Mercurial > repos > lecorguille > camera_annotate
view qsub.out @ 12:db270f704d93 draft
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835-dirty
| author | lecorguille |
|---|---|
| date | Thu, 14 Apr 2016 11:00:27 -0400 |
| parents | d33e0ed5f32a |
| children | ba7db5b70639 |
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git --git-dir /home/fr2424/sib/lecorguille/.planemo/gx_repo fetch >/dev/null 2>&1 cd /tmp/714419.1.short.q/tmp6zzhM3; 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/714419.1.short.q/tmp6zzhM3/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/714419.1.short.q/tmp6zzhM3/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/714419.1.short.q/tmp6zzhM3/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/714419.1.short.q/tmp6zzhM3/galaxy-dev Testing tools with command [cd /tmp/714419.1.short.q/tmp6zzhM3/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/714419.1.short.q/tmp6zzhM3/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/714419.1.short.q/tmp6xBwof/tmpacHkJy/new_files_path_3hEYGU'), ('app:main', 'database_connection', 'sqlite:////tmp/714419.1.short.q/tmp6xBwof/tmpacHkJy/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/714419.1.short.q/tmpUKxFhz'), ('app:main', 'template_cache_path', '/tmp/714419.1.short.q/tmp6xBwof/tmpacHkJy/database/compiled_templates'), ('app:main', 'job_working_directory', '/tmp/714419.1.short.q/tmp6xBwof/tmpacHkJy/job_working_directory_faEKBn'), ('app:main', 'tool_dependency_dir', '/tmp/714419.1.short.q/tmp6zzhM3/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/714419.1.short.q/tmp6xBwof/data_manager_test_tmp8bCYlG/data_manager_tool-data1dSWwR'), ('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/714419.1.short.q/tmp6xBwof/tmpacHkJy/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 16:47:16,672 Initalizing main Galaxy Queue Worker on sqlalchemy+sqlite:// tool_shed.tool_shed_registry DEBUG 2016-04-14 16:47:16,721 Loading references to tool sheds from /tmp/714419.1.short.q/tmp6zzhM3/tool_sheds_conf.xml tool_shed.tool_shed_registry DEBUG 2016-04-14 16:47:16,722 Loaded reference to tool shed: Target Shed galaxy.app DEBUG 2016-04-14 16:47:16,723 Using "galaxy.ini" config file: /tmp/714419.1.short.q/tmp6xBwof/functional_tests_wsgi.ini migrate.versioning.repository DEBUG 2016-04-14 16:47:16,813 Loading repository lib/galaxy/model/migrate... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,814 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,814 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,814 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,814 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,814 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,814 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,814 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,814 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,814 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,815 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,815 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,815 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,815 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,815 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,815 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,815 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,815 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,815 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,815 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,815 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,816 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,816 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,816 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,816 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,816 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,816 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,816 Loading script lib/galaxy/model/migrate/versions/0014_pages.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,816 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,816 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,816 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,817 Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,817 Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,817 Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,817 Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,817 Loading script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,817 Script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,817 Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,817 Script lib/galaxy/model/migrate/versions/0019_request_library_folder.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,817 Loading script lib/galaxy/model/migrate/versions/0020_library_upload_job.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,817 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 16:47:16,833 Script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Loading script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Loading script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Loading script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Loading script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,833 Script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 Loading script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 Script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 Loading script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 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 16:47:16,834 Loading script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 Script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 Loading script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 Script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 Loading script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,834 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 16:47:16,836 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,836 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,836 Loading script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,836 Script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,836 Loading script lib/galaxy/model/migrate/versions/0119_job_metrics.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,836 Script lib/galaxy/model/migrate/versions/0119_job_metrics.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,836 Loading script lib/galaxy/model/migrate/versions/0120_dataset_collections.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,836 Script lib/galaxy/model/migrate/versions/0120_dataset_collections.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,836 Loading script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,836 Script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Loading script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Loading script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,837 Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py... migrate.versioning.script.base DEBUG 2016-04-14 16:47:16,838 Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully migrate.versioning.repository DEBUG 2016-04-14 16:47:16,838 Repository lib/galaxy/model/migrate loaded successfully migrate.versioning.repository DEBUG 2016-04-14 16:47:16,839 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) galaxy.config INFO 2016-04-14 16:47:16,909 Install database targetting Galaxy's database configuration. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,961 Loading datatypes from /tmp/714419.1.short.q/tmp6zzhM3/tmp/tmp-toolshed-acalpd4oJfOX galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,966 Loading datatypes from /tmp/714419.1.short.q/tmp6zzhM3/tmp/tmp-toolshed-acalpdGiP3GN galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,966 Exception importing proprietary code file /tmp/714419.1.short.q/tmp6zzhM3/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 16:47:16,966 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,984 Loading datatypes from ./config/datatypes_conf.xml.sample galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,985 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,985 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,986 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,987 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,987 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,987 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,987 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,987 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,988 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,988 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,988 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,988 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,988 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,988 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,989 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,989 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,989 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,989 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,990 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,990 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,990 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,990 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,991 