Mercurial > repos > mmonsoor > camera_combinexsannos
view qsub.out @ 3:f5372f7c831a draft
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835-dirty
| author | lecorguille |
|---|---|
| date | Tue, 12 Apr 2016 04:14:10 -0400 |
| parents | |
| children |
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git --git-dir /home/fr2424/sib/lecorguille/.planemo/gx_repo fetch >/dev/null 2>&1 cd /tmp/713105.1.short.q/tmpP_qIg6; 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/713105.1.short.q/tmpP_qIg6/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/713105.1.short.q/tmpP_qIg6/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/713105.1.short.q/tmpP_qIg6/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/713105.1.short.q/tmpP_qIg6/galaxy-dev Testing tools with command [cd /tmp/713105.1.short.q/tmpP_qIg6/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_combinexsannos/tool_test_output.html --xunit_report_file /tmp/713105.1.short.q/tmpP_qIg6/xunit.xml --structured_data_report_file /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_combinexsannos/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/713105.1.short.q/tmpfSGfL4/tmpPCYVSx/new_files_path_LGMvXJ'), ('app:main', 'database_connection', 'sqlite:////tmp/713105.1.short.q/tmpfSGfL4/tmpPCYVSx/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/713105.1.short.q/tmpqRgQWq'), ('app:main', 'template_cache_path', '/tmp/713105.1.short.q/tmpfSGfL4/tmpPCYVSx/database/compiled_templates'), ('app:main', 'job_working_directory', '/tmp/713105.1.short.q/tmpfSGfL4/tmpPCYVSx/job_working_directory_O4asiE'), ('app:main', 'tool_dependency_dir', '/tmp/713105.1.short.q/tmpP_qIg6/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/713105.1.short.q/tmpfSGfL4/data_manager_test_tmpV3omAY/data_manager_tool-data38f9dn'), ('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/713105.1.short.q/tmpfSGfL4/tmpPCYVSx/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 2016-04-10 16:01:48,614 Initalizing main Galaxy Queue Worker on sqlalchemy+sqlite:// tool_shed.tool_shed_registry DEBUG 2016-04-10 16:01:48,686 Loading references to tool sheds from /tmp/713105.1.short.q/tmpP_qIg6/tool_sheds_conf.xml tool_shed.tool_shed_registry DEBUG 2016-04-10 16:01:48,686 Loaded reference to tool shed: Target Shed galaxy.app DEBUG 2016-04-10 16:01:48,687 Using "galaxy.ini" config file: /tmp/713105.1.short.q/tmpfSGfL4/functional_tests_wsgi.ini migrate.versioning.repository DEBUG 2016-04-10 16:01:48,808 Loading repository lib/galaxy/model/migrate... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,809 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,810 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0014_pages.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Script lib/galaxy/model/migrate/versions/0019_request_library_folder.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,811 Loading script lib/galaxy/model/migrate/versions/0020_library_upload_job.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,812 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 2016-04-10 16:01:48,823 Script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,823 Loading script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Loading script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 Loading script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,824 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 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0119_job_metrics.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Script lib/galaxy/model/migrate/versions/0119_job_metrics.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0120_dataset_collections.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Script lib/galaxy/model/migrate/versions/0120_dataset_collections.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,825 Loading script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,826 Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,827 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py... migrate.versioning.script.base DEBUG 2016-04-10 16:01:48,827 Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully migrate.versioning.repository DEBUG 2016-04-10 16:01:48,827 Repository lib/galaxy/model/migrate loaded successfully migrate.versioning.repository DEBUG 2016-04-10 16:01:48,827 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) galaxy.config INFO 2016-04-10 16:01:48,880 Install database targetting Galaxy's database configuration. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,918 Loading datatypes from /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmp-toolshed-acalpdiNKOAF galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,922 Loading datatypes from /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmp-toolshed-acalpdIGFyy7 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,923 Exception importing proprietary code file /tmp/713105.1.short.q/tmpP_qIg6/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 2016-04-10 16:01:48,923 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,936 Loading datatypes from ./config/datatypes_conf.xml.sample galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,936 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,937 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,938 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,938 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,938 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,938 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,938 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,938 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,938 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,939 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,939 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,939 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,939 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,939 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,939 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,939 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,940 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,940 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,940 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,940 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,940 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,941 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,942 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,943 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,943 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,943 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,943 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,943 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,943 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,943 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,944 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,944 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,944 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,944 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,944 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,944 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,945 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,945 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,945 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,945 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,945 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,945 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,945 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,946 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,948 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,948 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,948 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,949 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,949 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,949 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,949 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,949 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,949 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,950 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,951 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,952 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,953 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,954 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,955 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,956 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,957 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,958 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,958 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,958 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,958 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,958 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,958 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,959 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,960 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,960 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,961 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,961 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,961 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,961 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,962 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,962 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,962 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,963 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,964 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,964 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,964 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,965 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,965 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,965 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,965 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,965 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,966 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,966 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,966 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,966 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,966 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,966 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,966 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,967 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,967 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,967 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,967 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,967 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,967 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,968 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,968 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,968 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,968 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,968 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,968 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,969 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,969 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,969 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,969 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,969 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,969 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,970 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,970 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,970 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,970 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,970 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,970 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,971 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,971 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,971 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,971 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,971 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,971 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,972 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,972 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,972 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,972 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,972 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,972 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,973 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,973 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,973 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,973 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,973 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,973 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,974 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,974 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,974 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,974 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,974 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,974 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,974 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,975 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,975 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,975 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,975 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,975 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,975 