Mercurial > repos > lecorguille > camera_annotate
view qsub.out @ 11:d33e0ed5f32a draft
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835-dirty
| author | lecorguille |
|---|---|
| date | Thu, 14 Apr 2016 10:03:48 -0400 |
| parents | 01a900f2e464 |
| children | db270f704d93 |
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git --git-dir /home/fr2424/sib/lecorguille/.planemo/gx_repo fetch >/dev/null 2>&1 cd /tmp/714401.1.short.q/tmpAQxCGj; git clone --branch 'master' '/home/fr2424/sib/lecorguille/.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/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_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} Initialized empty Git repository in /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/.git/ 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 lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml from user_info.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 tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample Initializing tool-data/add_scores.loc from add_scores.loc.sample Initializing tool-data/alignseq.loc from alignseq.loc.sample Initializing tool-data/all_fasta.loc from all_fasta.loc.sample Initializing tool-data/bfast_indexes.loc from bfast_indexes.loc.sample Initializing tool-data/binned_scores.loc from binned_scores.loc.sample Initializing tool-data/codingSnps.loc from codingSnps.loc.sample Initializing tool-data/encode_datasets.loc from encode_datasets.loc.sample Initializing tool-data/faseq.loc from faseq.loc.sample Initializing tool-data/funDo.loc from funDo.loc.sample Initializing tool-data/liftOver.loc from liftOver.loc.sample Initializing tool-data/maf_index.loc from maf_index.loc.sample Initializing tool-data/maf_pairwise.loc from maf_pairwise.loc.sample Initializing tool-data/microbial_data.loc from microbial_data.loc.sample Initializing tool-data/mosaik_index.loc from mosaik_index.loc.sample Initializing tool-data/ngs_sim_fasta.loc from ngs_sim_fasta.loc.sample Initializing tool-data/perm_base_index.loc from perm_base_index.loc.sample Initializing tool-data/perm_color_index.loc from perm_color_index.loc.sample Initializing tool-data/phastOdds.loc from phastOdds.loc.sample Initializing tool-data/picard_index.loc from picard_index.loc.sample Initializing tool-data/quality_scores.loc from quality_scores.loc.sample Initializing tool-data/regions.loc from regions.loc.sample Initializing tool-data/sequence_index_base.loc from sequence_index_base.loc.sample Initializing tool-data/sequence_index_color.loc from sequence_index_color.loc.sample Initializing tool-data/sift_db.loc from sift_db.loc.sample Initializing tool-data/srma_index.loc from srma_index.loc.sample Initializing tool-data/twobit.loc from twobit.loc.sample Initializing static/welcome.html from welcome.html.sample Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv Ignoring indexes: https://pypi.python.org/simple Requirement already up-to-date: pip==8.0.2+gx2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt==0.4.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.30 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) Requirement already satisfied (use --upgrade to upgrade): nose in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1)) Requirement already satisfied (use --upgrade to upgrade): NoseHTML in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2)) Requirement already satisfied (use --upgrade to upgrade): twill==0.9.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) Requirement already satisfied (use --upgrade to upgrade): mock in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): funcsigs>=1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): six>=1.9 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): pbr>=0.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): ordereddict in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from funcsigs>=1->mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) Starting galaxy with command [cd /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_planemo/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/run.sh $COMMON_STARTUP_ARGS --daemon --wait] Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv Ignoring indexes: https://pypi.python.org/simple Requirement already up-to-date: pip==8.0.2+gx2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt==0.4.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.30 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv ............. Installing repositories - this may take some time... Testing using galaxy_root /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev Testing tools with command [cd /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/fr2424/sib/lecorguille/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /home/fr2424/sib/lecorguille/.venv_planemo/bin/virtualenv -p /home/fr2424/sib/lecorguille/.venv_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 /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_annotate/tool_test_output.html --xunit_report_file /tmp/714401.1.short.q/tmpAQxCGj/xunit.xml --structured_data_report_file /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_annotate/tool_test_output.json -installed] Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv Ignoring indexes: https://pypi.python.org/simple Requirement already up-to-date: pip==8.0.2+gx2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt==0.4.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.30 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) Requirement already satisfied (use --upgrade to upgrade): nose in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 1)) Requirement already satisfied (use --upgrade to upgrade): NoseHTML in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 2)) Requirement already satisfied (use --upgrade to upgrade): twill==0.9.1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 3)) Requirement already satisfied (use --upgrade to upgrade): mock in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from -r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): funcsigs>=1 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): six>=1.9 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): pbr>=0.11 in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): ordereddict in /home/fr2424/sib/lecorguille/.planemo/gx_venv/lib/python2.7/site-packages (from funcsigs>=1->mock->-r ./lib/galaxy/dependencies/dev-requirements.txt (line 4)) Activating virtualenv at /home/fr2424/sib/lecorguille/.planemo/gx_venv [('app:main', 'new_file_path', '/tmp/714401.1.short.q/tmpYE8cIL/tmpVeogQe/new_files_path_Zk6Uub'), ('app:main', 'database_connection', 'sqlite:////tmp/714401.1.short.q/tmpYE8cIL/tmpVeogQe/database/universe.sqlite'), ('app:main', 'data_manager_config_file', 'config/data_manager_conf.xml.sample,test/functional/tools/sample_data_manager_conf.xml'), ('app:main', 'job_queue_workers', 5), ('app:main', 'log_destination', 'stdout'), ('app:main', 'allow_user_deletion', True), ('app:main', 'master_api_key', 'test_key'), ('app:main', 'tool_config_file', '/tmp/714401.1.short.q/tmp3wnbXv'), ('app:main', 'template_cache_path', '/tmp/714401.1.short.q/tmpYE8cIL/tmpVeogQe/database/compiled_templates'), ('app:main', 'job_working_directory', '/tmp/714401.1.short.q/tmpYE8cIL/tmpVeogQe/job_working_directory_eYJfla'), ('app:main', 'tool_dependency_dir', '/tmp/714401.1.short.q/tmpAQxCGj/deps'), ('app:main', 'check_migrate_tools', False), ('app:main', 'tool_path', 'tools'), ('app:main', 'enable_beta_tool_formats', True), ('app:main', 'user_library_import_dir', None), ('app:main', 'galaxy_data_manager_data_path', '/tmp/714401.1.short.q/tmpYE8cIL/data_manager_test_tmpBMgb4s/data_manager_tool-dataFeK_yC'), ('app:main', 'tool_data_table_config_path', 'config/tool_data_table_conf.xml.sample,test/functional/tool-data/sample_tool_data_tables.xml'), ('app:main', 'file_path', '/tmp/714401.1.short.q/tmpYE8cIL/tmpVeogQe/database/files'), ('app:main', 'datatype_converters_config_file', 'datatype_converters_conf.xml.sample'), ('app:main', 'database_auto_migrate', True), ('app:main', 'use_tasked_jobs', True), ('app:main', 'auto_configure_logging', True), ('app:main', 'tool_parse_help', False), ('app:main', 'shed_tool_data_table_config', 'config/shed_tool_data_table_conf.xml'), ('app:main', 'update_integrated_tool_panel', False), ('app:main', 'admin_users', 'test@bx.psu.edu'), ('app:main', 'template_path', 'templates'), ('app:main', 'allow_user_creation', True), ('app:main', 'use_heartbeat', False), ('app:main', 'allow_library_path_paste', True), ('app:main', 'api_allow_run_as', 'test@bx.psu.edu'), ('app:main', 'test_conf', 'test.conf'), ('app:main', 'id_secret', 'changethisinproductiontoo'), ('app:main', 'library_import_dir', None), ('app:main', 'cleanup_job', 'onsuccess'), ('app:main', 'running_functional_tests', True)] galaxy.queue_worker INFO 2016-04-14 15:51:10,770 Initalizing main Galaxy Queue Worker on sqlalchemy+sqlite:// tool_shed.tool_shed_registry DEBUG 2016-04-14 15:51:10,811 Loading references to tool sheds from /tmp/714401.1.short.q/tmpAQxCGj/tool_sheds_conf.xml tool_shed.tool_shed_registry DEBUG 2016-04-14 15:51:10,811 Loaded reference to tool shed: Target Shed galaxy.app DEBUG 2016-04-14 15:51:10,812 Using "galaxy.ini" config file: /tmp/714401.1.short.q/tmpYE8cIL/functional_tests_wsgi.ini migrate.versioning.repository DEBUG 2016-04-14 15:51:10,886 Loading repository lib/galaxy/model/migrate... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,887 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,887 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,887 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,887 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,887 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,887 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,887 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,887 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,887 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,887 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,887 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,888 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,888 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,888 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,888 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,888 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,888 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,888 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,888 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,888 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,888 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,888 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,888 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,888 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,888 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,889 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,889 Loading script lib/galaxy/model/migrate/versions/0014_pages.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,889 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,889 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,889 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,889 Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,889 Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,889 Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,889 Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,889 Loading script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,889 Script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,889 Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,889 Script lib/galaxy/model/migrate/versions/0019_request_library_folder.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,890 Loading script lib/galaxy/model/migrate/versions/0020_library_upload_job.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,890 Script lib/galaxy/model/migrate/versions/0020_library_upload_job.py loaded 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lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,901 Script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,902 Loading script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,902 Script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,902 Loading script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,902 Script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,902 Loading script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,902 Script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,902 Loading script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,902 Script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,902 Loading script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,902 Script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,902 Loading script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,902 Script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,902 Loading script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,902 Script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,903 Loading script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,903 Script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,903 Loading script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,903 Script 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lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Loading script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Loading script lib/galaxy/model/migrate/versions/0119_job_metrics.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Script lib/galaxy/model/migrate/versions/0119_job_metrics.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Loading script lib/galaxy/model/migrate/versions/0120_dataset_collections.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Script lib/galaxy/model/migrate/versions/0120_dataset_collections.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Loading script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,904 Loading script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Loading script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,905 Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,906 Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,906 Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,906 Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,906 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py... migrate.versioning.script.base DEBUG 2016-04-14 15:51:10,906 Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully migrate.versioning.repository DEBUG 2016-04-14 15:51:10,906 Repository lib/galaxy/model/migrate loaded successfully migrate.versioning.repository DEBUG 2016-04-14 15:51:10,906 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) galaxy.config INFO 2016-04-14 15:51:10,960 Install database targetting Galaxy's database configuration. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:10,998 Loading datatypes from /tmp/714401.1.short.q/tmpAQxCGj/tmp/tmp-toolshed-acalpd1lhytY galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,003 Loading datatypes from /tmp/714401.1.short.q/tmpAQxCGj/tmp/tmp-toolshed-acalpdRs1z_c galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,003 Exception importing proprietary code file /tmp/714401.1.short.q/tmpAQxCGj/shed_tools/testtoolshed.g2.bx.psu.edu/repos/lecorguille/rdata_xcms_datatypes/bff835d58914/rdata_xcms_datatypes/binary: No module named binary galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,003 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,016 Loading datatypes from ./config/datatypes_conf.xml.sample galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,016 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,017 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,018 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,018 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,018 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,018 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,018 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,018 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,019 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,019 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,019 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,019 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,019 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,019 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,019 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,020 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,020 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,020 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,020 