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,991 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,991 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,991 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,991 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,992 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,992 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,992 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,992 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,992 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,992 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,993 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,993 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,993 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,993 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,993 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,993 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,994 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,994 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,994 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,994 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,994 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,994 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,995 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,995 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,995 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,995 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,996 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,996 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,996 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,996 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,997 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,997 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,997 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,997 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,997 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,997 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,998 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,998 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,998 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,998 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,998 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,998 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,999 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:16,999 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,001 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,001 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,001 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,002 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,002 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,002 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,002 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,003 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,003 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,003 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,003 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,003 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,003 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,004 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,004 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,004 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,004 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,004 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,004 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,005 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,005 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,005 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,005 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,005 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,005 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,006 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,006 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,006 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,006 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,006 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,006 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,007 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,007 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,007 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,007 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,007 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,007 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,008 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,008 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,008 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,008 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,008 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,008 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,009 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,009 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,009 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,009 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,009 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,009 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,010 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,010 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,010 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,010 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,010 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,010 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,011 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,011 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,011 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,011 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,011 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,011 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,012 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,012 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,012 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,012 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,012 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,012 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,013 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,013 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,013 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,013 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,013 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,013 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,014 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,014 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,014 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,014 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,014 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,015 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,015 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,015 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,015 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,019 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,019 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,019 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,020 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,020 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,020 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,020 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,020 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,021 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,021 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,021 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,021 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,021 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,021 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,022 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,022 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,022 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,022 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,022 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,022 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,023 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,024 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,024 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,025 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,025 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,025 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,025 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,025 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,026 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,028 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,028 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,028 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,028 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,028 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,029 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,029 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,029 