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,976 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,976 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,976 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,976 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,976 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,976 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,977 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,977 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,977 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,977 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,977 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,977 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,978 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,978 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,978 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,978 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,978 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,978 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,979 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,979 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,979 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,979 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,979 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,979 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,980 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,980 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,980 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,980 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,980 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,980 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,980 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,981 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,981 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,981 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,981 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,982 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,982 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,982 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,982 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,982 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,982 Overriding conflicting datatype with extension 'rdata', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,983 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,983 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,983 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,983 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,983 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,983 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,984 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,984 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,984 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,984 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,984 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,985 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,985 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,985 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,985 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,985 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,985 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,986 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,987 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Removed conflicting sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,988 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,989 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Removed conflicting sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,990 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,991 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,992 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,993 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,994 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,995 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,995 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,995 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,995 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,995 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,995 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,995 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,996 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 2016-04-10 16:01:48,996 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,996 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,996 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt galaxy.datatypes.registry DEBUG 2016-04-10 16:01:48,996 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt galaxy.jobs WARNING 2016-04-10 16:01:49,069 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/713105.1.short.q/tmpfSGfL4/functional_tests_wsgi.ini" instead galaxy.jobs DEBUG 2016-04-10 16:01:49,069 Loading job configuration from /tmp/713105.1.short.q/tmpfSGfL4/functional_tests_wsgi.ini galaxy.jobs DEBUG 2016-04-10 16:01:49,069 Done loading job configuration beaker.container DEBUG 2016-04-10 16:01:49,103 data file /tmp/713105.1.short.q/tmpP_qIg6/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache galaxy.tools.toolbox.watcher INFO 2016-04-10 16:01:49,104 Watchdog library unavailble, cannot monitor tools. galaxy.tools.toolbox.base INFO 2016-04-10 16:01:49,104 Parsing the tool configuration /tmp/713105.1.short.q/tmpP_qIg6/tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-10 16:01:49,115 Parsing the tool configuration /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev/config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-10 16:01:49,146 Parsing the tool configuration /tmp/713105.1.short.q/tmpP_qIg6/empty_tool_conf.xml galaxy.tools.toolbox.base DEBUG 2016-04-10 16:01:49,146 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2016-04-10 16:01:49,146 Loading section: Shed Installs galaxy.tools.toolbox.base DEBUG 2016-04-10 16:01:49,239 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3, version: 2.0.3 into tool panel.... galaxy.tools.deps DEBUG 2016-04-10 16:01:49,241 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.search DEBUG 2016-04-10 16:01:49,338 Starting to build toolbox index. galaxy.tools.search DEBUG 2016-04-10 16:01:49,730 Toolbox index finished. galaxy.tools.data_manager.manager DEBUG 2016-04-10 16:01:49,733 Loaded Data Manager: test_data_manager galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,736 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,738 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.display_applications.application ERROR 2016-04-10 16:01:49,741 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,741 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,741 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,742 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,742 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,745 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,745 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,748 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,748 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,754 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.display_applications.application ERROR 2016-04-10 16:01:49,756 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,757 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,757 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,763 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,773 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,774 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.display_applications.application ERROR 2016-04-10 16:01:49,776 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,776 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,778 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,781 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.display_applications.application ERROR 2016-04-10 16:01:49,784 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,784 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,785 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,785 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.display_applications.application ERROR 2016-04-10 16:01:49,788 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,788 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,788 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,788 Adding inherited display application 'igv_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,789 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,790 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,790 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,790 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,790 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,791 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,792 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,792 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,792 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,792 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,792 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,792 Adding inherited display application 'igv_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,793 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,793 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,793 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,793 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,794 Loaded converter: CONVERTER_Bam_Bai_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,795 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,796 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,797 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,798 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,799 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,800 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,802 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,802 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,803 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,804 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,806 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,807 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,808 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,809 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,810 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,811 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,812 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,813 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,814 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,815 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,816 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,817 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,818 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,819 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,820 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,821 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,822 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,823 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,824 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,825 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,826 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,827 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,828 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,829 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,830 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,831 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,832 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,833 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,834 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,835 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,836 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,837 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,838 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,839 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,840 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,841 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,842 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,843 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,844 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,846 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,847 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,848 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,848 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,849 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,850 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,852 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2016-04-10 16:01:49,854 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2016-04-10 16:01:49,856 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2016-04-10 16:01:49,857 Loaded history export tool: __EXPORT_HISTORY__ galaxy.web.base.pluginframework INFO 2016-04-10 16:01:49,858 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2016-04-10 16:01:49,859 Visualizations plugin disabled: Circster. Skipping... galaxy.visualization.plugins.config_parser INFO 2016-04-10 16:01:49,859 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2016-04-10 16:01:49,860 VisualizationsRegistry, loaded plugin: csg