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,020 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,020 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,021 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,021 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,021 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,021 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,021 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,021 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,022 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,023 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,024 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,024 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,024 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,024 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,024 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,024 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,025 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,025 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,025 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,025 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,026 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,027 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,027 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,027 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,027 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,029 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,029 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,029 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,029 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,029 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,029 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,030 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,030 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,030 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,030 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,030 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,030 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,030 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,031 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,032 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,033 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,033 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,033 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,033 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,033 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,033 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,033 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,034 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,035 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,036 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,036 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,036 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,036 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,036 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,036 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,036 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,037 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,038 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,039 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,039 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,039 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,039 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,039 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,041 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,041 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,041 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,042 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,042 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,042 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,042 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,042 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,042 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,042 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,043 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,044 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,044 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,045 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,046 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,046 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,046 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,046 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,047 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,047 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,047 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,047 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,047 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,047 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,047 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,048 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,049 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,050 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,050 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,050 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,050 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,050 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,051 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,052 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,052 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,052 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,052 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,052 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,052 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,053 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,053 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,053 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,053 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,053 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,053 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,053 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,054 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,054 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,054 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,054 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,054 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,054 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,055 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,055 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,055 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,055 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,055 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,056 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,056 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,056 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,056 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,056 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,056 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,057 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,057 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,057 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,057 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,057 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,057 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,057 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,058 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,058 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,058 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,058 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,058 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,058 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,059 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,059 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,059 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,059 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,059 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,059 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,060 