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,029 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,030 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,031 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,031 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,031 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,031 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,032 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,032 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,032 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,032 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,033 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,033 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,033 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,033 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,033 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,034 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,034 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,034 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,034 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,035 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,035 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,035 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,035 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,035 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,036 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,037 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,037 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,037 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,037 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,038 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,039 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,039 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,039 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,039 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,040 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,040 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,040 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,040 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,041 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,041 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,041 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,041 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,041 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,042 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,042 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,042 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,042 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,042 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,043 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,043 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,043 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,043 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,044 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,044 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,044 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,044 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,044 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,045 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,045 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,045 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,045 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,046 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,046 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,046 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,046 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,047 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,047 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,048 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,048 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,048 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,048 Overriding conflicting datatype with extension 'rdata', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,048 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,048 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,049 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,049 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,049 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,049 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,050 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,050 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,051 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,051 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,051 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,051 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,052 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,052 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,052 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,052 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,052 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,052 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,052 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,053 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,054 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,055 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,055 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,055 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,055 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,055 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,055 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,055 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Removed conflicting sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,056 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,057 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Removed conflicting sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,058 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,059 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,060 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,061 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,062 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,063 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,064 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,064 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,064 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,064 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,064 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,064 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,065 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,065 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,065 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,065 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,065 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,065 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,065 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,066 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,066 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,066 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 16:47:17,066 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 16:47:17,066 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,066 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,067 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt galaxy.datatypes.registry DEBUG 2016-04-14 16:47:17,067 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt galaxy.jobs WARNING 2016-04-14 16:47:17,140 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/714419.1.short.q/tmp6xBwof/functional_tests_wsgi.ini" instead galaxy.jobs DEBUG 2016-04-14 16:47:17,140 Loading job configuration from /tmp/714419.1.short.q/tmp6xBwof/functional_tests_wsgi.ini galaxy.jobs DEBUG 2016-04-14 16:47:17,140 Done loading job configuration beaker.container DEBUG 2016-04-14 16:47:17,171 data file /tmp/714419.1.short.q/tmp6zzhM3/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache galaxy.tools.toolbox.watcher INFO 2016-04-14 16:47:17,172 Watchdog library unavailble, cannot monitor tools. galaxy.tools.toolbox.base INFO 2016-04-14 16:47:17,172 Parsing the tool configuration /tmp/714419.1.short.q/tmp6zzhM3/tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-14 16:47:17,186 Parsing the tool configuration /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-14 16:47:17,233 Parsing the tool configuration /tmp/714419.1.short.q/tmp6zzhM3/empty_tool_conf.xml galaxy.tools.toolbox.base DEBUG 2016-04-14 16:47:17,233 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2016-04-14 16:47:17,233 Loading section: Shed Installs galaxy.tools.toolbox.base DEBUG 2016-04-14 16:47:17,463 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 16:47:17,465 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.search DEBUG 2016-04-14 16:47:17,552 Starting to build toolbox index. galaxy.tools.search DEBUG 2016-04-14 16:47:18,060 Toolbox index finished. galaxy.tools.data_manager.manager DEBUG 2016-04-14 16:47:18,064 Loaded Data Manager: test_data_manager galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,068 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,072 