbio_nextgen_install.py", line 290, in <module>
    main(parser.parse_args(), sys.argv[1:])
  File "/SAN/colcc/pillaylab-software/bcbio-pipeline/bcbio_nextgen_install.py", line 51, in main
    subprocess.check_call([bcbio, "upgrade"] + _clean_args(sys_argv, args))
  File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/SAN/colcc/pillaylab-software/bcbio-pipeline/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir', '/SAN/colcc/pillaylab-software/bcbio-pipeline/tools', '--datatarget', 'vep', '--datatarget', 'battenberg', '--datatarget', 'gnomad', '--genomes', 'hg38', '--genomes', 'hg19', '--genomes', 'GRCh37', '--genomes', 'mm9', '--genomes', 'mm10', '--genomes', 'phix', '--aligners', 'bwa', '--data']' returned non-zero exit status 1

Expected behavior Completed installation, including battenberg, vep and gnomad.

Log files Please attach (10MB max): bcbio_pipeline_installation.txt