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,060 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,060 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,060 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,060 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,061 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,061 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,061 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,061 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,061 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,061 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,061 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,062 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,062 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,062 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,062 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,062 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,062 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,063 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,063 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,063 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Overriding conflicting datatype with extension 'rdata', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,064 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,065 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,065 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,066 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,066 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,066 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,066 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,066 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,067 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,068 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,069 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Removed conflicting sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,070 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Removed conflicting sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,071 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,072 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,073 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,074 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,075 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,076 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,077 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,078 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,078 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,078 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt galaxy.jobs WARNING 2016-04-14 15:51:11,133 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/714401.1.short.q/tmpYE8cIL/functional_tests_wsgi.ini" instead galaxy.jobs DEBUG 2016-04-14 15:51:11,133 Loading job configuration from /tmp/714401.1.short.q/tmpYE8cIL/functional_tests_wsgi.ini galaxy.jobs DEBUG 2016-04-14 15:51:11,134 Done loading job configuration beaker.container DEBUG 2016-04-14 15:51:11,157 data file /tmp/714401.1.short.q/tmpAQxCGj/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache galaxy.tools.toolbox.watcher INFO 2016-04-14 15:51:11,158 Watchdog library unavailble, cannot monitor tools. galaxy.tools.toolbox.base INFO 2016-04-14 15:51:11,158 Parsing the tool configuration /tmp/714401.1.short.q/tmpAQxCGj/tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-14 15:51:11,169 Parsing the tool configuration /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-14 15:51:11,206 Parsing the tool configuration /tmp/714401.1.short.q/tmpAQxCGj/empty_tool_conf.xml galaxy.tools.toolbox.base DEBUG 2016-04-14 15:51:11,206 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2016-04-14 15:51:11,206 Loading section: Shed Installs galaxy.tools.toolbox.base DEBUG 2016-04-14 15:51:11,387 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3, version: 2.1.3 into tool panel.... galaxy.tools.deps DEBUG 2016-04-14 15:51:11,389 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.search DEBUG 2016-04-14 15:51:11,458 Starting to build toolbox index. galaxy.tools.search DEBUG 2016-04-14 15:51:11,851 Toolbox index finished. galaxy.tools.data_manager.manager DEBUG 2016-04-14 15:51:11,854 Loaded Data Manager: test_data_manager galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,857 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,859 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.display_applications.application ERROR 2016-04-14 15:51:11,862 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,862 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,863 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,863 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,864 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,866 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,867 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,869 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,870 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,876 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.display_applications.application ERROR 2016-04-14 15:51:11,878 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,878 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,879 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,885 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,894 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,895 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.display_applications.application ERROR 2016-04-14 15:51:11,897 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,897 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,900 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,903 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.display_applications.application ERROR 2016-04-14 15:51:11,905 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,905 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,906 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,907 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.display_applications.application ERROR 2016-04-14 15:51:11,909 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,909 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,910 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,910 Adding inherited display application 'igv_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,910 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,910 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,911 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,911 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,911 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,911 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,911 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,911 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,912 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,913 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,914 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,914 Adding inherited display application 'igv_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,914 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,914 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,914 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,914 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,916 Loaded converter: CONVERTER_Bam_Bai_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,917 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,918 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,919 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,920 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,921 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,922 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,923 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,924 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,925 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,926 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,928 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,928 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,930 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,931 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,932 