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.display_applications.application ERROR 2016-04-14 16:47:18,075 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 16:47:18,075 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,076 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,077 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,077 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,081 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,081 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,085 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,085 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,094 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.display_applications.application ERROR 2016-04-14 16:47:18,096 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 16:47:18,097 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,097 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,106 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,118 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,119 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.display_applications.application ERROR 2016-04-14 16:47:18,123 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 16:47:18,123 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,126 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,130 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.display_applications.application ERROR 2016-04-14 16:47:18,133 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 16:47:18,133 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,134 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,135 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.display_applications.application ERROR 2016-04-14 16:47:18,139 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 16:47:18,139 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,139 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,139 Adding inherited display application 'igv_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,140 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,140 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,140 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,141 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,141 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,141 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,141 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,141 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,142 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,142 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,142 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,142 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,143 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,143 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,143 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,143 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,144 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,145 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,145 Adding inherited display application 'igv_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,145 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,146 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,146 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,146 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,148 Loaded converter: CONVERTER_Bam_Bai_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,149 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,151 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,152 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,154 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,155 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,156 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,158 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,159 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,160 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,162 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,163 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,165 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,166 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,168 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,169 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,171 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,172 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,173 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,175 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,176 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,177 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,179 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,180 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,181 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,182 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,183 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,184 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,185 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,186 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,187 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,188 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,189 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,190 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,191 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,192 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,193 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,194 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,196 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,197 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,198 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,199 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,201 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,202 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,203 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,204 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,205 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,206 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,207 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,208 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,209 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,210 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,211 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,212 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,213 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,214 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,215 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2016-04-14 16:47:18,216 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2016-04-14 16:47:18,218 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2016-04-14 16:47:18,220 Loaded history export tool: __EXPORT_HISTORY__ galaxy.web.base.pluginframework INFO 2016-04-14 16:47:18,221 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2016-04-14 16:47:18,221 Visualizations plugin disabled: Circster. Skipping... galaxy.visualization.plugins.config_parser INFO 2016-04-14 16:47:18,222 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2016-04-14 16:47:18,222 VisualizationsRegistry, loaded plugin: csg galaxy.web.base.pluginframework INFO 2016-04-14 16:47:18,223 VisualizationsRegistry, loaded plugin: graphview galaxy.visualization.plugins.config_parser INFO 2016-04-14 16:47:18,224 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2016-04-14 16:47:18,224 VisualizationsRegistry, loaded plugin: graphviz galaxy.web.base.pluginframework INFO 2016-04-14 16:47:18,225 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2016-04-14 16:47:18,226 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2016-04-14 16:47:18,226 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2016-04-14 16:47:18,227 VisualizationsRegistry, loaded plugin: trackster galaxy.tours INFO 2016-04-14 16:47:18,261 Loaded tour 'core.history' galaxy.tours INFO 2016-04-14 16:47:18,304 Loaded tour 'core.galaxy_ui' galaxy.jobs.manager DEBUG 2016-04-14 16:47:18,308 Starting job handler galaxy.jobs INFO 2016-04-14 16:47:18,308 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-14 16:47:18,308 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2016-04-14 16:47:18,309 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2016-04-14 16:47:18,310 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-14 16:47:18,311 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2016-04-14 16:47:18,312 Starting 2 TaskRunner workers galaxy.jobs DEBUG 2016-04-14 16:47:18,312 Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks' galaxy.jobs DEBUG 2016-04-14 16:47:18,312 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2016-04-14 16:47:18,312 Loaded job runners plugins: tasks:local galaxy.jobs.handler INFO 2016-04-14 16:47:18,313 job handler stop queue started galaxy.jobs.handler INFO 2016-04-14 16:47:18,332 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2016-04-14 16:47:18,340 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2016-04-14 16:47:18,343 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.workflow.scheduling_manager DEBUG 2016-04-14 16:47:18,347 Starting workflow schedulers functional_tests.py INFO 2016-04-14 16:47:18,352 Embedded Universe application started galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,453 