Traceback (most recent call last):


 "/Users/cathywu/anaconda/envs/flow20181224/lib/python3.5/multiprocessing/process.py", line 249, in _bootstrap

self.run()


 "/Users/cathywu/anaconda/envs/flow20181224/lib/python3.5/site-packages/ray/autoscaler/updater.py", line 104, in run

raise e


 "/Users/cathywu/anaconda/envs/flow20181224/lib/python3.5/site-packages/ray/autoscaler/updater.py", line 89, in run

self.do_update()


 "/Users/cathywu/anaconda/envs/flow20181224/lib/python3.5/site-packages/ray/autoscaler/updater.py", line 176, in do_update

self.ssh_cmd(cmd, verbose=True)


 "/Users/cathywu/anaconda/envs/flow20181224/lib/python3.5/site-packages/ray/autoscaler/updater.py", line 244, in ssh_cmd

stderr=redirect or self.stderr)


 "/Users/cathywu/anaconda/envs/flow20181224/lib/python3.5/subprocess.py", line 581, in check_call

raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['ssh', '-o', 'ConnectTimeout=120s', '-o', 'StrictHostKeyChecking=no', '-i', '/Users/cathywu/.ssh/ray-autoscaler_us-west-1.pem', 'ubuntu@54.153.85.227', "bash --login -c 'set -i || true && source ~/.bashrc && export OMP_NUM_THREADS=1 PYTHONWARNINGS=ignore && cd flow && git fetch && git checkout `cat /tmp/path`'"]' returned non-zero exit status 128

Traceback (most recent call last):


 "/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 480, in _prep_genomes

retrieve_fn(env, manager, gid, idx)


 "/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 519, in _prep_raw_index

get_index_fn(idx)(env, ref_file)


 "/tmpbcbio-install/cloudbiolinux/cloudbio/biodata/genomes.py", line 850, in _index_rtg

subprocess.check_call(cmd.format(**locals()), shell=True)


 "/usr/local/share/bcbio-nextgen/anaconda/lib/python3.6/subprocess.py", line 311, in check_call

raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'export PATH=/usr/local/bin:$PATH && export RTG_JAVA_OPTS='-Xms1g' && export RTG_MEM=2g && rtg format -o rtg/GRCh37.sdf /mnt/biodata/genomes/Hsapiens/GRCh37/seq/GRCh37.fa' returned non-zero exit status 127.