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,933 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,934 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,935 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,936 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,937 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,938 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,939 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,940 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,941 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,942 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,943 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,944 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,945 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,946 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,947 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,948 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,949 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,950 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,951 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,952 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,953 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,954 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,957 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,957 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,959 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,960 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,961 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,962 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,963 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,964 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,965 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,966 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,967 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,968 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,969 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,970 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,971 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,972 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,973 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,974 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,975 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2016-04-14 15:51:11,977 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2016-04-14 15:51:11,978 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2016-04-14 15:51:11,980 Loaded history export tool: __EXPORT_HISTORY__ galaxy.web.base.pluginframework INFO 2016-04-14 15:51:11,981 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2016-04-14 15:51:11,982 Visualizations plugin disabled: Circster. Skipping... galaxy.visualization.plugins.config_parser INFO 2016-04-14 15:51:11,982 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2016-04-14 15:51:11,983 VisualizationsRegistry, loaded plugin: csg galaxy.web.base.pluginframework INFO 2016-04-14 15:51:11,983 VisualizationsRegistry, loaded plugin: graphview galaxy.visualization.plugins.config_parser INFO 2016-04-14 15:51:11,984 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2016-04-14 15:51:11,984 VisualizationsRegistry, loaded plugin: graphviz galaxy.web.base.pluginframework INFO 2016-04-14 15:51:11,985 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2016-04-14 15:51:11,986 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2016-04-14 15:51:11,987 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2016-04-14 15:51:11,988 VisualizationsRegistry, loaded plugin: trackster galaxy.tours INFO 2016-04-14 15:51:12,032 Loaded tour 'core.galaxy_ui' galaxy.tours INFO 2016-04-14 15:51:12,065 Loaded tour 'core.history' galaxy.jobs.manager DEBUG 2016-04-14 15:51:12,069 Starting job handler galaxy.jobs INFO 2016-04-14 15:51:12,069 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-14 15:51:12,069 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2016-04-14 15:51:12,069 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2016-04-14 15:51:12,071 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-14 15:51:12,072 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2016-04-14 15:51:12,073 Starting 2 TaskRunner workers galaxy.jobs DEBUG 2016-04-14 15:51:12,073 Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks' galaxy.jobs DEBUG 2016-04-14 15:51:12,073 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2016-04-14 15:51:12,073 Loaded job runners plugins: tasks:local galaxy.jobs.handler INFO 2016-04-14 15:51:12,074 job handler stop queue started galaxy.jobs.handler INFO 2016-04-14 15:51:12,091 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2016-04-14 15:51:12,098 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2016-04-14 15:51:12,100 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.workflow.scheduling_manager DEBUG 2016-04-14 15:51:12,103 Starting workflow schedulers functional_tests.py INFO 2016-04-14 15:51:12,110 Embedded Universe application started galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,117 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,120 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,121 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,121 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,123 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,126 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,126 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,128 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,134 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,134 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,134 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,135 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,135 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,135 Enabling 'search' controller, class: SearchController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,136 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,136 Enabling 'mobile' controller, class: Mobile galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,203 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,203 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,204 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,204 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,205 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,205 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,207 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,208 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,208 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,209 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,209 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,209 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,209 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,211 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,212 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,213 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,213 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,214 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,214 Enabling 'tours' API controller, class: ToursController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,215 Enabling 'remote_files' API controller, class: RemoteFilesAPIController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,215 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,215 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,216 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,216 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,216 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,216 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,217 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,217 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,218 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,218 Enabling 'page_revisions' API controller, class: PageRevisionsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,218 Enabling 'pages' API controller, class: PagesController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,218 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,219 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,219 Enabling 'metrics' API controller, class: MetricsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,219 