galaxy.web.base.pluginframework INFO 2016-04-10 16:01:49,860 VisualizationsRegistry, loaded plugin: graphview galaxy.visualization.plugins.config_parser INFO 2016-04-10 16:01:49,861 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2016-04-10 16:01:49,861 VisualizationsRegistry, loaded plugin: graphviz galaxy.web.base.pluginframework INFO 2016-04-10 16:01:49,862 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2016-04-10 16:01:49,863 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2016-04-10 16:01:49,864 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2016-04-10 16:01:49,864 VisualizationsRegistry, loaded plugin: trackster galaxy.tours INFO 2016-04-10 16:01:49,898 Loaded tour 'core.history' galaxy.tours INFO 2016-04-10 16:01:49,942 Loaded tour 'core.galaxy_ui' galaxy.jobs.manager DEBUG 2016-04-10 16:01:49,945 Starting job handler galaxy.jobs INFO 2016-04-10 16:01:49,945 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-10 16:01:49,946 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2016-04-10 16:01:49,946 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2016-04-10 16:01:49,947 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-10 16:01:49,949 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2016-04-10 16:01:49,949 Starting 2 TaskRunner workers galaxy.jobs DEBUG 2016-04-10 16:01:49,949 Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks' galaxy.jobs DEBUG 2016-04-10 16:01:49,949 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2016-04-10 16:01:49,950 Loaded job runners plugins: tasks:local galaxy.jobs.handler INFO 2016-04-10 16:01:49,950 job handler stop queue started galaxy.jobs.handler INFO 2016-04-10 16:01:49,968 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2016-04-10 16:01:49,974 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2016-04-10 16:01:49,976 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.workflow.scheduling_manager DEBUG 2016-04-10 16:01:49,980 Starting workflow schedulers functional_tests.py INFO 2016-04-10 16:01:49,986 Embedded Universe application started galaxy.web.framework.base DEBUG 2016-04-10 16:01:49,999 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,002 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,002 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,002 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,004 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,004 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,005 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,005 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,138 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,138 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,139 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,140 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,142 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,142 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,144 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,144 Enabling 'search' controller, class: SearchController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,145 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,145 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,146 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,146 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,146 Enabling 'mobile' controller, class: Mobile galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,147 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,148 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,148 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,149 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,151 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,151 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,152 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,153 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,155 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,155 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,155 Enabling 'tours' API controller, class: ToursController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,156 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,156 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,156 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,157 Enabling 'pages' API controller, class: PagesController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,157 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,157 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,158 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,158 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,158 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,158 Enabling 'metrics' API controller, class: MetricsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,159 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,159 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,159 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,159 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,160 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,160 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,161 Enabling 'remote_files' API controller, class: RemoteFilesAPIController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,162 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,163 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,163 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,163 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,164 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,164 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,164 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,165 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,165 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,166 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,185 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,185 Enabling 'page_revisions' API controller, class: PageRevisionsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,186 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,186 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,186 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,187 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,187 Enabling 'tool_data' API controller, class: ToolData galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,187 Enabling 'jobs' API controller, class: JobController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,188 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,188 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,188 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,188 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,189 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,189 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,190 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,190 Enabling 'job_files' API controller, class: JobFilesAPIController galaxy.web.framework.base DEBUG 2016-04-10 16:01:50,190 Enabling 'authenticate' API controller, class: AuthenticationController galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,646 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,647 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,661 Enabling 'error' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,662 Enabling 'x-forwarded-host' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,662 Enabling 'Request ID' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,669 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,670 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,670 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,670 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-10 16:01:50,670 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.queue_worker INFO 2016-04-10 16:01:50,671 Binding and starting galaxy control worker for main functional_tests.py DEBUG 2016-04-10 16:01:50,680 Attempting to serve app on randomly chosen port: 8260 functional_tests.py INFO 2016-04-10 16:01:50,810 Embedded web server started functional_tests.py INFO 2016-04-10 16:01:50,811 Functional tests will be run against localhost:8260 galaxy.tools.toolbox.watcher INFO 2016-04-10 16:01:50,812 Watchdog library unavailble, cannot monitor tools. galaxy.tools.toolbox.base INFO 2016-04-10 16:01:50,812 Parsing the tool configuration /tmp/713105.1.short.q/tmpP_qIg6/tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-10 16:01:50,812 Parsing the tool configuration /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev/config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-10 16:01:50,838 Parsing the tool configuration /tmp/713105.1.short.q/tmpP_qIg6/empty_tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-10 16:01:50,838 Parsing the tool configuration /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev/config/shed_tool_conf.xml galaxy.tools.toolbox.base DEBUG 2016-04-10 16:01:50,884 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2016-04-10 16:01:50,884 Loading section: Shed Installs galaxy.tools.toolbox.base DEBUG 2016-04-10 16:01:50,971 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3, version: 2.0.3 into tool panel.... galaxy.tools.deps DEBUG 2016-04-10 16:01:50,972 Unable to find config file './dependency_resolvers_conf.xml' [?1034hbase.asserts DEBUG 2016-04-10 16:01:51,117 base.asserts.text base.asserts DEBUG 2016-04-10 16:01:51,117 base.asserts.tabular base.asserts DEBUG 2016-04-10 16:01:51,118 base.asserts.xml nose.plugins.manager DEBUG 2016-04-10 16:01:51,134 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:51,212 Starting new HTTP connection (1): localhost galaxy.web.framework.webapp INFO 2016-04-10 16:01:51,216 Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:51,232 "GET /api/users?key=test_key HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:51,273 Starting new HTTP connection (1): localhost galaxy.web.framework.webapp INFO 2016-04-10 16:01:51,277 Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:51,736 "POST /api/users HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:51,737 Starting new HTTP connection (1): localhost galaxy.web.framework.webapp INFO 2016-04-10 16:01:51,742 Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:51,808 "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:51,810 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:51,972 "POST /api/histories HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:51,993 Starting new HTTP connection (1): localhost galaxy.tools DEBUG 2016-04-10 16:01:52,284 Validated and populated state for tool request (18.604 ms) galaxy.tools.actions.upload DEBUG 2016-04-10 16:01:52,327 Persisted uploads (20.794 ms) galaxy.tools.actions.upload DEBUG 2016-04-10 16:01:52,749 Checked and cleaned uploads (421.616 ms) galaxy.tools.actions.upload_common INFO 2016-04-10 16:01:52,854 tool upload1 created job id 1 galaxy.tools.actions.upload DEBUG 2016-04-10 16:01:52,977 Created upload job (227.243 ms) galaxy.tools.execute DEBUG 2016-04-10 16:01:52,977 Tool [upload1] created job [1] (670.247 ms) galaxy.tools.execute DEBUG 2016-04-10 16:01:52,996 Executed all jobs for tool request: (711.689 ms) requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:53,031 "POST /api/tools HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:53,033 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:53,118 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:53,120 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:53,212 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:53,214 Starting new HTTP connection (1): localhost galaxy.jobs DEBUG 2016-04-10 16:01:53,274 (1) Working directory for job is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1 galaxy.jobs.handler DEBUG 2016-04-10 16:01:53,321 (1) Dispatching to local runner galaxy.jobs DEBUG 2016-04-10 16:01:53,425 (1) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:53,431 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:53,433 Starting new HTTP connection (1): localhost galaxy.jobs.runners DEBUG 2016-04-10 16:01:53,483 Job [1] queued (162.272 ms) galaxy.jobs.handler INFO 2016-04-10 16:01:53,595 (1) Job dispatched requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:53,697 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:53,699 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:53,986 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:53,988 Starting new HTTP connection (1): localhost galaxy.tools.deps DEBUG 2016-04-10 16:01:54,120 Building dependency shell command for dependency 'samtools' galaxy.tools.deps DEBUG 2016-04-10 16:01:54,121 Find dependency samtools version None galaxy.tools.deps DEBUG 2016-04-10 16:01:54,121 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:01:54,121 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:01:54,121 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:01:54,123 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:01:54,124 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps WARNING 2016-04-10 16:01:54,124 Failed to resolve dependency on 'samtools', ignoring requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:54,145 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:54,147 Starting new HTTP connection (1): localhost galaxy.jobs.command_factory INFO 2016-04-10 16:01:54,222 Built script [/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev/tools/data_source/upload.py /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmp07yIbk 1:/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/dataset_1_files:/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_1.dat] requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:54,320 