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bcbio / bcbio-nextgen-vm

Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines
MIT License
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test_docker_ipython does not run to completion #185

Open hackdna opened 4 years ago

hackdna commented 4 years ago

Command:

pytest -s -v tests/test_docker.py::test_docker_ipython

Output:

platform linux -- Python 3.7.6, pytest-5.4.1, py-1.8.1, pluggy-0.13.1 -- /home/vagrant/bcbio-vm/anaconda/bin/python
cachedir: .pytest_cache
rootdir: /vagrant
plugins: cov-2.8.1, mock-3.1.0
collected 1 item

tests/test_docker.py::test_docker_ipython [2020-05-20T15:43Z] bcbio-vm: System YAML configuration: /tmp/bcbio/test_automated_output/bcbio_system-prep.yaml.
[2020-05-20T15:43Z] bcbio-vm: Locale set to C.UTF-8.
[2020-05-20T15:43Z] bcbio-vm: Resource requests: bwa, gatk, sambamba, samtools; memory: 3.00, 3.00, 3.00, 3.00; cores: 2, 2, 2, 2
[2020-05-20T15:43Z] bcbio-vm: Configuring 1 jobs to run, using 1 cores each with 3.00g of memory reserved for each job
[ProfileCreate] Generating default config file: '/tmp/bcbio/test_automated_output/log/ipython/ipython_config.py'
[ProfileCreate] Generating default config file: '/tmp/bcbio/test_automated_output/log/ipython/ipython_kernel_config.py'
[ProfileCreate] Generating default config file: '/tmp/bcbio/test_automated_output/log/ipython/ipcontroller_config.py'
[ProfileCreate] Generating default config file: '/tmp/bcbio/test_automated_output/log/ipython/ipengine_config.py'
[ProfileCreate] Generating default config file: '/tmp/bcbio/test_automated_output/log/ipython/ipcluster_config.py'
2020-05-20 11:43:37.063 [IPClusterStart] Using existing profile dir: '/tmp/bcbio/test_automated_output/log/ipython'
2020-05-20 11:43:37.064 [IPClusterStart] Searching path ['/tmp/bcbio/test_automated_output', '/tmp/bcbio/test_automated_output/log/ipython', '/home/vagrant/bcbio-vm/anaconda/etc/ipython', '/usr/local/etc/ipython', '/etc/ipython'] for config files
2020-05-20 11:43:37.064 [IPClusterStart] Attempting to load config file: ipython_config.py
2020-05-20 11:43:37.065 [IPClusterStart] Looking for ipython_config in /etc/ipython
2020-05-20 11:43:37.066 [IPClusterStart] Looking for ipython_config in /usr/local/etc/ipython
2020-05-20 11:43:37.066 [IPClusterStart] Looking for ipython_config in /home/vagrant/bcbio-vm/anaconda/etc/ipython
2020-05-20 11:43:37.066 [IPClusterStart] Looking for ipython_config in /tmp/bcbio/test_automated_output/log/ipython
2020-05-20 11:43:37.067 [IPClusterStart] Loaded config file: /tmp/bcbio/test_automated_output/log/ipython/ipython_config.py
2020-05-20 11:43:37.067 [IPClusterStart] Looking for ipython_config in /tmp/bcbio/test_automated_output
2020-05-20 11:43:37.068 [IPClusterStart] Attempting to load config file: ipclusteripcluster_13af4483_bdc2_489e_b8f5_90adf5224cf9_config.py
2020-05-20 11:43:37.069 [IPClusterStart] Looking for ipcontroller_config in /etc/ipython
2020-05-20 11:43:37.069 [IPClusterStart] Looking for ipcontroller_config in /usr/local/etc/ipython
2020-05-20 11:43:37.069 [IPClusterStart] Looking for ipcontroller_config in /home/vagrant/bcbio-vm/anaconda/etc/ipython
2020-05-20 11:43:37.070 [IPClusterStart] Looking for ipcontroller_config in /tmp/bcbio/test_automated_output/log/ipython
2020-05-20 11:43:37.070 [IPClusterStart] Loaded config file: /tmp/bcbio/test_automated_output/log/ipython/ipcontroller_config.py
2020-05-20 11:43:37.071 [IPClusterStart] Looking for ipcontroller_config in /tmp/bcbio/test_automated_output
2020-05-20 11:43:37.071 [IPClusterStart] Attempting to load config file: ipclusteripcluster_13af4483_bdc2_489e_b8f5_90adf5224cf9_config.py
2020-05-20 11:43:37.072 [IPClusterStart] Looking for ipengine_config in /etc/ipython
2020-05-20 11:43:37.072 [IPClusterStart] Looking for ipengine_config in /usr/local/etc/ipython
2020-05-20 11:43:37.073 [IPClusterStart] Looking for ipengine_config in /home/vagrant/bcbio-vm/anaconda/etc/ipython
2020-05-20 11:43:37.073 [IPClusterStart] Looking for ipengine_config in /tmp/bcbio/test_automated_output/log/ipython
2020-05-20 11:43:37.074 [IPClusterStart] Loaded config file: /tmp/bcbio/test_automated_output/log/ipython/ipengine_config.py
2020-05-20 11:43:37.074 [IPClusterStart] Looking for ipengine_config in /tmp/bcbio/test_automated_output
2020-05-20 11:43:37.075 [IPClusterStart] Attempting to load config file: ipclusteripcluster_13af4483_bdc2_489e_b8f5_90adf5224cf9_config.py
2020-05-20 11:43:37.075 [IPClusterStart] Looking for ipcluster_config in /etc/ipython
2020-05-20 11:43:37.075 [IPClusterStart] Looking for ipcluster_config in /usr/local/etc/ipython
2020-05-20 11:43:37.076 [IPClusterStart] Looking for ipcluster_config in /home/vagrant/bcbio-vm/anaconda/etc/ipython
2020-05-20 11:43:37.076 [IPClusterStart] Looking for ipcluster_config in /tmp/bcbio/test_automated_output/log/ipython
2020-05-20 11:43:37.076 [IPClusterStart] Loaded config file: /tmp/bcbio/test_automated_output/log/ipython/ipcluster_config.py
2020-05-20 11:43:37.077 [IPClusterStart] Looking for ipcluster_config in /tmp/bcbio/test_automated_output
0 Engines running

The test hangs at this point.