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,220 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,220 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,220 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,220 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,221 Enabling 'jobs' API controller, class: JobController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,238 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,238 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,239 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,240 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,240 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,240 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,241 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,241 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,242 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,242 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,242 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,243 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,243 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,244 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,244 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,244 Enabling 'job_files' API controller, class: JobFilesAPIController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,245 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,245 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,245 Enabling 'tool_data' API controller, class: ToolData galaxy.web.framework.base DEBUG 2016-04-14 15:51:12,246 Enabling 'authenticate' API controller, class: AuthenticationController galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,706 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,707 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,716 Enabling 'error' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,716 Enabling 'x-forwarded-host' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,716 Enabling 'Request ID' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,722 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,722 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,722 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,722 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 15:51:12,722 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.queue_worker INFO 2016-04-14 15:51:12,723 Binding and starting galaxy control worker for main functional_tests.py DEBUG 2016-04-14 15:51:12,732 Attempting to serve app on randomly chosen port: 9732 functional_tests.py INFO 2016-04-14 15:51:12,874 Embedded web server started functional_tests.py INFO 2016-04-14 15:51:12,875 Functional tests will be run against localhost:9732 galaxy.tools.toolbox.watcher INFO 2016-04-14 15:51:12,876 Watchdog library unavailble, cannot monitor tools. galaxy.tools.toolbox.base INFO 2016-04-14 15:51:12,876 Parsing the tool configuration /tmp/714401.1.short.q/tmpAQxCGj/tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-14 15:51:12,876 Parsing the tool configuration /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-14 15:51:12,902 Parsing the tool configuration /tmp/714401.1.short.q/tmpAQxCGj/empty_tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-14 15:51:12,902 Parsing the tool configuration /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/config/shed_tool_conf.xml galaxy.tools.toolbox.base DEBUG 2016-04-14 15:51:12,980 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2016-04-14 15:51:12,980 Loading section: Shed Installs galaxy.tools.toolbox.base DEBUG 2016-04-14 15:51:13,221 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3, version: 2.1.3 into tool panel.... galaxy.tools.deps DEBUG 2016-04-14 15:51:13,221 Unable to find config file './dependency_resolvers_conf.xml' [?1034hbase.asserts DEBUG 2016-04-14 15:51:13,594 base.asserts.text base.asserts DEBUG 2016-04-14 15:51:13,595 base.asserts.tabular base.asserts DEBUG 2016-04-14 15:51:13,595 base.asserts.xml nose.plugins.manager DEBUG 2016-04-14 15:51:13,605 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:13,786 Starting new HTTP connection (1): localhost galaxy.web.framework.webapp INFO 2016-04-14 15:51:13,791 Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:13,802 "GET /api/users?key=test_key HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:14,070 Starting new HTTP connection (1): localhost galaxy.web.framework.webapp INFO 2016-04-14 15:51:14,073 Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:14,563 "POST /api/users HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:14,564 Starting new HTTP connection (1): localhost galaxy.web.framework.webapp INFO 2016-04-14 15:51:14,570 Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:14,637 "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:14,639 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:14,809 "POST /api/histories HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:14,825 Starting new HTTP connection (1): localhost galaxy.tools DEBUG 2016-04-14 15:51:15,045 Validated and populated state for tool request (19.760 ms) galaxy.tools.actions.upload DEBUG 2016-04-14 15:51:15,091 Persisted uploads (22.581 ms) galaxy.tools.actions.upload DEBUG 2016-04-14 15:51:15,578 Checked and cleaned uploads (487.187 ms) galaxy.tools.actions.upload_common INFO 2016-04-14 15:51:15,694 tool upload1 created job id 1 galaxy.tools.actions.upload DEBUG 2016-04-14 15:51:15,821 Created upload job (242.417 ms) galaxy.tools.execute DEBUG 2016-04-14 15:51:15,821 Tool [upload1] created job [1] (752.711 ms) galaxy.tools.execute DEBUG 2016-04-14 15:51:15,840 Executed all jobs for tool request: (795.117 ms) requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:15,876 "POST /api/tools HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:15,878 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:15,962 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:15,964 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:16,048 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:16,050 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:16,134 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:16,136 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:16,220 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:16,222 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:16,302 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:16,304 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:16,392 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:16,394 Starting new HTTP connection (1): localhost galaxy.jobs DEBUG 2016-04-14 15:51:16,469 (1) Working directory for job is: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1 galaxy.jobs.handler DEBUG 2016-04-14 15:51:16,519 (1) Dispatching to local runner galaxy.jobs DEBUG 2016-04-14 15:51:16,623 (1) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:16,655 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:16,657 Starting new HTTP connection (1): localhost galaxy.jobs.runners DEBUG 2016-04-14 15:51:16,713 Job [1] queued (194.097 ms) galaxy.jobs.handler INFO 2016-04-14 15:51:16,754 (1) Job dispatched requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:16,930 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:16,933 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:17,176 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:17,177 Starting new HTTP connection (1): localhost galaxy.tools.deps DEBUG 2016-04-14 15:51:17,460 Building dependency shell command for dependency 'samtools' galaxy.tools.deps DEBUG 2016-04-14 15:51:17,460 Find dependency samtools version None galaxy.tools.deps DEBUG 2016-04-14 15:51:17,461 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 15:51:17,461 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 15:51:17,461 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 15:51:17,462 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 15:51:17,462 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:17,462 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None galaxy.tools.deps WARNING 2016-04-14 15:51:17,462 Failed to resolve dependency on 'samtools', ignoring requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:17,467 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:17,579 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None galaxy.jobs.command_factory INFO 2016-04-14 