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pvanheus/planemo.log

Created July 5, 2018 11:57
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planemo.log
git --git-dir /home/pvh/.planemo/gx_repo fetch >/dev/null 2>&1
cd /tmp/tmp7eiSQ_; git clone --branch 'master' '/home/pvh/.planemo/gx_repo' 'galaxy-dev'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/pvh/.planemo/gx_venv_None; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/pvh/.virtualenvs/planemo/bin/virtualenv -p /home/pvh/.virtualenvs/planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}
Cloning into 'galaxy-dev'...
done.
Set COMMON_STARTUP_ARGS to --dev-wheels
Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample
Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample
Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample
Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample
Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample
Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample
Initializing static/welcome.html from welcome.html.sample
Activating virtualenv at /home/pvh/.planemo/gx_venv_None
Requirement already satisfied: pip>=8.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (10.0.1)
Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple
Requirement already satisfied: numpy==1.9.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 4)) (1.9.2)
Requirement already satisfied: bx-python==0.7.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 5)) (0.7.3)
Requirement already satisfied: MarkupSafe==1.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 6)) (1.0)
Requirement already satisfied: PyYAML==3.12 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 7)) (3.12)
Requirement already satisfied: SQLAlchemy==1.0.15 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 8)) (1.0.15)
Requirement already satisfied: sqlalchemy-utils==0.32.19 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 9)) (0.32.19)
Requirement already satisfied: mercurial==3.7.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 10)) (3.7.3)
Requirement already satisfied: pycrypto==2.6.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 11)) (2.6.1)
Requirement already satisfied: uWSGI==2.0.15 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 12)) (2.0.15)
Requirement already satisfied: pysam==0.14 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 14)) (0.14)
Requirement already satisfied: bz2file==0.98 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 21)) (0.98)
Requirement already satisfied: ipaddress==1.0.18 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 22)) (1.0.18)
Requirement already satisfied: boltons==17.1.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 23)) (17.1.0)
Requirement already satisfied: Paste==2.0.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 24)) (2.0.2)
Requirement already satisfied: PasteDeploy==1.5.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 25)) (1.5.2)
Requirement already satisfied: docutils==0.14 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 26)) (0.14)
Requirement already satisfied: repoze.lru==0.6 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 27)) (0.6)
Requirement already satisfied: Routes==2.4.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 28)) (2.4.1)
Requirement already satisfied: WebOb==1.4.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 29)) (1.4.1)
Requirement already satisfied: WebHelpers==1.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 30)) (1.3)
Requirement already satisfied: Mako==1.0.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 31)) (1.0.2)
Requirement already satisfied: pytz==2017.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 32)) (2017.3)
Requirement already satisfied: Babel==2.5.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 33)) (2.5.1)
Requirement already satisfied: Beaker==1.7.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 34)) (1.7.0)
Requirement already satisfied: dictobj==0.3.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 35)) (0.3.1)
Requirement already satisfied: nose==1.3.7 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 36)) (1.3.7)
Requirement already satisfied: Parsley==1.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 37)) (1.3)
Requirement already satisfied: six==1.11.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 38)) (1.11.0)
Requirement already satisfied: Whoosh==2.7.4 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 39)) (2.7.4)
Requirement already satisfied: galaxy_sequence_utils==1.0.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 40)) (1.0.2)
Requirement already satisfied: h5py==2.7.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 41)) (2.7.1)
Requirement already satisfied: packaging==16.8 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 42)) (16.8)
Requirement already satisfied: pykwalify==1.6.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 45)) (1.6.0)
Requirement already satisfied: python-dateutil==2.5.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 46)) (2.5.3)
Requirement already satisfied: docopt==0.6.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 47)) (0.6.2)
Requirement already satisfied: Cheetah==2.4.4 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 50)) (2.4.4)
Requirement already satisfied: Markdown==2.6.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 51)) (2.6.3)
Requirement already satisfied: requests==2.18.4 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 54)) (2.18.4)
Requirement already satisfied: certifi==2017.7.27.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 55)) (2017.7.27.1)
Requirement already satisfied: urllib3==1.22 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 56)) (1.22)
Requirement already satisfied: chardet==3.0.4 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 57)) (3.0.4)
Requirement already satisfied: idna==2.6 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 58)) (2.6)
Requirement already satisfied: bioblend==0.7.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 61)) (0.7.0)
Requirement already satisfied: boto==2.38.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 62)) (2.38.0)
Requirement already satisfied: requests-toolbelt==0.8.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 63)) (0.8.0)
Requirement already satisfied: kombu==3.0.30 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 67)) (3.0.30)
Requirement already satisfied: amqp==1.4.8 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 68)) (1.4.8)
Requirement already satisfied: anyjson==0.3.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 69)) (0.3.3)
Requirement already satisfied: psutil==4.1.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 72)) (4.1.0)
Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 73)) (0.8.0)
Requirement already satisfied: sqlalchemy-migrate==0.11.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 76)) (0.11.0)
Requirement already satisfied: decorator==4.0.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 77)) (4.0.2)
Requirement already satisfied: Tempita==0.5.3dev in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 78)) (0.5.3.dev0)
Requirement already satisfied: sqlparse==0.1.16 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 79)) (0.1.16)
Requirement already satisfied: pbr==3.1.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 80)) (3.1.1)
Requirement already satisfied: svgwrite==1.1.6 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 83)) (1.1.6)
Requirement already satisfied: pyparsing==2.1.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 84)) (2.1.1)
Requirement already satisfied: Fabric==1.13.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 87)) (1.13.2)
Requirement already satisfied: paramiko==2.2.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 88)) (2.2.1)
Requirement already satisfied: ecdsa==0.13 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 89)) (0.13)
Requirement already satisfied: python-genomespaceclient==0.1.8 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 92)) (0.1.8)
Requirement already satisfied: funcsigs==1.0.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1)) (1.0.2)
Requirement already satisfied: recommonmark==0.4.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2)) (0.4.0)
Requirement already satisfied: snowballstemmer==1.2.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (1.2.1)
Requirement already satisfied: nosehtml==0.4.4 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) (0.4.4)
Requirement already satisfied: pygments==2.2.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) (2.2.0)
Requirement already satisfied: watchdog==0.8.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 6)) (0.8.3)
Requirement already satisfied: lxml==4.1.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 7)) (4.1.0)
Requirement already satisfied: selenium==3.6.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 10)) (3.6.0)
Requirement already satisfied: commonmark==0.5.4 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 11)) (0.5.4)
Requirement already satisfied: typing==3.6.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 13)) (3.6.2)
Requirement already satisfied: mock==2.0.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 15)) (2.0.0)
Requirement already satisfied: testfixtures==5.3.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 16)) (5.3.0)