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:54,322 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:54,479 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:54,481 Starting new HTTP connection (1): localhost galaxy.jobs.runners DEBUG 2016-04-10 16:01:54,644 (1) command is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/set_metadata_4tX2I5.py" "/tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/galaxy.json" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_kS0IBD,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_5pLbDY,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_ZeSkpU,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_WCkLAe,/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_1.dat,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_0JObw3" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2016-04-10 16:01:54,658 (1) executing job script: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/galaxy_1.sh galaxy.jobs DEBUG 2016-04-10 16:01:54,667 (1) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:54,692 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:57,700 Starting new HTTP connection (1): localhost galaxy.jobs.runners.local DEBUG 2016-04-10 16:01:57,701 execution finished: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/1/galaxy_1.sh requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:57,953 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:57,955 Starting new HTTP connection (1): localhost galaxy.datatypes.metadata DEBUG 2016-04-10 16:01:58,024 loading metadata from file for: HistoryDatasetAssociation 1 requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:58,124 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:58,127 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:58,487 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:58,505 Starting new HTTP connection (1): localhost galaxy.jobs DEBUG 2016-04-10 16:01:58,599 job 1 ended (finish() executed in (898.090 ms)) galaxy.tools DEBUG 2016-04-10 16:01:58,806 Validated and populated state for tool request (32.481 ms) galaxy.tools.actions.upload DEBUG 2016-04-10 16:01:58,997 Persisted uploads (22.787 ms) galaxy.tools.actions.upload DEBUG 2016-04-10 16:01:59,432 Checked and cleaned uploads (434.549 ms) galaxy.tools.actions.upload_common INFO 2016-04-10 16:01:59,536 tool upload1 created job id 2 galaxy.tools.actions.upload DEBUG 2016-04-10 16:01:59,650 Created upload job (217.822 ms) galaxy.tools.execute DEBUG 2016-04-10 16:01:59,650 Tool [upload1] created job [2] (675.753 ms) galaxy.tools.execute DEBUG 2016-04-10 16:01:59,668 Executed all jobs for tool request: (861.378 ms) requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:59,700 "POST /api/tools HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:59,703 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:59,782 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:59,785 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:59,870 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:59,872 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:01:59,954 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:01:59,956 Starting new HTTP connection (1): localhost galaxy.jobs DEBUG 2016-04-10 16:02:00,032 (2) Working directory for job is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2 galaxy.jobs.handler DEBUG 2016-04-10 16:02:00,065 (2) Dispatching to local runner galaxy.jobs DEBUG 2016-04-10 16:02:00,127 (2) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:00,146 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:00,148 Starting new HTTP connection (1): localhost galaxy.jobs.runners DEBUG 2016-04-10 16:02:00,191 Job [2] queued (125.385 ms) galaxy.jobs.handler INFO 2016-04-10 16:02:00,269 (2) Job dispatched requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:00,454 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:00,456 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:00,764 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:00,768 Starting new HTTP connection (1): localhost galaxy.tools.deps DEBUG 2016-04-10 16:02:00,909 Building dependency shell command for dependency 'samtools' galaxy.tools.deps DEBUG 2016-04-10 16:02:00,909 Find dependency samtools version None galaxy.tools.deps DEBUG 2016-04-10 16:02:00,909 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:00,909 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:00,909 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:00,910 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:00,910 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps WARNING 2016-04-10 16:02:00,910 Failed to resolve dependency on 'samtools', ignoring requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:00,922 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:00,924 Starting new HTTP connection (1): localhost galaxy.jobs.command_factory INFO 2016-04-10 16:02:01,000 Built script [/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/tool_script.sh] for tool command[python /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev/tools/data_source/upload.py /tmp/713105.1.short.q/tmpP_qIg6/galaxy-dev /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz /tmp/713105.1.short.q/tmpP_qIg6/tmp/tmp5kH8fC 2:/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/dataset_2_files:/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_2.dat] requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:01,154 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:01,157 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:01,392 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:01,395 Starting new HTTP connection (1): localhost galaxy.jobs.runners DEBUG 2016-04-10 16:02:01,543 (2) command is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/tool_script.sh; return_code=$?; python "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/set_metadata_2M0z36.py" "/tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/galaxy.json" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_Ai0pDn,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_buBNt6,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_dXSFS6,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_z1HNLN,/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_2.dat,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_ZRIfiw" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2016-04-10 16:02:01,561 (2) executing job script: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/galaxy_2.sh galaxy.jobs DEBUG 2016-04-10 16:02:01,570 (2) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:01,606 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:04,658 Starting new HTTP connection (1): localhost galaxy.jobs.runners.local DEBUG 2016-04-10 16:02:04,658 execution finished: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/2/galaxy_2.sh requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:04,986 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:04,988 Starting new HTTP connection (1): localhost galaxy.datatypes.metadata DEBUG 2016-04-10 16:02:05,001 loading metadata from file for: HistoryDatasetAssociation 2 requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:05,181 "GET /api/histories/2891970512fa2d5a?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:05,184 Starting new HTTP connection (1): localhost galaxy.tools DEBUG 2016-04-10 16:02:05,395 Validated and populated state for tool request (97.725 ms) galaxy.tools.actions INFO 2016-04-10 16:02:05,615 Handled output (164.454 ms) galaxy.jobs DEBUG 2016-04-10 16:02:05,649 job 2 ended (finish() executed in (990.195 ms)) galaxy.tools.actions INFO 2016-04-10 16:02:05,736 Verified access to datasets (15.574 ms) galaxy.tools.execute DEBUG 2016-04-10 16:02:05,810 Tool [testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3] created job [3] (392.452 ms) galaxy.tools.execute DEBUG 2016-04-10 16:02:05,827 Executed all jobs for tool request: (431.967 ms) requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:05,863 "POST /api/tools HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:05,864 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:06,021 "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:06,223 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:06,374 "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None galaxy.jobs DEBUG 2016-04-10 16:02:06,532 (3) Working directory for job is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3 galaxy.jobs.handler DEBUG 2016-04-10 16:02:06,547 (3) Dispatching to local runner galaxy.jobs DEBUG 2016-04-10 16:02:06,591 (3) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2016-04-10 16:02:06,650 Job [3] queued (103.168 ms) galaxy.jobs.handler INFO 2016-04-10 16:02:06,688 (3) Job dispatched requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:06,805 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:07,145 "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None galaxy.tools.deps DEBUG 2016-04-10 16:02:07,311 Building dependency shell command for dependency 'R' galaxy.tools.deps DEBUG 2016-04-10 16:02:07,311 Find dependency R version 3.1.2 galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b13981cb5d0> (isnull? False) galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Building dependency shell command for dependency 'r-snow' galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Find dependency r-snow version 0.4_1 galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:07,320 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps WARNING 2016-04-10 16:02:07,321 Failed to resolve dependency on 'r-snow', ignoring galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Building dependency shell command for dependency 'bioconductor-camera' galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Find dependency bioconductor-camera version 1.44.0 galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps WARNING 2016-04-10 16:02:07,321 Failed to resolve dependency on 'bioconductor-camera', ignoring galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Building dependency shell command for dependency 'r-batch' galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Find dependency r-batch version 1.1_4 galaxy.tools.deps DEBUG 2016-04-10 16:02:07,321 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:07,322 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:07,322 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:07,322 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-10 16:02:07,322 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x3a24090> (isnull? True) galaxy.tools.deps WARNING 2016-04-10 16:02:07,322 Failed to resolve dependency on 'r-batch', ignoring galaxy.tools.deps DEBUG 2016-04-10 16:02:07,322 Building dependency shell command for dependency 'graphicsmagick' galaxy.tools.deps DEBUG 2016-04-10 16:02:07,322 Find dependency graphicsmagick version 1.3.20 galaxy.tools.deps DEBUG 2016-04-10 16:02:07,322 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2b13503a0710> (isnull? False) galaxy.jobs.command_factory INFO 2016-04-10 16:02:07,397 Built script [/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/713105.1.short.q/tmpP_qIg6/deps/R/3.1.2/mmonsoor/camera_combinexsannos/2591056df814; export PACKAGE_BASE; . /tmp/713105.1.short.q/tmpP_qIg6/deps/R/3.1.2/mmonsoor/camera_combinexsannos/2591056df814/env.sh; PACKAGE_BASE=/tmp/713105.1.short.q/tmpP_qIg6/deps/graphicsmagick/1.3.20/mmonsoor/camera_combinexsannos/2591056df814; export PACKAGE_BASE; . /tmp/713105.1.short.q/tmpP_qIg6/deps/graphicsmagick/1.3.20/mmonsoor/camera_combinexsannos/2591056df814/env.sh; LANG=C Rscript /tmp/713105.1.short.q/tmpP_qIg6/shed_tools/testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/2591056df814/camera_combinexsannos/CAMERA.r xfunction combinexsAnnos image_pos /tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_1.dat image_neg /tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_2.dat variableMetadataOutput /tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_3.dat pos TRUE tol 2 ruleset 1,1 convert_param FALSE keep_meta TRUE] galaxy.jobs.runners DEBUG 2016-04-10 16:02:07,665 (3) command is: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/tool_script.sh; return_code=$?; python "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/set_metadata_d9wj8r.py" "/tmp/713105.1.short.q/tmpP_qIg6/tmp/tmpkDelnz" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/galaxy.json" "/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_3_LtRgbi,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_3_7WM6NQ,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_3_BhIIkJ,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_3_kfKhlZ,/tmp/713105.1.short.q/tmpP_qIg6/files/000/dataset_3.dat,/tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_3_n87Fib" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2016-04-10 16:02:07,677 (3) executing job script: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/galaxy_3.sh galaxy.jobs DEBUG 2016-04-10 16:02:07,685 (3) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:07,948 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:08,104 "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:09,708 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:09,906 "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None galaxy.jobs.runners.local DEBUG 2016-04-10 16:02:10,324 execution finished: /tmp/713105.1.short.q/tmpP_qIg6/job_working_directory/000/3/galaxy_3.sh galaxy.jobs.output_checker INFO 2016-04-10 16:02:10,364 Job 3: Fatal error: Exit code 1 () galaxy.jobs.output_checker DEBUG 2016-04-10 16:02:10,365 Tool exit code indicates an error, failing job. galaxy.jobs DEBUG 2016-04-10 16:02:10,433 (3) setting dataset 3 state to ERROR galaxy.jobs DEBUG 2016-04-10 16:02:10,749 job 3 ended (finish() executed in (424.557 ms)) requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:13,111 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:13,271 "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:13,274 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:13,331 "GET /api/histories/2891970512fa2d5a/contents?