Traceback (most recent call last):


 "/mnt/projects/dlho/tancrc/bcbio_pipeline/bin/bcbio_nextgen.py", line 215, in <module>

install.upgrade_bcbio(kwargs["args"])


 "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/install.py", line 96, in upgrade_bcbio

upgrade_bcbio_data(args, REMOTES)


 "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/site-packages/bcbio/install.py", line 293, in upgrade_bcbio_data

cbl_deploy.deploy(s)


 "/home/dlho/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py", line 65, in deploy

_setup_vm(options, vm_launcher, actions)


 "/home/dlho/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py", line 110, in _setup_vm

configure_instance(options, actions)


 "/home/dlho/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py", line 268, in configure_instance

setup_biodata(options)


 "/home/dlho/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py", line 250, in setup_biodata

install_proc(options["genomes"], ["ggd", "s3", "raw"])


 "/home/dlho/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 338, in install_data

_prep_genomes(env, genomes, genome_indexes, ready_approaches)


 "/home/dlho/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 467, in _prep_genomes

retrieve_fn(env, manager, gid, idx)


 "/home/dlho/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 812, in _install_with_ggd

ggd.install_recipe(env.cwd, recipe_file, gid)


 "/home/dlho/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/ggd.py", line 31, in install_recipe

recipe["recipe"]["full"]["recipe_type"])


 "/home/dlho/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/ggd.py", line 63, in _run_recipe

subprocess.check_output(["bash", run_file])


 "/mnt/projects/dlho/tancrc/bcbio_pipeline/anaconda/lib/python2.7/subprocess.py", line 574, in check_output

raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command '['bash', '/mnt/projects/dlho/tancrc/bcbio_pipeline/genomes/Hsapiens/GRCh37/txtmp/ggd-run.sh']' returned non-zero exit status 8

continuing in /usr/share/vim/vim81/syntax/Traceback (most recent call last):


 "/usr/lib/python3.7/encodings/__init__.py", line 31, in <module>

import codecs


 "/usr/lib/python3.7/codecs.py", line 96

*, _is_text_encoding=None):

^

SyntaxError: invalid syntax

%

```