Requirement already satisfied: imagesize==0.7.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (0.7.1)
Requirement already satisfied: alabaster==0.7.10 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 18)) (0.7.10)
Requirement already satisfied: argh==0.26.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (0.26.2)
Requirement already satisfied: jinja2==2.9.6 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 23)) (2.9.6)
Requirement already satisfied: twill==0.9.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 24)) (0.9.1)
Requirement already satisfied: pygithub3==0.5.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 25)) (0.5.1)
Requirement already satisfied: sphinx==1.6.5 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (1.6.5)
Requirement already satisfied: sphinxcontrib-websupport==1.0.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 29)) (1.0.1)
Requirement already satisfied: pathtools==0.1.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 30)) (0.1.2)
Requirement already satisfied: sphinx-rtd-theme==0.2.4 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 31)) (0.2.4)
Requirement already satisfied: nodeenv==1.2.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 36)) (1.2.0)
Requirement already satisfied: PasteScript in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 73)) (2.0.2)
Requirement already satisfied: pynacl>=1.0.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 88)) (1.2.1)
Requirement already satisfied: pyasn1>=0.1.7 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 88)) (0.4.3)
Requirement already satisfied: bcrypt>=3.1.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 88)) (3.1.4)
Requirement already satisfied: cryptography>=1.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 88)) (2.2.2)
Requirement already satisfied: boto3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 92)) (1.7.48)
Requirement already satisfied: python-swiftclient in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 92)) (3.5.0)
Requirement already satisfied: setuptools in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from sphinx==1.6.5->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (39.2.0)
Requirement already satisfied: cffi>=1.4.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 88)) (1.11.5)
Requirement already satisfied: enum34; python_version < "3" in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 88)) (1.1.6)
Requirement already satisfied: asn1crypto>=0.21.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 88)) (0.24.0)
Requirement already satisfied: botocore<1.11.0,>=1.10.48 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 92)) (1.10.48)
Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 92)) (0.9.3)
Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 92)) (0.1.13)
Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 92)) (3.2.0)
Requirement already satisfied: pycparser in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 88)) (2.18)
Testing using galaxy_root /tmp/tmp7eiSQ_/galaxy-dev
Testing tools with command [cd /tmp/tmp7eiSQ_/galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/pvh/.planemo/gx_venv_None; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/pvh/.virtualenvs/planemo/bin/virtualenv -p /home/pvh/.virtualenvs/planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/tools/jbrowse/tool_test_output.html --xunit_report_file /tmp/tmp7eiSQ_/xunit.xml --structured_data_report_file /home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/tools/jbrowse/tool_test_output.json functional.test_toolbox]
Activating virtualenv at /home/pvh/.planemo/gx_venv_None
Requirement already satisfied: pip>=8.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (10.0.1)
Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple
Requirement already satisfied: numpy==1.9.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 4)) (1.9.2)
Requirement already satisfied: bx-python==0.7.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 5)) (0.7.3)
Requirement already satisfied: MarkupSafe==1.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 6)) (1.0)
Requirement already satisfied: PyYAML==3.12 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 7)) (3.12)
Requirement already satisfied: SQLAlchemy==1.0.15 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 8)) (1.0.15)
Requirement already satisfied: sqlalchemy-utils==0.32.19 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 9)) (0.32.19)
Requirement already satisfied: mercurial==3.7.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 10)) (3.7.3)
Requirement already satisfied: pycrypto==2.6.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 11)) (2.6.1)
Requirement already satisfied: uWSGI==2.0.15 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 12)) (2.0.15)
Requirement already satisfied: pysam==0.14 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 14)) (0.14)
Requirement already satisfied: bz2file==0.98 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 21)) (0.98)
Requirement already satisfied: ipaddress==1.0.18 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 22)) (1.0.18)
Requirement already satisfied: boltons==17.1.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 23)) (17.1.0)
Requirement already satisfied: Paste==2.0.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 24)) (2.0.2)
Requirement already satisfied: PasteDeploy==1.5.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 25)) (1.5.2)
Requirement already satisfied: docutils==0.14 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 26)) (0.14)
Requirement already satisfied: repoze.lru==0.6 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 27)) (0.6)
Requirement already satisfied: Routes==2.4.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 28)) (2.4.1)
Requirement already satisfied: WebOb==1.4.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 29)) (1.4.1)
Requirement already satisfied: WebHelpers==1.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 30)) (1.3)
Requirement already satisfied: Mako==1.0.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 31)) (1.0.2)
Requirement already satisfied: pytz==2017.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 32)) (2017.3)
Requirement already satisfied: Babel==2.5.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 33)) (2.5.1)
Requirement already satisfied: Beaker==1.7.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 34)) (1.7.0)
Requirement already satisfied: dictobj==0.3.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 35)) (0.3.1)
Requirement already satisfied: nose==1.3.7 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 36)) (1.3.7)
Requirement already satisfied: Parsley==1.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 37)) (1.3)
Requirement already satisfied: six==1.11.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 38)) (1.11.0)
Requirement already satisfied: Whoosh==2.7.4 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 39)) (2.7.4)
Requirement already satisfied: galaxy_sequence_utils==1.0.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 40)) (1.0.2)
Requirement already satisfied: h5py==2.7.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 41)) (2.7.1)
Requirement already satisfied: packaging==16.8 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 42)) (16.8)
Requirement already satisfied: pykwalify==1.6.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 45)) (1.6.0)
Requirement already satisfied: python-dateutil==2.5.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 46)) (2.5.3)
Requirement already satisfied: docopt==0.6.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 47)) (0.6.2)
Requirement already satisfied: Cheetah==2.4.4 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 50)) (2.4.4)
Requirement already satisfied: Markdown==2.6.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 51)) (2.6.3)
Requirement already satisfied: requests==2.18.4 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 54)) (2.18.4)
Requirement already satisfied: certifi==2017.7.27.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 55)) (2017.7.27.1)
Requirement already satisfied: urllib3==1.22 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 56)) (1.22)
Requirement already satisfied: chardet==3.0.4 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 57)) (3.0.4)
Requirement already satisfied: idna==2.6 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 58)) (2.6)
Requirement already satisfied: bioblend==0.7.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 61)) (0.7.0)
Requirement already satisfied: boto==2.38.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 62)) (2.38.0)
Requirement already satisfied: requests-toolbelt==0.8.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 63)) (0.8.0)
Requirement already satisfied: kombu==3.0.30 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 67)) (3.0.30)
Requirement already satisfied: amqp==1.4.8 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 68)) (1.4.8)
Requirement already satisfied: anyjson==0.3.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 69)) (0.3.3)
Requirement already satisfied: psutil==4.1.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 72)) (4.1.0)
Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 73)) (0.8.0)
Requirement already satisfied: sqlalchemy-migrate==0.11.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 76)) (0.11.0)