15:51:17,580 Built script [/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev/tools/data_source/upload.py /tmp/714401.1.short.q/tmpAQxCGj/galaxy-dev /tmp/714401.1.short.q/tmpAQxCGj/tmp/tmpLPOdzn /tmp/714401.1.short.q/tmpAQxCGj/tmp/tmp0jkGJc 1:/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/dataset_1_files:/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat] requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:17,585 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:17,877 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:17,879 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:18,065 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:18,067 Starting new HTTP connection (1): localhost galaxy.jobs.runners DEBUG 2016-04-14 15:51:18,069 (1) command is: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/set_metadata_XVRZb9.py" "/tmp/714401.1.short.q/tmpAQxCGj/tmp/tmpLPOdzn" "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/galaxy.json" "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_2H7S7g,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_bwLNVA,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_jembhp,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_7Ch0tX,/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_lR53Ty" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2016-04-14 15:51:18,085 (1) executing job script: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/galaxy_1.sh galaxy.jobs DEBUG 2016-04-14 15:51:18,094 (1) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:18,245 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None galaxy.jobs.runners.local DEBUG 2016-04-14 15:51:21,083 execution finished: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/1/galaxy_1.sh requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:21,084 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:21,293 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:21,295 Starting new HTTP connection (1): localhost galaxy.datatypes.metadata DEBUG 2016-04-14 15:51:21,348 loading metadata from file for: HistoryDatasetAssociation 1 requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:21,606 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:21,608 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:21,789 "GET /api/histories/2891970512fa2d5a?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:21,791 Starting new HTTP connection (1): localhost galaxy.tools DEBUG 2016-04-14 15:51:21,898 Validated and populated state for tool request (72.417 ms) galaxy.tools.actions INFO 2016-04-14 15:51:22,068 Handled output (99.542 ms) galaxy.jobs DEBUG 2016-04-14 15:51:22,129 job 1 ended (finish() executed in (1044.369 ms)) galaxy.tools.actions INFO 2016-04-14 15:51:22,213 Handled output (144.572 ms) galaxy.tools.actions INFO 2016-04-14 15:51:22,303 Handled output (90.577 ms) galaxy.tools.actions INFO 2016-04-14 15:51:22,388 Handled output (84.692 ms) galaxy.tools.actions INFO 2016-04-14 15:51:22,477 Verified access to datasets (7.993 ms) galaxy.tools.execute DEBUG 2016-04-14 15:51:22,596 Tool [testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3] created job [2] (651.728 ms) galaxy.tools.execute DEBUG 2016-04-14 15:51:22,614 Executed all jobs for tool request: (715.204 ms) requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:22,719 "POST /api/tools HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:22,721 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:22,870 "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None galaxy.jobs DEBUG 2016-04-14 15:51:23,004 (2) Working directory for job is: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2 galaxy.jobs.handler DEBUG 2016-04-14 15:51:23,020 (2) Dispatching to local runner galaxy.jobs DEBUG 2016-04-14 15:51:23,062 (2) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:23,073 Starting new HTTP connection (1): localhost galaxy.jobs.runners DEBUG 2016-04-14 15:51:23,141 Job [2] queued (121.409 ms) galaxy.jobs.handler INFO 2016-04-14 15:51:23,213 (2) Job dispatched requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:23,326 "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None galaxy.tools.deps DEBUG 2016-04-14 15:51:23,695 Building dependency shell command for dependency 'R' galaxy.tools.deps DEBUG 2016-04-14 15:51:23,696 Find dependency R version 3.1.2 galaxy.tools.deps DEBUG 2016-04-14 15:51:23,704 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b7e7c239b10> (isnull? False) galaxy.tools.deps DEBUG 2016-04-14 15:51:23,704 Building dependency shell command for dependency 'r-snow' galaxy.tools.deps DEBUG 2016-04-14 15:51:23,704 Find dependency r-snow version 0.4_1 galaxy.tools.deps DEBUG 2016-04-14 15:51:23,704 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps WARNING 2016-04-14 15:51:23,705 Failed to resolve dependency on 'r-snow', ignoring galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Building dependency shell command for dependency 'bioconductor-camera' galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Find dependency bioconductor-camera version 1.22.0 galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b7e7c268890> (isnull? False) galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Building dependency shell command for dependency 'r-batch' galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Find dependency r-batch version 1.1_4 galaxy.tools.deps DEBUG 2016-04-14 15:51:23,705 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 15:51:23,706 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 15:51:23,706 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 15:51:23,706 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 15:51:23,706 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x47bf090> (isnull? True) galaxy.tools.deps WARNING 2016-04-14 15:51:23,706 Failed to resolve dependency on 'r-batch', ignoring galaxy.tools.deps DEBUG 2016-04-14 15:51:23,706 Building dependency shell command for dependency 'graphicsmagick' galaxy.tools.deps DEBUG 2016-04-14 15:51:23,706 Find dependency graphicsmagick version 1.3.20 galaxy.tools.deps DEBUG 2016-04-14 15:51:23,706 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b7ec80fead0> (isnull? False) requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:23,729 Starting new HTTP connection (1): localhost galaxy.jobs.command_factory INFO 2016-04-14 15:51:23,830 Built script [/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/714401.1.short.q/tmpAQxCGj/deps/R/3.1.2/lecorguille/camera_annotate/01a900f2e464; export PACKAGE_BASE; . /tmp/714401.1.short.q/tmpAQxCGj/deps/R/3.1.2/lecorguille/camera_annotate/01a900f2e464/env.sh; PACKAGE_BASE=/tmp/714401.1.short.q/tmpAQxCGj/deps/bioconductor-camera/1.22.0/lecorguille/camera_annotate/01a900f2e464; export PACKAGE_BASE; . /tmp/714401.1.short.q/tmpAQxCGj/deps/bioconductor-camera/1.22.0/lecorguille/camera_annotate/01a900f2e464/env.sh; PACKAGE_BASE=/tmp/714401.1.short.q/tmpAQxCGj/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/01a900f2e464; export PACKAGE_BASE; . /tmp/714401.1.short.q/tmpAQxCGj/deps/graphicsmagick/1.3.20/lecorguille/camera_annotate/01a900f2e464/env.sh; LANG=C Rscript /tmp/714401.1.short.q/tmpAQxCGj/shed_tools/testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/01a900f2e464/camera_annotate/CAMERA.r xfunction annotatediff image /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_1.dat variableMetadataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat dataMatrixOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat xsetRdataOutput /tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat convert_param FALSE num_digits 0 nSlaves ${GALAXY_SLOTS:-1} sigma 6 perfwhm 0.6 maxcharge 3 maxiso 4 minfrac 0.5 ppm 5 mzabs 0.015 intval into max_peaks 100 quick FALSE polarity negative cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE multiplier 3 runDiffreport TRUE eicmax 200 eicwidth 200 value into sortpval FALSE h 480 w 640 mzdec 2 new_file_path /tmp/714401.1.short.q/tmpAQxCGj/tmp/primary_5_] requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:23,968 "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:24,771 Starting new HTTP connection (1): localhost galaxy.jobs.runners DEBUG 2016-04-14 15:51:24,772 (2) command is: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/tool_script.sh; return_code=$?; python "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/set_metadata_nPFswU.py" "/tmp/714401.1.short.q/tmpAQxCGj/tmp/tmpLPOdzn" "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/galaxy.json" "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_bsNzU9,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_ktNnvu,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_6PXLPl,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_db7cVH,/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_2.dat,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_7qIivj" "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_3_j4Mjr6,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_3_ir7l9Z,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_3_SuHDrD,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_3_ruts7J,/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_3.dat,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_3_jvOjlv" "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_4_3zPwDY,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_4_2ztBlR,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_4_jkuI4N,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_4_ADypZO,/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_4.dat,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_4_xI2Wdp" "/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_5_ASl36X,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_5_QmXDdz,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_5_I6RNNV,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_5_SGtGLd,/tmp/714401.1.short.q/tmpAQxCGj/files/000/dataset_5.dat,/tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_5_V21r1c" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2016-04-14 15:51:24,795 (2) executing job script: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/galaxy_2.sh galaxy.jobs DEBUG 2016-04-14 15:51:24,808 (2) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:25,115 "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None galaxy.jobs.runners.local DEBUG 2016-04-14 15:51:47,359 execution finished: /tmp/714401.1.short.q/tmpAQxCGj/job_working_directory/000/2/galaxy_2.sh galaxy.jobs.output_checker INFO 2016-04-14 15:51:47,404 Job 2: Fatal error: Exit code 1 () galaxy.jobs.output_checker DEBUG 2016-04-14 15:51:47,404 Tool exit code indicates an error, failing job. galaxy.jobs DEBUG 2016-04-14 15:51:47,491 (2) setting dataset 2 state to ERROR galaxy.jobs DEBUG 2016-04-14 15:51:47,531 (2) setting dataset 3 state to ERROR galaxy.jobs DEBUG 2016-04-14 15:51:47,571 (2) setting dataset 4 state to ERROR galaxy.jobs DEBUG 2016-04-14 15:51:47,610 (2) setting dataset 5 state to ERROR galaxy.jobs DEBUG 2016-04-14 15:51:48,011 job 2 ended (finish() executed in (650.423 ms)) requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:48,962 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:49,130 "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:49,136 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:49,196 "GET /api/histories/2891970512fa2d5a/contents?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:49,198 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:49,375 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:49,377 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:49,509 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:49,511 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:49,680 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:49,682 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:49,805 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:49,808 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:49,997 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:49,999 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:50,149 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:50,152 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:50,490 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:50,492 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:50,615 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:50,617 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:50,786 "GET /api/jobs/5729865256bc2525?full=true&key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:50,788 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:50,969 "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:50,971 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:51,027 "GET /api/histories/2891970512fa2d5a/contents?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:51,028 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:51,229 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:51,231 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:51,352 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:51,354 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:51,547 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:51,549 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:51,669 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:51,672 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:51,842 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:51,844 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:51,963 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:51,965 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:52,209 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:52,212 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:52,336 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:52,339 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:52,493 "GET /api/jobs/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:52,496 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:52,565 "GET /api/histories/2891970512fa2d5a/contents?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:52,567 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:52,739 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:52,741 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:52,859 "GET /api/histories/2891970512fa2d5a/contents/5729865256bc2525/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:52,862 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:53,031 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:53,033 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:53,191 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:53,193 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:53,361 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:53,363 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:53,479 "GET /api/histories/2891970512fa2d5a/contents/8155e4b4bf1581ff/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:53,482 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:53,669 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 15:51:53,671 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 15:51:53,793 "GET /api/histories/2891970512fa2d5a/contents/7b55dbb89df8f4e5/provenance?key=7ce8ea2c34065bcdfd7a8363392dae90 HTTP/1.1" 200 None functional_tests.py INFO 2016-04-14 15:51:53,821 Shutting down functional_tests.py INFO 2016-04-14 15:51:53,821 Shutting down embedded web server functional_tests.py INFO 2016-04-14 15:51:53,823 Embedded web server stopped functional_tests.py INFO 2016-04-14 15:51:53,823 Shutting down app galaxy.jobs.handler INFO 2016-04-14 15:51:53,824 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-14 15:51:53,824 job handler queue stopped galaxy.jobs.runners INFO 2016-04-14 15:51:53,824 TaskRunner: Sending stop signal to 2 worker threads galaxy.jobs.runners INFO 2016-04-14 15:51:53,824 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2016-04-14 15:51:53,825 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-14 15:51:53,825 job handler stop queue stopped functional_tests.py INFO 2016-04-14 15:51:53,826 Embedded Universe application stopped functional_tests.py INFO 2016-04-14 15:51:53,826 Cleaning up temporary files in /tmp/714401.1.short.q/tmpYE8cIL/tmpVeogQe galaxy.jobs.handler INFO 2016-04-14 15:51:54,673 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-14 15:51:54,673 job handler queue stopped galaxy.jobs.runners INFO 2016-04-14 15:51:54,673 TaskRunner: Sending stop signal to 2 worker threads galaxy.jobs.runners INFO 2016-04-14 15:51:54,673 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2016-04-14 15:51:54,674 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-14 15:51:54,674 job handler stop queue stopped testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3[0]: failed