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:13,333 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:13,703 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:13,706 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:13,845 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:13,847 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:14,043 "GET /api/jobs/54f2a3a23292eb07?full=true&key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:14,045 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:14,195 "GET /api/jobs/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:14,196 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:14,250 "GET /api/histories/2891970512fa2d5a/contents?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:14,252 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:14,438 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-10 16:02:14,440 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-10 16:02:14,557 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=e26b8119477946474c5d2c9523746e14 HTTP/1.1" 200 None functional_tests.py INFO 2016-04-10 16:02:14,574 Shutting down functional_tests.py INFO 2016-04-10 16:02:14,574 Shutting down embedded web server functional_tests.py INFO 2016-04-10 16:02:14,577 Embedded web server stopped functional_tests.py INFO 2016-04-10 16:02:14,577 Shutting down app galaxy.jobs.handler INFO 2016-04-10 16:02:14,577 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-10 16:02:14,577 job handler queue stopped galaxy.jobs.runners INFO 2016-04-10 16:02:14,577 TaskRunner: Sending stop signal to 2 worker threads galaxy.jobs.runners INFO 2016-04-10 16:02:14,577 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2016-04-10 16:02:14,578 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-10 16:02:14,578 job handler stop queue stopped functional_tests.py INFO 2016-04-10 16:02:14,578 Embedded Universe application stopped functional_tests.py INFO 2016-04-10 16:02:14,579 Cleaning up temporary files in /tmp/713105.1.short.q/tmpfSGfL4/tmpPCYVSx galaxy.jobs.handler INFO 2016-04-10 16:02:15,442 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-10 16:02:15,442 job handler queue stopped galaxy.jobs.runners INFO 2016-04-10 16:02:15,442 TaskRunner: Sending stop signal to 2 worker threads galaxy.jobs.runners INFO 2016-04-10 16:02:15,442 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2016-04-10 16:02:15,442 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-10 16:02:15,442 job handler stop queue stopped testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3[0]: failed testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3[0]: failed git --git-dir /home/fr2424/sib/lecorguille/.planemo/gx_repo fetch >/dev/null 2>&1 cd /tmp/713334.1.short.q/tmpsEEpi3; 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/713334.1.short.q/tmpsEEpi3/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/713334.1.short.q/tmpsEEpi3/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/713334.1.short.q/tmpsEEpi3/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/713334.1.short.q/tmpsEEpi3/galaxy-dev Testing tools with command [cd /tmp/713334.1.short.q/tmpsEEpi3/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_combinexsannos/tool_test_output.html --xunit_report_file /tmp/713334.1.short.q/tmpsEEpi3/xunit.xml --structured_data_report_file /projet/fr2424/sib/lecorguille/script/git/w4m/camera/galaxy/camera_combinexsannos/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/713334.1.short.q/tmpi0htl5/tmpWnIGuv/new_files_path_KTg1gx'), ('app:main', 'database_connection', 'sqlite:////tmp/713334.1.short.q/tmpi0htl5/tmpWnIGuv/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/713334.1.short.q/tmpPqLFGI'), ('app:main', 'template_cache_path', '/tmp/713334.1.short.q/tmpi0htl5/tmpWnIGuv/database/compiled_templates'), ('app:main', 'job_working_directory', '/tmp/713334.1.short.q/tmpi0htl5/tmpWnIGuv/job_working_directory_jsZpiI'), ('app:main', 'tool_dependency_dir', '/tmp/713334.1.short.q/tmpsEEpi3/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/713334.1.short.q/tmpi0htl5/data_manager_test_tmpW7p51M/data_manager_tool-data0kK9J0'), ('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/713334.1.short.q/tmpi0htl5/tmpWnIGuv/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 2016-04-11 15:37:49,725 Initalizing main Galaxy Queue Worker on sqlalchemy+sqlite:// tool_shed.tool_shed_registry DEBUG 2016-04-11 15:37:49,767 Loading references to tool sheds from /tmp/713334.1.short.q/tmpsEEpi3/tool_sheds_conf.xml tool_shed.tool_shed_registry DEBUG 2016-04-11 15:37:49,767 Loaded reference to tool shed: Target Shed galaxy.app DEBUG 2016-04-11 15:37:49,768 Using "galaxy.ini" config file: /tmp/713334.1.short.q/tmpi0htl5/functional_tests_wsgi.ini migrate.versioning.repository DEBUG 2016-04-11 15:37:49,845 Loading repository lib/galaxy/model/migrate... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,846 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,846 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,846 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,846 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,846 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,846 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,846 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,847 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Loading script lib/galaxy/model/migrate/versions/0014_pages.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,848 Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Loading script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Script lib/galaxy/model/migrate/versions/0019_request_library_folder.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Loading script lib/galaxy/model/migrate/versions/0020_library_upload_job.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Script lib/galaxy/model/migrate/versions/0020_library_upload_job.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Loading script lib/galaxy/model/migrate/versions/0021_user_prefs.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Script lib/galaxy/model/migrate/versions/0021_user_prefs.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Loading script lib/galaxy/model/migrate/versions/0022_visualization_tables.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Script lib/galaxy/model/migrate/versions/0022_visualization_tables.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Loading script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Script lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,849 Loading script 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lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,861 Loading script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Loading script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Loading script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Loading script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Loading script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Loading script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,862 Script 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migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Loading script lib/galaxy/model/migrate/versions/0120_dataset_collections.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Script lib/galaxy/model/migrate/versions/0120_dataset_collections.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Loading script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Loading script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Loading script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,864 Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py... migrate.versioning.script.base DEBUG 2016-04-11 15:37:49,865 Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully migrate.versioning.repository DEBUG 2016-04-11 15:37:49,865 Repository lib/galaxy/model/migrate loaded successfully migrate.versioning.repository DEBUG 2016-04-11 15:37:49,865 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) galaxy.config INFO 2016-04-11 15:37:49,921 Install database targetting Galaxy's database configuration. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,961 Loading datatypes from /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp-toolshed-acalpduZyvbh galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,965 Loading datatypes from /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp-toolshed-acalpdFPNzfa galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,965 Exception importing proprietary code file /tmp/713334.1.short.q/tmpsEEpi3/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 2016-04-11 15:37:49,965 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,979 Loading datatypes from ./config/datatypes_conf.xml.sample galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,980 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,980 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,981 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,981 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,981 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,982 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,982 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,982 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,982 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,982 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,982 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,982 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,983 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,983 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,983 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,983 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,983 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,983 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,984 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,984 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,984 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,984 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,984 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Overriding conflicting datatype with extension 'data', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,985 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,986 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,987 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,987 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,987 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,987 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,987 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,987 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,987 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,988 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,988 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,988 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,988 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,988 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,989 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,989 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,989 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,989 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,989 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,989 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,989 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,990 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,991 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,992 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,992 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,993 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,993 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,993 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,993 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,993 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,994 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,995 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,996 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,997 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,997 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,997 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,997 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,997 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,997 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,998 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:49,999 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,000 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,001 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,002 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,002 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,002 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,002 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,002 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,002 