Requirement already satisfied: decorator==4.0.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 77)) (4.0.2)
Requirement already satisfied: Tempita==0.5.3dev in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 78)) (0.5.3.dev0)
Requirement already satisfied: sqlparse==0.1.16 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 79)) (0.1.16)
Requirement already satisfied: pbr==3.1.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 80)) (3.1.1)
Requirement already satisfied: svgwrite==1.1.6 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 83)) (1.1.6)
Requirement already satisfied: pyparsing==2.1.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 84)) (2.1.1)
Requirement already satisfied: Fabric==1.13.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 87)) (1.13.2)
Requirement already satisfied: paramiko==2.2.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 88)) (2.2.1)
Requirement already satisfied: ecdsa==0.13 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 89)) (0.13)
Requirement already satisfied: python-genomespaceclient==0.1.8 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r requirements.txt (line 92)) (0.1.8)
Requirement already satisfied: funcsigs==1.0.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1)) (1.0.2)
Requirement already satisfied: recommonmark==0.4.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2)) (0.4.0)
Requirement already satisfied: snowballstemmer==1.2.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) (1.2.1)
Requirement already satisfied: nosehtml==0.4.4 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) (0.4.4)
Requirement already satisfied: pygments==2.2.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 5)) (2.2.0)
Requirement already satisfied: watchdog==0.8.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 6)) (0.8.3)
Requirement already satisfied: lxml==4.1.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 7)) (4.1.0)
Requirement already satisfied: selenium==3.6.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 10)) (3.6.0)
Requirement already satisfied: commonmark==0.5.4 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 11)) (0.5.4)
Requirement already satisfied: typing==3.6.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 13)) (3.6.2)
Requirement already satisfied: mock==2.0.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 15)) (2.0.0)
Requirement already satisfied: testfixtures==5.3.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 16)) (5.3.0)
Requirement already satisfied: imagesize==0.7.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 17)) (0.7.1)
Requirement already satisfied: alabaster==0.7.10 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 18)) (0.7.10)
Requirement already satisfied: argh==0.26.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 20)) (0.26.2)
Requirement already satisfied: jinja2==2.9.6 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 23)) (2.9.6)
Requirement already satisfied: twill==0.9.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 24)) (0.9.1)
Requirement already satisfied: pygithub3==0.5.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 25)) (0.5.1)
Requirement already satisfied: sphinx==1.6.5 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (1.6.5)
Requirement already satisfied: sphinxcontrib-websupport==1.0.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 29)) (1.0.1)
Requirement already satisfied: pathtools==0.1.2 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 30)) (0.1.2)
Requirement already satisfied: sphinx-rtd-theme==0.2.4 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 31)) (0.2.4)
Requirement already satisfied: nodeenv==1.2.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 36)) (1.2.0)
Requirement already satisfied: PasteScript in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 73)) (2.0.2)
Requirement already satisfied: pynacl>=1.0.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 88)) (1.2.1)
Requirement already satisfied: pyasn1>=0.1.7 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 88)) (0.4.3)
Requirement already satisfied: bcrypt>=3.1.3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 88)) (3.1.4)
Requirement already satisfied: cryptography>=1.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 88)) (2.2.2)
Requirement already satisfied: boto3 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 92)) (1.7.48)
Requirement already satisfied: python-swiftclient in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 92)) (3.5.0)
Requirement already satisfied: setuptools in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from sphinx==1.6.5->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 27)) (39.2.0)
Requirement already satisfied: cffi>=1.4.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 88)) (1.11.5)
Requirement already satisfied: enum34; python_version < "3" in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 88)) (1.1.6)
Requirement already satisfied: asn1crypto>=0.21.0 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 88)) (0.24.0)
Requirement already satisfied: botocore<1.11.0,>=1.10.48 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 92)) (1.10.48)
Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 92)) (0.9.3)
Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 92)) (0.1.13)
Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 92)) (3.2.0)
Requirement already satisfied: pycparser in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 88)) (2.18)
Looking in indexes: https://wheels.galaxyproject.org/simple, https://pypi.python.org/simple
Requirement already satisfied: watchdog in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from -r /dev/stdin (line 1)) (0.8.3)
Requirement already satisfied: argh>=0.24.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from watchdog->-r /dev/stdin (line 1)) (0.26.2)
Requirement already satisfied: PyYAML>=3.10 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from watchdog->-r /dev/stdin (line 1)) (3.12)
Requirement already satisfied: pathtools>=0.1.1 in /home/pvh/.planemo/gx_venv_None/lib/python2.7/site-packages (from watchdog->-r /dev/stdin (line 1)) (0.1.2)
Activating virtualenv at /home/pvh/.planemo/gx_venv_None
2018-07-05 13:51:50,891 INFO [galaxy.queue_worker] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite://
2018-07-05 13:51:51,063 INFO [galaxy.model.migrate.check] Migrating 127 -> 128...
2018-07-05 13:51:51,458 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:51,458 INFO [galaxy.model.migrate.check] Migration script to add session update time (used for timeouts)
2018-07-05 13:51:51,458 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:51,458 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:51,458 INFO [galaxy.model.migrate.check] Migrating 128 -> 129...
2018-07-05 13:51:51,860 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:51,860 INFO [galaxy.model.migrate.check] Migration script to allow invalidation of job external output metadata temp files
2018-07-05 13:51:51,860 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:51,860 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:51,860 INFO [galaxy.model.migrate.check] Migrating 129 -> 130...
2018-07-05 13:51:52,324 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:52,325 INFO [galaxy.model.migrate.check] Migration script to change the 'value' column of 'user_preference' table from varchar to text.
2018-07-05 13:51:52,325 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:52,325 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:52,325 INFO [galaxy.model.migrate.check] Migrating 130 -> 131...
2018-07-05 13:51:53,074 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:53,075 INFO [galaxy.model.migrate.check] Migration script to support subworkflows and workflow request input parameters
2018-07-05 13:51:53,075 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:53,075 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:53,076 INFO [galaxy.model.migrate.check] Migrating 131 -> 132...
2018-07-05 13:51:53,138 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:53,138 INFO [galaxy.model.migrate.check] Migrating 132 -> 133...
2018-07-05 13:51:53,524 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:53,524 INFO [galaxy.model.migrate.check] Add dependencies column to jobs table
2018-07-05 13:51:53,524 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:53,524 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:53,524 INFO [galaxy.model.migrate.check] Migrating 133 -> 134...
2018-07-05 13:51:53,547 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:53,547 INFO [galaxy.model.migrate.check] Migration script to set the 'deleted' column of the
2018-07-05 13:51:53,547 INFO [galaxy.model.migrate.check] 'history_dataset_association' table to True if 'purged' is True.
2018-07-05 13:51:53,547 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:53,547 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:53,547 INFO [galaxy.model.migrate.check] Migrating 134 -> 135...
2018-07-05 13:51:54,039 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:54,040 INFO [galaxy.model.migrate.check] This migration script adds support for storing tags in the context of a dataset in a library
2018-07-05 13:51:54,040 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:54,040 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:54,041 INFO [galaxy.model.migrate.check] Migrating 135 -> 136...