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,453 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,456 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,462 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,464 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,464 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,464 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,466 Enabling 'mobile' controller, class: Mobile galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,466 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,467 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,468 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,469 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,469 Enabling 'search' controller, class: SearchController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,470 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,471 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,471 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,471 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,471 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,473 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,474 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,476 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,477 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,478 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,478 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,478 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,479 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,480 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,480 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,481 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,484 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,484 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,485 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,485 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,486 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,486 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,486 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,487 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,488 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,488 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,488 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,489 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,490 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,490 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,491 Enabling 'pages' API controller, class: PagesController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,492 Enabling 'remote_files' API controller, class: RemoteFilesAPIController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,492 Enabling 'page_revisions' API controller, class: PageRevisionsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,493 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,494 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,494 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,517 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,517 Enabling 'tours' API controller, class: ToursController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,518 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,518 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,519 Enabling 'metrics' API controller, class: MetricsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,519 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,520 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,521 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,522 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,522 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,523 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,523 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,524 Enabling 'tool_data' API controller, class: ToolData galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,524 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,524 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,525 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,525 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,525 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,526 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,526 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,526 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,527 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,527 Enabling 'authenticate' API controller, class: AuthenticationController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,527 Enabling 'job_files' API controller, class: JobFilesAPIController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,528 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,529 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2016-04-14 16:47:18,529 Enabling 'jobs' API controller, class: JobController galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,121 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,123 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,133 Enabling 'error' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,133 Enabling 'x-forwarded-host' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,133 Enabling 'Request ID' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,140 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,140 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,141 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,141 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-14 16:47:19,141 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.queue_worker INFO 2016-04-14 16:47:19,141 Binding and starting galaxy control worker for main functional_tests.py DEBUG 2016-04-14 16:47:19,153 Attempting to serve app on randomly chosen port: 9558 functional_tests.py INFO 2016-04-14 16:47:19,592 Embedded web server started functional_tests.py INFO 2016-04-14 16:47:19,592 Functional tests will be run against localhost:9558 galaxy.tools.toolbox.watcher INFO 2016-04-14 16:47:19,594 Watchdog library unavailble, cannot monitor tools. galaxy.tools.toolbox.base INFO 2016-04-14 16:47:19,594 Parsing the tool configuration /tmp/714419.1.short.q/tmp6zzhM3/tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-14 16:47:19,594 Parsing the tool configuration /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-14 16:47:19,626 Parsing the tool configuration /tmp/714419.1.short.q/tmp6zzhM3/empty_tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-14 16:47:19,627 Parsing the tool configuration /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/config/shed_tool_conf.xml galaxy.tools.toolbox.base DEBUG 2016-04-14 16:47:19,724 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2016-04-14 16:47:19,724 Loading section: Shed Installs galaxy.tools.toolbox.base DEBUG 2016-04-14 16:47:19,909 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 16:47:19,910 Unable to find config file './dependency_resolvers_conf.xml' [?1034hbase.asserts DEBUG 2016-04-14 16:47:20,293 base.asserts.text base.asserts DEBUG 2016-04-14 16:47:20,293 base.asserts.tabular base.asserts DEBUG 2016-04-14 16:47:20,294 base.asserts.xml nose.plugins.manager DEBUG 2016-04-14 16:47:20,314 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:20,514 Starting new HTTP connection (1): localhost galaxy.web.framework.webapp INFO 2016-04-14 16:47:20,519 Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:20,533 "GET /api/users?key=test_key HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:20,788 Starting new HTTP connection (1): localhost galaxy.web.framework.webapp INFO 2016-04-14 16:47:20,792 Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:21,379 "POST /api/users HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:21,381 Starting new HTTP connection (1): localhost galaxy.web.framework.webapp INFO 2016-04-14 16:47:21,385 Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:21,446 "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:21,448 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:21,624 "POST /api/histories HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:21,644 Starting new HTTP connection (1): localhost galaxy.tools DEBUG 2016-04-14 16:47:21,914 Validated and populated state for tool request (26.178 ms) galaxy.tools.actions.upload DEBUG 2016-04-14 16:47:21,974 Persisted uploads (29.632 ms) galaxy.tools.actions.upload DEBUG 2016-04-14 16:47:22,425 Checked and cleaned uploads (450.856 ms) galaxy.tools.actions.upload_common INFO 2016-04-14 16:47:22,521 tool upload1 created job id 1 galaxy.tools.actions.upload DEBUG 2016-04-14 16:47:22,655 Created upload job (229.375 ms) galaxy.tools.execute DEBUG 2016-04-14 16:47:22,655 Tool [upload1] created job [1] (710.457 ms) galaxy.tools.execute DEBUG 2016-04-14 16:47:22,674 Executed all jobs for tool request: (759.156 ms) requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:22,708 "POST /api/tools HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:22,710 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:22,813 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:22,816 Starting new HTTP connection (1): localhost galaxy.jobs DEBUG 2016-04-14 16:47:22,927 (1) Working directory for job is: /tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1 requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:22,959 