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,002 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,003 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,003 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,003 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,003 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,003 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,005 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,005 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,005 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,006 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,006 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,006 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,007 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,007 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,007 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,008 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,008 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,008 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,008 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,008 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,008 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,008 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,009 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,009 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,009 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,009 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,010 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,010 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,010 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,011 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,011 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,011 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,011 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,011 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,011 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,011 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,012 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,012 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,012 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,012 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,012 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,012 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,013 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,013 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,013 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,013 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,013 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,014 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,014 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,014 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,014 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,014 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,014 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,015 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,015 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,015 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,015 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,015 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,015 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,016 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,016 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,016 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,016 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,016 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,016 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,017 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,017 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,017 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,017 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,017 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,017 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,018 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,018 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,018 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,018 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,018 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,019 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,019 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,019 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,019 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,019 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,019 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,020 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,020 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,020 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,020 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,020 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,020 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,021 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,021 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,021 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,021 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,021 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,021 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,022 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,022 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,022 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,022 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,022 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,022 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,023 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,023 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,023 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,023 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,023 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,023 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,024 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,024 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,024 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,024 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,024 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,025 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,026 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,027 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,028 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,028 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,028 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,028 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Overriding conflicting datatype with extension 'rdata', using datatype from ./config/datatypes_conf.xml.sample. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,029 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,030 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,030 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,030 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,031 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,031 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,031 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,031 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,031 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,031 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,032 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Removed conflicting sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,033 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,034 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Removed conflicting sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,035 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Removed conflicting sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Removed conflicting sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,036 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Removed conflicting sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,037 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Removed conflicting sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,038 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Removed conflicting sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,039 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,040 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,041 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,042 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,042 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,042 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,042 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,042 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,042 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,042 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 2016-04-11 15:37:50,043 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,043 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,043 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,043 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt galaxy.jobs WARNING 2016-04-11 15:37:50,102 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/713334.1.short.q/tmpi0htl5/functional_tests_wsgi.ini" instead galaxy.jobs DEBUG 2016-04-11 15:37:50,102 Loading job configuration from /tmp/713334.1.short.q/tmpi0htl5/functional_tests_wsgi.ini galaxy.jobs DEBUG 2016-04-11 15:37:50,102 Done loading job configuration beaker.container DEBUG 2016-04-11 15:37:50,131 data file /tmp/713334.1.short.q/tmpsEEpi3/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache galaxy.tools.toolbox.watcher INFO 2016-04-11 15:37:50,131 Watchdog library unavailble, cannot monitor tools. galaxy.tools.toolbox.base INFO 2016-04-11 15:37:50,131 Parsing the tool configuration /tmp/713334.1.short.q/tmpsEEpi3/tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-11 15:37:50,142 Parsing the tool configuration /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev/config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-11 15:37:50,173 Parsing the tool configuration /tmp/713334.1.short.q/tmpsEEpi3/empty_tool_conf.xml galaxy.tools.toolbox.base DEBUG 2016-04-11 15:37:50,177 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2016-04-11 15:37:50,177 Loading section: Shed Installs galaxy.tools.toolbox.base DEBUG 2016-04-11 15:37:50,271 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3, version: 2.0.3 into tool panel.... galaxy.tools.deps DEBUG 2016-04-11 15:37:50,272 Unable to find config file './dependency_resolvers_conf.xml' galaxy.tools.search DEBUG 2016-04-11 15:37:50,347 Starting to build toolbox index. galaxy.tools.search DEBUG 2016-04-11 15:37:50,735 Toolbox index finished. galaxy.tools.data_manager.manager DEBUG 2016-04-11 15:37:50,737 Loaded Data Manager: test_data_manager galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,740 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,743 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.display_applications.application ERROR 2016-04-11 15:37:50,745 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,745 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,746 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,747 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,747 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,750 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,750 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,753 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,753 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,760 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.display_applications.application ERROR 2016-04-11 15:37:50,762 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,762 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,763 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,769 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,780 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,781 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.display_applications.application ERROR 2016-04-11 15:37:50,783 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,783 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,786 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,789 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.display_applications.application ERROR 2016-04-11 15:37:50,791 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,791 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,792 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,793 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.display_applications.application ERROR 2016-04-11 15:37:50,795 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,795 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,796 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,796 Adding inherited display application 'igv_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,796 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,797 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,797 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,797 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,797 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,797 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,797 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,797 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,798 