2018-07-05 13:51:55,035 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:55,036 INFO [galaxy.model.migrate.check] Migration script for collections and workflows connections.
2018-07-05 13:51:55,036 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:55,036 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:55,036 INFO [galaxy.model.migrate.check] Migrating 136 -> 137...
2018-07-05 13:51:55,471 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:55,471 INFO [galaxy.model.migrate.check] Add copied_from_job_id column to jobs table
2018-07-05 13:51:55,472 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:55,472 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:55,472 INFO [galaxy.model.migrate.check] Migrating 137 -> 138...
2018-07-05 13:51:55,866 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:55,866 INFO [galaxy.model.migrate.check] Add version column to history_dataset_association table
2018-07-05 13:51:55,866 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:55,867 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:55,867 INFO [galaxy.model.migrate.check] Migrating 138 -> 139...
2018-07-05 13:51:56,281 DEBUG [0139_add_history_dataset_association_history_table] Created history_dataset_association_history table
2018-07-05 13:51:56,304 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:56,304 INFO [galaxy.model.migrate.check] Migration script to add the history_dataset_association_history table.
2018-07-05 13:51:56,304 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:56,304 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:56,304 INFO [galaxy.model.migrate.check] Migrating 139 -> 140...
2018-07-05 13:51:57,006 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:57,007 INFO [galaxy.model.migrate.check] Add dataset_version column to job_to_input_dataset table
2018-07-05 13:51:57,007 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:57,007 INFO [galaxy.model.migrate.check]
2018-07-05 13:51:57,028 INFO [galaxy.config] Install database targetting Galaxy's database configuration.
2018-07-05 13:51:57,193 ERROR [galaxy.visualization.genomes] Error reading twobit.loc
Traceback (most recent call last):
File "/tmp/tmp7eiSQ_/galaxy-dev/lib/galaxy/visualization/genomes.py", line 212, in reload_genomes
for line in open(os.path.join(self.app.config.tool_data_path, "twobit.loc")):
IOError: [Errno 2] No such file or directory: '/tmp/tmp7eiSQ_/galaxy-dev/tool-data/twobit.loc'
2018-07-05 13:51:57,242 INFO [galaxy.util.handlers] Setting <handlers> default to child with id 'main'
2018-07-05 13:51:57,242 INFO [galaxy.jobs] Did not find job handler pool managed by application stack, this server (main) will handle jobs submitted to it
2018-07-05 13:51:57,307 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp7eiSQ_/tool_conf.xml
2018-07-05 13:51:57,391 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp7eiSQ_/shed_tools_conf.xml
2018-07-05 13:51:57,391 INFO [galaxy.tools.toolbox.base] Parsing the tool configuration /tmp/tmp7eiSQ_/empty_tool_conf.xml
No handlers could be found for logger "galaxy.datatypes.display_applications.application"
2018-07-05 13:51:57,742 INFO [galaxy.jobs] Handler 'main' will load all configured runner plugins
2018-07-05 13:51:57,748 INFO [galaxy.jobs.handler] job handler stop queue started
2018-07-05 13:51:57,758 INFO [galaxy.jobs.handler] job handler queue started
2018-07-05 13:51:57,765 INFO [galaxy.jobs.handler] job handler stop queue started
2018-07-05 13:51:57,777 INFO [galaxy.app] Galaxy app startup finished (6961.332 ms)
2018-07-05 13:51:58,528 INFO [galaxy.queue_worker] Binding and starting galaxy control worker for main
/home/pvh/.planemo/gx_venv_None/local/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.
'storage.' % (dialect.name, dialect.driver))
JBrowse ( jbrowse ) > Test-1 ... 2018-07-05 13:51:59,592 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 1
2018-07-05 13:52:00,021 INFO [galaxy.jobs.handler] (1) Job dispatched
2018-07-05 13:52:00,424 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/1/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/1/registry.xml /tmp/tmpUV7l_C 1:/tmp/tmp7eiSQ_/job_working_directory/000/1/dataset_1_files:/tmp/tmp7eiSQ_/files/000/dataset_1.dat]
2018-07-05 13:52:00,672 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:00,673 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:03,600 INFO [galaxy.tools.actions] Handled output named output for tool jbrowse (27.021 ms)
2018-07-05 13:52:03,624 INFO [galaxy.tools.actions] Added output datasets to history (23.970 ms)
2018-07-05 13:52:03,661 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=jbrowse] (11.952 ms)
2018-07-05 13:52:03,662 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=jbrowse] complete, ready to flush (37.057 ms)
2018-07-05 13:52:03,706 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=2,tool_id=jbrowse] (44.592 ms)
2018-07-05 13:52:04,318 INFO [galaxy.jobs.handler] (2) Job dispatched
2018-07-05 13:52:04,534 WARNI [galaxy.util.object_wrapper] Unable to create dynamic subclass for <class 'galaxy.model.metadata.MetadataCollection'>, {'data_lines': 2881, 'dbkey': u'hg17', 'sequences': 1}: metaclass conflict: the metaclass of a derived class must be a (non-strict) subclass of the metaclasses of all its bases
2018-07-05 13:52:04,535 WARNI [galaxy.util.object_wrapper] Unable to create dynamic subclass for <type 'listiterator'>, <listiterator object at 0x7fd5b13c3e50>: type 'listiterator' is not an acceptable base type
2018-07-05 13:52:04,569 DEBUG [galaxy.tools.deps] Using dependency jbrowse version 1.12.3 of type conda
2018-07-05 13:52:04,570 DEBUG [galaxy.tools.deps] Using dependency python version 2.7 of type conda
2018-07-05 13:52:04,570 DEBUG [galaxy.tools.deps] Using dependency biopython version 1.66 of type conda
2018-07-05 13:52:04,570 DEBUG [galaxy.tools.deps] Using dependency bcbiogff version 0.6.2 of type conda
2018-07-05 13:52:04,570 DEBUG [galaxy.tools.deps] Using dependency samtools version 1.2 of type conda
2018-07-05 13:52:04,570 DEBUG [galaxy.tools.deps] Using dependency pyyaml version 3.11 of type conda
2018-07-05 13:52:04,571 DEBUG [galaxy.tools.deps] Using dependency jbrowse version 1.12.3 of type conda
2018-07-05 13:52:04,571 DEBUG [galaxy.tools.deps] Using dependency python version 2.7 of type conda
2018-07-05 13:52:04,571 DEBUG [galaxy.tools.deps] Using dependency biopython version 1.66 of type conda
2018-07-05 13:52:04,571 DEBUG [galaxy.tools.deps] Using dependency bcbiogff version 0.6.2 of type conda
2018-07-05 13:52:04,571 DEBUG [galaxy.tools.deps] Using dependency samtools version 1.2 of type conda