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:22,963 Starting new HTTP connection (1): localhost galaxy.jobs.handler DEBUG 2016-04-14 16:47:22,964 (1) Dispatching to local runner galaxy.jobs DEBUG 2016-04-14 16:47:23,090 (1) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2016-04-14 16:47:23,172 Job [1] queued (204.971 ms) galaxy.jobs.handler INFO 2016-04-14 16:47:23,227 (1) Job dispatched requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:23,290 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:23,293 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:23,562 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:23,568 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:23,913 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:23,915 Starting new HTTP connection (1): localhost galaxy.tools.deps DEBUG 2016-04-14 16:47:23,998 Building dependency shell command for dependency 'samtools' galaxy.tools.deps DEBUG 2016-04-14 16:47:23,998 Find dependency samtools version None galaxy.tools.deps DEBUG 2016-04-14 16:47:23,998 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 16:47:23,999 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 16:47:23,999 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 16:47:24,000 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) galaxy.tools.deps DEBUG 2016-04-14 16:47:24,001 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x420c0d0> (isnull? True) galaxy.tools.deps WARNING 2016-04-14 16:47:24,001 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.command_factory INFO 2016-04-14 16:47:24,110 Built script [/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev/tools/data_source/upload.py /tmp/714419.1.short.q/tmp6zzhM3/galaxy-dev /tmp/714419.1.short.q/tmp6zzhM3/tmp/tmpjP3KUB /tmp/714419.1.short.q/tmp6zzhM3/tmp/tmpNZ2o6u 1:/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/dataset_1_files:/tmp/714419.1.short.q/tmp6zzhM3/files/000/dataset_1.dat] requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:24,160 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:24,164 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:24,477 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:24,480 Starting new HTTP connection (1): localhost galaxy.jobs.runners DEBUG 2016-04-14 16:47:24,679 (1) command is: /tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/set_metadata_MqaJuZ.py" "/tmp/714419.1.short.q/tmp6zzhM3/tmp/tmpjP3KUB" "/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/galaxy.json" "/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_GavpWf,/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_X9MeXX,/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_SKjWPt,/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_WKXGCU,/tmp/714419.1.short.q/tmp6zzhM3/files/000/dataset_1.dat,/tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_48OdEJ" 5242880; sh -c "exit $return_code" requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:24,695 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None galaxy.jobs.runners.local DEBUG 2016-04-14 16:47:24,698 (1) executing job script: /tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/galaxy_1.sh requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:24,704 Starting new HTTP connection (1): localhost galaxy.jobs DEBUG 2016-04-14 16:47:24,711 (1) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:24,969 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:24,972 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,131 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,133 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,237 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,239 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,387 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,397 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,499 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,502 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,605 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,607 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,752 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,754 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,856 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,858 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:25,961 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:25,964 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,065 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,068 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,171 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,173 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,277 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,280 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,380 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,383 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,528 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,530 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,631 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,633 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,750 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,753 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,858 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,860 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:26,962 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:26,965 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,067 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,069 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,171 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,174 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,275 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,277 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,378 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,380 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,548 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,550 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,651 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,653 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,767 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,770 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,870 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,872 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:27,975 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:27,977 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:28,080 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:28,083 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:28,184 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:28,185 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:28,287 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:28,288 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:28,400 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:28,402 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:28,504 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:28,506 Starting new HTTP connection (1): localhost galaxy.jobs.runners.local DEBUG 2016-04-14 16:47:28,549 execution finished: /tmp/714419.1.short.q/tmp6zzhM3/job_working_directory/000/1/galaxy_1.sh requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:28,869 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:28,871 Starting new HTTP connection (1): localhost galaxy.datatypes.metadata DEBUG 2016-04-14 16:47:29,058 loading metadata from file for: HistoryDatasetAssociation 1 requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:29,102 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-14 16:47:29,105 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-14 16:47:29,415 "GET /api/histories/2891970512fa2d5a?key=d60dee226c7d93c090d051c4571345f0 HTTP/1.1" 200 None functional_tests.py INFO 2016-04-14 16:47:29,425 Shutting down functional_tests.py INFO 2016-04-14 16:47:29,425 Shutting down embedded web server functional_tests.py INFO 2016-04-14 16:47:29,428 Embedded web server stopped functional_tests.py INFO 2016-04-14 16:47:29,428 Shutting down app galaxy.jobs.handler INFO 2016-04-14 16:47:29,428 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-14 16:47:29,428 job handler queue stopped galaxy.jobs.runners INFO 2016-04-14 16:47:29,428 TaskRunner: Sending stop signal to 2 worker threads galaxy.jobs.runners INFO 2016-04-14 16:47:29,428 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2016-04-14 16:47:29,429 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-14 16:47:29,429 job handler stop queue stopped functional_tests.py INFO 2016-04-14 16:47:29,429 Embedded Universe application stopped functional_tests.py INFO 2016-04-14 16:47:29,429 Cleaning up temporary files in /tmp/714419.1.short.q/tmp6xBwof/tmpacHkJy galaxy.jobs DEBUG 2016-04-14 16:47:29,555 job 1 ended (finish() executed in (1006.205 ms)) galaxy.jobs.handler INFO 2016-04-14 16:47:30,107 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-14 16:47:30,107 job handler queue stopped galaxy.jobs.runners INFO 2016-04-14 16:47:30,107 TaskRunner: Sending stop signal to 2 worker threads galaxy.jobs.runners INFO 2016-04-14 16:47:30,107 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2016-04-14 16:47:30,107 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-14 16:47:30,107 job handler stop queue stopped testtoolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3[0]: failed