Adding inherited display application 'ensembl_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,798 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,798 Adding inherited display application 'rviewer_interval' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,798 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,798 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,798 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,798 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,799 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,800 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,800 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,800 Adding inherited display application 'igv_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,800 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,800 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,800 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,801 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,802 Loaded converter: CONVERTER_Bam_Bai_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,803 Loaded converter: CONVERTER_bam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,804 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,805 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,806 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,808 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,809 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,810 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,811 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,812 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,813 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,814 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,815 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,816 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,817 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,818 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,819 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,821 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,822 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,823 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,824 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,825 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,826 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,827 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,828 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,829 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,830 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,831 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,832 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,833 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,834 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,835 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,836 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,837 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,838 Loaded converter: CONVERTER_interval_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,839 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,840 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,841 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,843 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,844 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,845 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,846 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,847 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,848 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,849 Loaded converter: CONVERTER_sam_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,850 Loaded converter: tabular_to_dbnsfp galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,851 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,852 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,853 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,855 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,856 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,857 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,858 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,859 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,860 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,861 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,863 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2016-04-11 15:37:50,864 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.special_tools DEBUG 2016-04-11 15:37:50,866 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.special_tools DEBUG 2016-04-11 15:37:50,867 Loaded history export tool: __EXPORT_HISTORY__ galaxy.web.base.pluginframework INFO 2016-04-11 15:37:50,869 VisualizationsRegistry, loaded plugin: charts galaxy.visualization.plugins.config_parser INFO 2016-04-11 15:37:50,870 Visualizations plugin disabled: Circster. Skipping... galaxy.visualization.plugins.config_parser INFO 2016-04-11 15:37:50,870 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2016-04-11 15:37:50,871 VisualizationsRegistry, loaded plugin: csg galaxy.web.base.pluginframework INFO 2016-04-11 15:37:50,871 VisualizationsRegistry, loaded plugin: graphview galaxy.visualization.plugins.config_parser INFO 2016-04-11 15:37:50,872 template syntax is deprecated: use entry_point instead galaxy.web.base.pluginframework INFO 2016-04-11 15:37:50,872 VisualizationsRegistry, loaded plugin: graphviz galaxy.web.base.pluginframework INFO 2016-04-11 15:37:50,873 VisualizationsRegistry, loaded plugin: phyloviz galaxy.web.base.pluginframework INFO 2016-04-11 15:37:50,874 VisualizationsRegistry, loaded plugin: scatterplot galaxy.visualization.plugins.config_parser INFO 2016-04-11 15:37:50,875 Visualizations plugin disabled: Sweepster. Skipping... galaxy.web.base.pluginframework INFO 2016-04-11 15:37:50,876 VisualizationsRegistry, loaded plugin: trackster galaxy.tours INFO 2016-04-11 15:37:50,922 Loaded tour 'core.galaxy_ui' galaxy.tours INFO 2016-04-11 15:37:50,956 Loaded tour 'core.history' galaxy.jobs.manager DEBUG 2016-04-11 15:37:50,959 Starting job handler galaxy.jobs INFO 2016-04-11 15:37:50,959 Handler 'main' will load all configured runner plugins galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-11 15:37:50,960 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2016-04-11 15:37:50,960 Starting 5 LocalRunner workers galaxy.jobs DEBUG 2016-04-11 15:37:50,961 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' galaxy.jobs.runners.state_handler_factory DEBUG 2016-04-11 15:37:50,963 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit galaxy.jobs.runners DEBUG 2016-04-11 15:37:50,963 Starting 2 TaskRunner workers galaxy.jobs DEBUG 2016-04-11 15:37:50,964 Loaded job runner 'galaxy.jobs.runners.tasks:TaskedJobRunner' as 'tasks' galaxy.jobs DEBUG 2016-04-11 15:37:50,964 Legacy destination with id 'local:///', url 'local:///' converted, got params: galaxy.jobs.handler DEBUG 2016-04-11 15:37:50,964 Loaded job runners plugins: tasks:local galaxy.jobs.handler INFO 2016-04-11 15:37:50,965 job handler stop queue started galaxy.jobs.handler INFO 2016-04-11 15:37:50,979 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2016-04-11 15:37:50,989 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2016-04-11 15:37:50,990 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.workflow.scheduling_manager DEBUG 2016-04-11 15:37:50,994 Starting workflow schedulers functional_tests.py INFO 2016-04-11 15:37:51,005 Embedded Universe application started galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,015 Enabling 'search' controller, class: SearchController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,019 Enabling 'admin' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,021 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,022 Enabling 'request_type' controller, class: RequestType galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,025 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,026 Enabling 'tool_runner' controller, class: ToolRunner galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,029 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,030 Enabling 'visualization' controller, class: VisualizationController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,031 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,032 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,032 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,032 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,033 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,033 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,034 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,034 Enabling 'userskeys' controller, class: User galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,035 Enabling 'external_service' controller, class: ExternalService galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,036 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,036 Enabling 'external_services' controller, class: ExternalServiceController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,038 Enabling 'biostar' controller, class: BiostarController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,039 Enabling 'user' controller, class: User galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,039 Enabling 'mobile' controller, class: Mobile galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,039 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,039 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,040 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,108 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,108 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,109 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,110 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,131 Enabling 'search' API controller, class: SearchController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,132 Enabling 'datatypes' API controller, class: DatatypesController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,132 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,132 Enabling 'pages' API controller, class: PagesController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,133 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,133 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,133 Enabling 'history_tags' API controller, class: HistoryTagsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,133 Enabling 'workflow_tags' API controller, class: WorkflowTagsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,133 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,134 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,134 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,135 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,136 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,136 Enabling 'authenticate' API controller, class: AuthenticationController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,137 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,137 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,137 Enabling 'jobs' API controller, class: JobController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,138 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,138 Enabling 'configuration' API controller, class: ConfigurationController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,139 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,139 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,139 Enabling 'page_revisions' API controller, class: PageRevisionsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,140 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,140 Enabling 'folder_contents' API controller, class: FolderContentsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,140 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,141 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,141 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,142 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,142 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,143 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,143 Enabling 'tool_data' API controller, class: ToolData galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,144 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,144 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,145 Enabling 'folders' API controller, class: FoldersController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,145 Enabling 'job_files' API controller, class: JobFilesAPIController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,146 Enabling 'remote_files' API controller, class: RemoteFilesAPIController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,146 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,147 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,147 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,147 Enabling 'metrics' API controller, class: MetricsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,148 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,148 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,148 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,149 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,149 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,149 Enabling 'tours' API controller, class: ToursController galaxy.web.framework.base DEBUG 2016-04-11 15:37:51,150 Enabling 'histories' API controller, class: HistoriesController galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,633 