2018-07-05 13:52:04,571 DEBUG [galaxy.tools.deps] Using dependency pyyaml version 3.11 of type conda
2018-07-05 13:52:04,617 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/2/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; python '/home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/tools/jbrowse/jbrowse.py' --version > /tmp/tmp7eiSQ_/tmp/GALAXY_VERSION_STRING_2 2>&1; mkdir -p /tmp/tmp7eiSQ_/job_working_directory/000/2/dataset_2_files && cp /tmp/tmp7eiSQ_/job_working_directory/000/2/tmpgM3gVE /tmp/tmp7eiSQ_/job_working_directory/000/2/dataset_2_files/galaxy.xml && python '/home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/tools/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --outdir /tmp/tmp7eiSQ_/job_working_directory/000/2/dataset_2_files /tmp/tmp7eiSQ_/job_working_directory/000/2/tmpgM3gVE && mv /tmp/tmp7eiSQ_/job_working_directory/000/2/tmp4sbq7Y /tmp/tmp7eiSQ_/files/000/dataset_2.dat; mv /tmp/tmp7eiSQ_/job_working_directory/000/2/tmpgM3gVE /tmp/tmp7eiSQ_/files/000/dataset_2.dat]
2018-07-05 13:52:04,746 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:04,747 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
ok
JBrowse ( jbrowse ) > Test-2 ... 2018-07-05 13:52:12,865 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 3
2018-07-05 13:52:13,699 INFO [galaxy.jobs.handler] (3) Job dispatched
2018-07-05 13:52:14,142 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/3/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/3/registry.xml /tmp/tmphpljKp 3:/tmp/tmp7eiSQ_/job_working_directory/000/3/dataset_3_files:/tmp/tmp7eiSQ_/files/000/dataset_3.dat]
2018-07-05 13:52:14,388 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:14,388 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:17,956 INFO [galaxy.tools.actions] Handled output named output for tool jbrowse (94.421 ms)
2018-07-05 13:52:18,025 INFO [galaxy.tools.actions] Added output datasets to history (68.555 ms)
2018-07-05 13:52:18,065 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=jbrowse] (16.815 ms)
2018-07-05 13:52:18,066 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=jbrowse] complete, ready to flush (41.489 ms)
2018-07-05 13:52:18,106 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=4,tool_id=jbrowse] (39.337 ms)
2018-07-05 13:52:19,093 INFO [galaxy.jobs.handler] (4) Job dispatched
2018-07-05 13:52:19,317 DEBUG [galaxy.tools.deps] Using dependency jbrowse version 1.12.3 of type conda
2018-07-05 13:52:19,317 DEBUG [galaxy.tools.deps] Using dependency python version 2.7 of type conda
2018-07-05 13:52:19,317 DEBUG [galaxy.tools.deps] Using dependency biopython version 1.66 of type conda
2018-07-05 13:52:19,317 DEBUG [galaxy.tools.deps] Using dependency bcbiogff version 0.6.2 of type conda
2018-07-05 13:52:19,317 DEBUG [galaxy.tools.deps] Using dependency samtools version 1.2 of type conda
2018-07-05 13:52:19,318 DEBUG [galaxy.tools.deps] Using dependency pyyaml version 3.11 of type conda
2018-07-05 13:52:19,318 DEBUG [galaxy.tools.deps] Using dependency jbrowse version 1.12.3 of type conda
2018-07-05 13:52:19,318 DEBUG [galaxy.tools.deps] Using dependency python version 2.7 of type conda
2018-07-05 13:52:19,318 DEBUG [galaxy.tools.deps] Using dependency biopython version 1.66 of type conda
2018-07-05 13:52:19,319 DEBUG [galaxy.tools.deps] Using dependency bcbiogff version 0.6.2 of type conda
2018-07-05 13:52:19,319 DEBUG [galaxy.tools.deps] Using dependency samtools version 1.2 of type conda
2018-07-05 13:52:19,319 DEBUG [galaxy.tools.deps] Using dependency pyyaml version 3.11 of type conda
2018-07-05 13:52:19,359 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/4/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; python '/home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/tools/jbrowse/jbrowse.py' --version > /tmp/tmp7eiSQ_/tmp/GALAXY_VERSION_STRING_4 2>&1; mkdir -p /tmp/tmp7eiSQ_/job_working_directory/000/4/dataset_4_files && cp /tmp/tmp7eiSQ_/job_working_directory/000/4/tmpgkrEIt /tmp/tmp7eiSQ_/job_working_directory/000/4/dataset_4_files/galaxy.xml && python '/home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/tools/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --outdir /tmp/tmp7eiSQ_/job_working_directory/000/4/dataset_4_files /tmp/tmp7eiSQ_/job_working_directory/000/4/tmpgkrEIt && mv /tmp/tmp7eiSQ_/job_working_directory/000/4/tmpuOhHuy /tmp/tmp7eiSQ_/files/000/dataset_4.dat; mv /tmp/tmp7eiSQ_/job_working_directory/000/4/tmpgkrEIt /tmp/tmp7eiSQ_/files/000/dataset_4.dat]
2018-07-05 13:52:19,539 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:19,539 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
ok
JBrowse ( jbrowse ) > Test-3 ... 2018-07-05 13:52:27,509 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 5
2018-07-05 13:52:28,436 INFO [galaxy.jobs.handler] (5) Job dispatched
2018-07-05 13:52:28,749 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/5/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/5/registry.xml /tmp/tmpkl79co 5:/tmp/tmp7eiSQ_/job_working_directory/000/5/dataset_5_files:/tmp/tmp7eiSQ_/files/000/dataset_5.dat]
2018-07-05 13:52:28,946 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:28,948 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:31,823 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 6
2018-07-05 13:52:32,662 INFO [galaxy.jobs.handler] (6) Job dispatched
2018-07-05 13:52:32,999 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/6/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/6/registry.xml /tmp/tmpRSZsCm 6:/tmp/tmp7eiSQ_/job_working_directory/000/6/dataset_6_files:/tmp/tmp7eiSQ_/files/000/dataset_6.dat]
2018-07-05 13:52:33,201 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:33,201 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:35,988 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 7
2018-07-05 13:52:36,892 INFO [galaxy.jobs.handler] (7) Job dispatched
2018-07-05 13:52:37,271 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/7/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/7/registry.xml /tmp/tmpzvOFVM 7:/tmp/tmp7eiSQ_/job_working_directory/000/7/dataset_7_files:/tmp/tmp7eiSQ_/files/000/dataset_7.dat]
2018-07-05 13:52:37,474 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:37,475 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:40,277 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 8
2018-07-05 13:52:41,147 INFO [galaxy.jobs.handler] (8) Job dispatched
2018-07-05 13:52:41,519 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/8/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/8/registry.xml /tmp/tmpfQhCHy 8:/tmp/tmp7eiSQ_/job_working_directory/000/8/dataset_8_files:/tmp/tmp7eiSQ_/files/000/dataset_8.dat]
2018-07-05 13:52:41,696 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:41,699 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:44,857 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 9
2018-07-05 13:52:45,406 INFO [galaxy.jobs.handler] (9) Job dispatched
2018-07-05 13:52:45,778 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/9/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/9/registry.xml /tmp/tmp1yLAPb 9:/tmp/tmp7eiSQ_/job_working_directory/000/9/dataset_9_files:/tmp/tmp7eiSQ_/files/000/dataset_9.dat]
2018-07-05 13:52:46,019 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:46,019 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:49,013 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 10
2018-07-05 13:52:49,627 INFO [galaxy.jobs.handler] (10) Job dispatched
2018-07-05 13:52:49,984 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/10/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/10/registry.xml /tmp/tmpRx3QNt 10:/tmp/tmp7eiSQ_/job_working_directory/000/10/dataset_10_files:/tmp/tmp7eiSQ_/files/000/dataset_10.dat]
2018-07-05 13:52:50,185 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:50,186 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:53,069 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 11
2018-07-05 13:52:53,853 INFO [galaxy.jobs.handler] (11) Job dispatched
2018-07-05 13:52:54,226 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/11/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/11/registry.xml /tmp/tmpe6wTSh 11:/tmp/tmp7eiSQ_/job_working_directory/000/11/dataset_11_files:/tmp/tmp7eiSQ_/files/000/dataset_11.dat]
2018-07-05 13:52:54,467 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:54,467 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:57,245 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 12
2018-07-05 13:52:58,088 INFO [galaxy.jobs.handler] (12) Job dispatched
2018-07-05 13:52:58,416 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/12/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/12/registry.xml /tmp/tmp517zr0 12:/tmp/tmp7eiSQ_/job_working_directory/000/12/dataset_12_files:/tmp/tmp7eiSQ_/files/000/dataset_12.dat]
2018-07-05 13:52:58,620 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:52:58,621 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:02,315 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 13
2018-07-05 13:53:03,417 INFO [galaxy.jobs.handler] (13) Job dispatched
2018-07-05 13:53:03,844 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/13/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/13/registry.xml /tmp/tmpx7vDQz 13:/tmp/tmp7eiSQ_/job_working_directory/000/13/dataset_13_files:/tmp/tmp7eiSQ_/files/000/dataset_13.dat]
2018-07-05 13:53:04,169 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:04,170 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:07,556 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 14
2018-07-05 13:53:08,701 INFO [galaxy.jobs.handler] (14) Job dispatched
2018-07-05 13:53:09,090 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/14/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/14/registry.xml /tmp/tmpYjL9CH 14:/tmp/tmp7eiSQ_/job_working_directory/000/14/dataset_14_files:/tmp/tmp7eiSQ_/files/000/dataset_14.dat]
2018-07-05 13:53:09,334 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:09,334 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:12,518 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 15
2018-07-05 13:53:13,031 INFO [galaxy.jobs.handler] (15) Job dispatched
2018-07-05 13:53:13,362 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/15/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/15/registry.xml /tmp/tmpWhn6fA 15:/tmp/tmp7eiSQ_/job_working_directory/000/15/dataset_15_files:/tmp/tmp7eiSQ_/files/000/dataset_15.dat]
2018-07-05 13:53:13,622 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:13,624 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:16,737 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 16
2018-07-05 13:53:17,319 INFO [galaxy.jobs.handler] (16) Job dispatched
2018-07-05 13:53:17,720 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/16/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/16/registry.xml /tmp/tmpWtF84B 16:/tmp/tmp7eiSQ_/job_working_directory/000/16/dataset_16_files:/tmp/tmp7eiSQ_/files/000/dataset_16.dat]
2018-07-05 13:53:17,973 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:17,974 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:21,039 INFO [galaxy.tools.actions] Handled output named output for tool jbrowse (33.104 ms)
2018-07-05 13:53:21,068 INFO [galaxy.tools.actions] Added output datasets to history (29.161 ms)
2018-07-05 13:53:21,200 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=jbrowse] (69.275 ms)
2018-07-05 13:53:21,201 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=jbrowse] complete, ready to flush (132.431 ms)
2018-07-05 13:53:21,237 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=17,tool_id=jbrowse] (35.836 ms)
2018-07-05 13:53:21,556 INFO [galaxy.jobs.handler] (17) Job dispatched
2018-07-05 13:53:22,143 DEBUG [galaxy.tools.deps] Using dependency jbrowse version 1.12.3 of type conda
2018-07-05 13:53:22,144 DEBUG [galaxy.tools.deps] Using dependency python version 2.7 of type conda
2018-07-05 13:53:22,144 DEBUG [galaxy.tools.deps] Using dependency biopython version 1.66 of type conda
2018-07-05 13:53:22,144 DEBUG [galaxy.tools.deps] Using dependency bcbiogff version 0.6.2 of type conda
2018-07-05 13:53:22,144 DEBUG [galaxy.tools.deps] Using dependency samtools version 1.2 of type conda
2018-07-05 13:53:22,144 DEBUG [galaxy.tools.deps] Using dependency pyyaml version 3.11 of type conda
2018-07-05 13:53:22,145 DEBUG [galaxy.tools.deps] Using dependency jbrowse version 1.12.3 of type conda
2018-07-05 13:53:22,145 DEBUG [galaxy.tools.deps] Using dependency python version 2.7 of type conda
2018-07-05 13:53:22,145 DEBUG [galaxy.tools.deps] Using dependency biopython version 1.66 of type conda
2018-07-05 13:53:22,145 DEBUG [galaxy.tools.deps] Using dependency bcbiogff version 0.6.2 of type conda
2018-07-05 13:53:22,145 DEBUG [galaxy.tools.deps] Using dependency samtools version 1.2 of type conda
2018-07-05 13:53:22,146 DEBUG [galaxy.tools.deps] Using dependency pyyaml version 3.11 of type conda
2018-07-05 13:53:22,194 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/17/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; python '/home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/tools/jbrowse/jbrowse.py' --version > /tmp/tmp7eiSQ_/tmp/GALAXY_VERSION_STRING_17 2>&1; mkdir -p /tmp/tmp7eiSQ_/job_working_directory/000/17/dataset_17_files && cp /tmp/tmp7eiSQ_/job_working_directory/000/17/tmpDoD80s /tmp/tmp7eiSQ_/job_working_directory/000/17/dataset_17_files/galaxy.xml && python '/home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/tools/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --outdir /tmp/tmp7eiSQ_/job_working_directory/000/17/dataset_17_files /tmp/tmp7eiSQ_/job_working_directory/000/17/tmpDoD80s && mv /tmp/tmp7eiSQ_/job_working_directory/000/17/tmpdEkNa6 /tmp/tmp7eiSQ_/files/000/dataset_17.dat; mv /tmp/tmp7eiSQ_/job_working_directory/000/17/tmpDoD80s /tmp/tmp7eiSQ_/files/000/dataset_17.dat]
2018-07-05 13:53:22,397 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:22,398 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
ok
JBrowse ( jbrowse ) > Test-4 ... 2018-07-05 13:53:30,464 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 18
2018-07-05 13:53:30,950 INFO [galaxy.jobs.handler] (18) Job dispatched
2018-07-05 13:53:31,316 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/18/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/18/registry.xml /tmp/tmp7pN8RF 18:/tmp/tmp7eiSQ_/job_working_directory/000/18/dataset_18_files:/tmp/tmp7eiSQ_/files/000/dataset_18.dat]
2018-07-05 13:53:31,507 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:31,508 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:34,296 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 19
2018-07-05 13:53:35,216 INFO [galaxy.jobs.handler] (19) Job dispatched
2018-07-05 13:53:35,558 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/19/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/19/registry.xml /tmp/tmpRMzme2 19:/tmp/tmp7eiSQ_/job_working_directory/000/19/dataset_19_files:/tmp/tmp7eiSQ_/files/000/dataset_19.dat]
2018-07-05 13:53:35,777 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:35,778 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:38,607 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 20
2018-07-05 13:53:39,460 INFO [galaxy.jobs.handler] (20) Job dispatched
2018-07-05 13:53:40,149 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/20/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/20/registry.xml /tmp/tmpoXqqzE 20:/tmp/tmp7eiSQ_/job_working_directory/000/20/dataset_20_files:/tmp/tmp7eiSQ_/files/000/dataset_20.dat]
2018-07-05 13:53:40,364 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:40,365 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:43,029 INFO [galaxy.tools.actions] Handled output named output for tool jbrowse (65.217 ms)
2018-07-05 13:53:43,052 INFO [galaxy.tools.actions] Added output datasets to history (22.876 ms)
2018-07-05 13:53:43,091 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=jbrowse] (19.743 ms)
2018-07-05 13:53:43,092 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=jbrowse] complete, ready to flush (39.499 ms)
2018-07-05 13:53:43,129 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=21,tool_id=jbrowse] (36.646 ms)
2018-07-05 13:53:43,719 INFO [galaxy.jobs.handler] (21) Job dispatched
2018-07-05 13:53:43,919 DEBUG [galaxy.tools.deps] Using dependency jbrowse version 1.12.3 of type conda
2018-07-05 13:53:43,919 DEBUG [galaxy.tools.deps] Using dependency python version 2.7 of type conda
2018-07-05 13:53:43,919 DEBUG [galaxy.tools.deps] Using dependency biopython version 1.66 of type conda
2018-07-05 13:53:43,920 DEBUG [galaxy.tools.deps] Using dependency bcbiogff version 0.6.2 of type conda
2018-07-05 13:53:43,920 DEBUG [galaxy.tools.deps] Using dependency samtools version 1.2 of type conda
2018-07-05 13:53:43,920 DEBUG [galaxy.tools.deps] Using dependency pyyaml version 3.11 of type conda
2018-07-05 13:53:43,921 DEBUG [galaxy.tools.deps] Using dependency jbrowse version 1.12.3 of type conda
2018-07-05 13:53:43,921 DEBUG [galaxy.tools.deps] Using dependency python version 2.7 of type conda
2018-07-05 13:53:43,921 DEBUG [galaxy.tools.deps] Using dependency biopython version 1.66 of type conda
2018-07-05 13:53:43,921 DEBUG [galaxy.tools.deps] Using dependency bcbiogff version 0.6.2 of type conda
2018-07-05 13:53:43,921 DEBUG [galaxy.tools.deps] Using dependency samtools version 1.2 of type conda
2018-07-05 13:53:43,921 DEBUG [galaxy.tools.deps] Using dependency pyyaml version 3.11 of type conda
2018-07-05 13:53:43,960 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/21/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; python '/home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/tools/jbrowse/jbrowse.py' --version > /tmp/tmp7eiSQ_/tmp/GALAXY_VERSION_STRING_21 2>&1; mkdir -p /tmp/tmp7eiSQ_/job_working_directory/000/21/dataset_21_files && cp /tmp/tmp7eiSQ_/job_working_directory/000/21/tmpwItgi4 /tmp/tmp7eiSQ_/job_working_directory/000/21/dataset_21_files/galaxy.xml && python '/home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/tools/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --outdir /tmp/tmp7eiSQ_/job_working_directory/000/21/dataset_21_files /tmp/tmp7eiSQ_/job_working_directory/000/21/tmpwItgi4 && mv /tmp/tmp7eiSQ_/job_working_directory/000/21/tmpoda923 /tmp/tmp7eiSQ_/files/000/dataset_21.dat; mv /tmp/tmp7eiSQ_/job_working_directory/000/21/tmpwItgi4 /tmp/tmp7eiSQ_/files/000/dataset_21.dat]
2018-07-05 13:53:44,069 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:44,070 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
ok
JBrowse ( jbrowse ) > Test-5 ... 2018-07-05 13:53:57,423 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 22
2018-07-05 13:53:58,176 INFO [galaxy.jobs.handler] (22) Job dispatched
2018-07-05 13:53:58,577 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/22/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/22/registry.xml /tmp/tmpmzjvO9 22:/tmp/tmp7eiSQ_/job_working_directory/000/22/dataset_22_files:/tmp/tmp7eiSQ_/files/000/dataset_22.dat]
2018-07-05 13:53:58,818 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:53:58,819 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:54:01,666 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 23
2018-07-05 13:54:02,444 INFO [galaxy.jobs.handler] (23) Job dispatched
2018-07-05 13:54:02,909 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/23/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/23/registry.xml /tmp/tmpPdFTaZ 23:/tmp/tmp7eiSQ_/job_working_directory/000/23/dataset_23_files:/tmp/tmp7eiSQ_/files/000/dataset_23.dat]
2018-07-05 13:54:03,163 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:54:03,163 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:54:06,243 INFO [galaxy.tools.actions] Handled output named output for tool jbrowse (28.021 ms)
2018-07-05 13:54:06,268 INFO [galaxy.tools.actions] Added output datasets to history (24.440 ms)
2018-07-05 13:54:06,311 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=jbrowse] (19.323 ms)
2018-07-05 13:54:06,312 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=jbrowse] complete, ready to flush (43.931 ms)
2018-07-05 13:54:06,350 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=24,tool_id=jbrowse] (38.164 ms)
2018-07-05 13:54:06,620 INFO [galaxy.jobs.handler] (24) Job dispatched
2018-07-05 13:54:07,025 DEBUG [galaxy.tools.deps] Using dependency jbrowse version 1.12.3 of type conda
2018-07-05 13:54:07,025 DEBUG [galaxy.tools.deps] Using dependency python version 2.7 of type conda
2018-07-05 13:54:07,025 DEBUG [galaxy.tools.deps] Using dependency biopython version 1.66 of type conda
2018-07-05 13:54:07,025 DEBUG [galaxy.tools.deps] Using dependency bcbiogff version 0.6.2 of type conda
2018-07-05 13:54:07,025 DEBUG [galaxy.tools.deps] Using dependency samtools version 1.2 of type conda
2018-07-05 13:54:07,026 DEBUG [galaxy.tools.deps] Using dependency pyyaml version 3.11 of type conda
2018-07-05 13:54:07,026 DEBUG [galaxy.tools.deps] Using dependency jbrowse version 1.12.3 of type conda
2018-07-05 13:54:07,026 DEBUG [galaxy.tools.deps] Using dependency python version 2.7 of type conda
2018-07-05 13:54:07,027 DEBUG [galaxy.tools.deps] Using dependency biopython version 1.66 of type conda
2018-07-05 13:54:07,027 DEBUG [galaxy.tools.deps] Using dependency bcbiogff version 0.6.2 of type conda
2018-07-05 13:54:07,027 DEBUG [galaxy.tools.deps] Using dependency samtools version 1.2 of type conda
2018-07-05 13:54:07,027 DEBUG [galaxy.tools.deps] Using dependency pyyaml version 3.11 of type conda
2018-07-05 13:54:07,123 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/24/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/mulled-v1-4f60687598c40f0675c7de956d89c6ebcb6abb8d1faef576907dbea7330e0778' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; python '/home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/tools/jbrowse/jbrowse.py' --version > /tmp/tmp7eiSQ_/tmp/GALAXY_VERSION_STRING_24 2>&1; mkdir -p /tmp/tmp7eiSQ_/job_working_directory/000/24/dataset_24_files && cp /tmp/tmp7eiSQ_/job_working_directory/000/24/tmpuqxJtB /tmp/tmp7eiSQ_/job_working_directory/000/24/dataset_24_files/galaxy.xml && python '/home/pvh/Documents/code/SANBI/pvh-forks/tools-iuc/tools/jbrowse/jbrowse.py' --jbrowse ${JBROWSE_SOURCE_DIR} --outdir /tmp/tmp7eiSQ_/job_working_directory/000/24/dataset_24_files /tmp/tmp7eiSQ_/job_working_directory/000/24/tmpuqxJtB && mv /tmp/tmp7eiSQ_/job_working_directory/000/24/tmp1BABxh /tmp/tmp7eiSQ_/files/000/dataset_24.dat; mv /tmp/tmp7eiSQ_/job_working_directory/000/24/tmpuqxJtB /tmp/tmp7eiSQ_/files/000/dataset_24.dat]
2018-07-05 13:54:07,298 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:54:07,299 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
ok
JBrowse ( jbrowse ) > Test-6 ... 2018-07-05 13:54:21,016 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 25
2018-07-05 13:54:22,211 INFO [galaxy.jobs.handler] (25) Job dispatched
2018-07-05 13:54:22,589 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/25/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/25/registry.xml /tmp/tmpg6_Xt9 25:/tmp/tmp7eiSQ_/job_working_directory/000/25/dataset_25_files:/tmp/tmp7eiSQ_/files/000/dataset_25.dat]
2018-07-05 13:54:22,794 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:54:22,795 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:54:25,661 INFO [galaxy.tools.actions.upload_common] tool upload1 created job id 26
2018-07-05 13:54:26,435 INFO [galaxy.jobs.handler] (26) Job dispatched
2018-07-05 13:54:26,801 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/26/tool_script.sh] for tool command [python /tmp/tmp7eiSQ_/galaxy-dev/tools/data_source/upload.py /tmp/tmp7eiSQ_/galaxy-dev /tmp/tmp7eiSQ_/job_working_directory/000/26/registry.xml /tmp/tmpayjDQw 26:/tmp/tmp7eiSQ_/job_working_directory/000/26/dataset_26_files:/tmp/tmp7eiSQ_/files/000/dataset_26.dat]
2018-07-05 13:54:27,012 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:54:27,013 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:54:30,135 INFO [galaxy.tools.actions] Handled output named output for tool CONVERTER_bam_to_coodinate_sorted_bam (30.478 ms)
2018-07-05 13:54:30,142 INFO [galaxy.tools.actions] Added output datasets to history (6.092 ms)
2018-07-05 13:54:30,166 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=CONVERTER_bam_to_coodinate_sorted_bam] (10.782 ms)
2018-07-05 13:54:30,167 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=CONVERTER_bam_to_coodinate_sorted_bam] complete, ready to flush (24.971 ms)
2018-07-05 13:54:30,204 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=27,tool_id=CONVERTER_bam_to_coodinate_sorted_bam] (37.056 ms)
2018-07-05 13:54:30,338 INFO [galaxy.tools.actions] Handled output named output for tool jbrowse (48.645 ms)
2018-07-05 13:54:30,365 INFO [galaxy.tools.actions] Added output datasets to history (27.483 ms)
2018-07-05 13:54:30,397 INFO [galaxy.tools.actions] Verified access to datasets for Job[unflushed,tool_id=jbrowse] (16.267 ms)
2018-07-05 13:54:30,398 INFO [galaxy.tools.actions] Setup for job Job[unflushed,tool_id=jbrowse] complete, ready to flush (32.482 ms)
2018-07-05 13:54:30,439 INFO [galaxy.tools.actions] Flushed transaction for job Job[id=28,tool_id=jbrowse] (40.914 ms)
2018-07-05 13:54:30,703 INFO [galaxy.jobs.handler] (27) Job dispatched
2018-07-05 13:54:30,903 DEBUG [galaxy.tools.deps] Using dependency samtools version 1.6 of type conda
2018-07-05 13:54:30,904 DEBUG [galaxy.tools.deps] Using dependency samtools version 1.6 of type conda
2018-07-05 13:54:31,005 INFO [galaxy.jobs.command_factory] Built script [/tmp/tmp7eiSQ_/job_working_directory/000/27/tool_script.sh] for tool command [[ "$CONDA_DEFAULT_ENV" = "/home/pvh/miniconda3/envs/__samtools@1.6" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/pvh/miniconda3/bin/activate '/home/pvh/miniconda3/envs/__samtools@1.6' > conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; samtools sort -@ ${GALAXY_SLOTS:-1} -o '/tmp/tmp7eiSQ_/files/000/dataset_27.dat' -O bam -T dataset '/tmp/tmp7eiSQ_/files/000/dataset_26.dat']
2018-07-05 13:54:31,161 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:54:31,162 DEBUG [galaxy.tools.deps] Using dependency bcftools version 1.5 of type conda
2018-07-05 13:54:33,497 INFO [galaxy.jobs.output_checker] Job 27: Fatal error: Exit code 1 ()
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