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,635 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,645 Enabling 'error' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,645 Enabling 'x-forwarded-host' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,645 Enabling 'Request ID' middleware galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,651 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,651 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,652 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,652 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static galaxy.webapps.galaxy.buildapp DEBUG 2016-04-11 15:37:51,652 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static galaxy.queue_worker INFO 2016-04-11 15:37:51,652 Binding and starting galaxy control worker for main functional_tests.py DEBUG 2016-04-11 15:37:51,659 Attempting to serve app on randomly chosen port: 9960 functional_tests.py INFO 2016-04-11 15:37:51,830 Embedded web server started functional_tests.py INFO 2016-04-11 15:37:51,830 Functional tests will be run against localhost:9960 galaxy.tools.toolbox.watcher INFO 2016-04-11 15:37:51,831 Watchdog library unavailble, cannot monitor tools. galaxy.tools.toolbox.base INFO 2016-04-11 15:37:51,832 Parsing the tool configuration /tmp/713334.1.short.q/tmpsEEpi3/tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-11 15:37:51,832 Parsing the tool configuration /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev/config/shed_tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-11 15:37:51,856 Parsing the tool configuration /tmp/713334.1.short.q/tmpsEEpi3/empty_tool_conf.xml galaxy.tools.toolbox.base INFO 2016-04-11 15:37:51,857 Parsing the tool configuration /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev/config/shed_tool_conf.xml galaxy.tools.toolbox.base DEBUG 2016-04-11 15:37:51,902 Loaded tool id: upload1, version: 1.1.4 into tool panel.. galaxy.tools.toolbox.base DEBUG 2016-04-11 15:37:51,902 Loading section: Shed Installs galaxy.tools.toolbox.base DEBUG 2016-04-11 15:37:51,987 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3, version: 2.0.3 into tool panel.... galaxy.tools.deps DEBUG 2016-04-11 15:37:51,987 Unable to find config file './dependency_resolvers_conf.xml' [?1034hbase.asserts DEBUG 2016-04-11 15:37:52,453 base.asserts.text base.asserts DEBUG 2016-04-11 15:37:52,454 base.asserts.tabular base.asserts DEBUG 2016-04-11 15:37:52,454 base.asserts.xml nose.plugins.manager DEBUG 2016-04-11 15:37:52,463 DefaultPluginManager load plugin nosehtml = nosehtml.plugin:NoseHTML requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:52,663 Starting new HTTP connection (1): localhost galaxy.web.framework.webapp INFO 2016-04-11 15:37:52,667 Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:52,679 "GET /api/users?key=test_key HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:52,935 Starting new HTTP connection (1): localhost galaxy.web.framework.webapp INFO 2016-04-11 15:37:52,943 Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:53,515 "POST /api/users HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:53,516 Starting new HTTP connection (1): localhost galaxy.web.framework.webapp INFO 2016-04-11 15:37:53,521 Session authenticated using Galaxy master api key requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:53,590 "POST /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:53,592 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:53,748 "POST /api/histories HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:53,769 Starting new HTTP connection (1): localhost galaxy.tools DEBUG 2016-04-11 15:37:54,037 Validated and populated state for tool request (19.293 ms) galaxy.tools.actions.upload DEBUG 2016-04-11 15:37:54,081 Persisted uploads (21.733 ms) galaxy.tools.actions.upload DEBUG 2016-04-11 15:37:54,548 Checked and cleaned uploads (465.971 ms) galaxy.tools.actions.upload_common INFO 2016-04-11 15:37:54,651 tool upload1 created job id 1 galaxy.tools.actions.upload DEBUG 2016-04-11 15:37:54,785 Created upload job (236.755 ms) galaxy.tools.execute DEBUG 2016-04-11 15:37:54,785 Tool [upload1] created job [1] (725.060 ms) galaxy.tools.execute DEBUG 2016-04-11 15:37:54,804 Executed all jobs for tool request: (766.715 ms) requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:54,841 "POST /api/tools HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:54,843 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:54,922 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:54,924 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,005 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,007 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,084 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,086 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,164 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,165 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,245 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,252 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,333 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,335 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,413 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,415 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,493 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,495 Starting new HTTP connection (1): localhost galaxy.jobs DEBUG 2016-04-11 15:37:55,571 (1) Working directory for job is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1 galaxy.jobs.handler DEBUG 2016-04-11 15:37:55,638 (1) Dispatching to local runner requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,736 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:55,738 Starting new HTTP connection (1): localhost galaxy.jobs DEBUG 2016-04-11 15:37:55,744 (1) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2016-04-11 15:37:55,828 Job [1] queued (189.303 ms) galaxy.jobs.handler INFO 2016-04-11 15:37:55,872 (1) Job dispatched requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:55,995 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:56,001 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:56,257 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:56,268 Starting new HTTP connection (1): localhost galaxy.tools.deps DEBUG 2016-04-11 15:37:56,441 Building dependency shell command for dependency 'samtools' galaxy.tools.deps DEBUG 2016-04-11 15:37:56,441 Find dependency samtools version None galaxy.tools.deps DEBUG 2016-04-11 15:37:56,441 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:37:56,441 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:37:56,444 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:37:56,444 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:37:56,444 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps WARNING 2016-04-11 15:37:56,444 Failed to resolve dependency on 'samtools', ignoring requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:56,463 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:56,465 Starting new HTTP connection (1): localhost galaxy.jobs.command_factory INFO 2016-04-11 15:37:56,542 Built script [/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/tool_script.sh] for tool command[python /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev/tools/data_source/upload.py /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmpfJ5r0e 1:/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/dataset_1_files:/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_1.dat] requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:56,647 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:56,650 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:56,866 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:37:56,868 Starting new HTTP connection (1): localhost galaxy.jobs.runners DEBUG 2016-04-11 15:37:57,002 (1) command is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/tool_script.sh; return_code=$?; python "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/set_metadata_JxYGz5.py" "/tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/galaxy.json" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_onqmr5,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_Pjphbp,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1__nrzej,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_vGIlJV,/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_1.dat,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_aZcMtE" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2016-04-11 15:37:57,020 (1) executing job script: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/galaxy_1.sh galaxy.jobs DEBUG 2016-04-11 15:37:57,029 (1) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:37:57,053 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:00,147 Starting new HTTP connection (1): localhost galaxy.jobs.runners.local DEBUG 2016-04-11 15:38:00,147 execution finished: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/1/galaxy_1.sh requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:00,404 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:00,425 Starting new HTTP connection (1): localhost galaxy.datatypes.metadata DEBUG 2016-04-11 15:38:00,439 loading metadata from file for: HistoryDatasetAssociation 1 requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:00,568 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:00,570 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:00,723 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:00,741 Starting new HTTP connection (1): localhost galaxy.jobs DEBUG 2016-04-11 15:38:00,856 job 1 ended (finish() executed in (705.703 ms)) galaxy.tools DEBUG 2016-04-11 15:38:01,067 Validated and populated state for tool request (23.639 ms) galaxy.tools.actions.upload DEBUG 2016-04-11 15:38:01,115 Persisted uploads (22.461 ms) galaxy.tools.actions.upload DEBUG 2016-04-11 15:38:01,556 Checked and cleaned uploads (440.896 ms) galaxy.tools.actions.upload_common INFO 2016-04-11 15:38:01,660 tool upload1 created job id 2 galaxy.tools.actions.upload DEBUG 2016-04-11 15:38:01,794 Created upload job (237.941 ms) galaxy.tools.execute DEBUG 2016-04-11 15:38:01,794 Tool [upload1] created job [2] (701.946 ms) galaxy.tools.execute DEBUG 2016-04-11 15:38:01,811 Executed all jobs for tool request: (744.709 ms) requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:01,844 "POST /api/tools HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:01,846 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:01,924 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:01,926 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:02,006 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:02,009 Starting new HTTP connection (1): localhost galaxy.jobs DEBUG 2016-04-11 15:38:02,099 (2) Working directory for job is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2 galaxy.jobs.handler DEBUG 2016-04-11 15:38:02,149 (2) Dispatching to local runner requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:02,167 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:02,169 Starting new HTTP connection (1): localhost galaxy.jobs DEBUG 2016-04-11 15:38:02,368 (2) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2016-04-11 15:38:02,445 Job [2] queued (295.954 ms) galaxy.jobs.handler INFO 2016-04-11 15:38:02,487 (2) Job dispatched requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:02,624 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:02,626 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:02,854 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:02,856 Starting new HTTP connection (1): localhost galaxy.tools.deps DEBUG 2016-04-11 15:38:03,096 Building dependency shell command for dependency 'samtools' galaxy.tools.deps DEBUG 2016-04-11 15:38:03,096 Find dependency samtools version None galaxy.tools.deps DEBUG 2016-04-11 15:38:03,096 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:03,096 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:03,096 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:03,096 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:03,097 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps WARNING 2016-04-11 15:38:03,097 Failed to resolve dependency on 'samtools', ignoring requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:03,103 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:03,105 Starting new HTTP connection (1): localhost galaxy.jobs.command_factory INFO 2016-04-11 15:38:03,174 Built script [/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/tool_script.sh] for tool command[python /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev/tools/data_source/upload.py /tmp/713334.1.short.q/tmpsEEpi3/galaxy-dev /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb /tmp/713334.1.short.q/tmpsEEpi3/tmp/tmpbDMWgG 2:/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/dataset_2_files:/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_2.dat] requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:03,239 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:03,242 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:03,407 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:03,409 Starting new HTTP connection (1): localhost galaxy.jobs.runners DEBUG 2016-04-11 15:38:03,609 (2) command is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/tool_script.sh; return_code=$?; python "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/set_metadata_gjY7n6.py" "/tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/galaxy.json" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_uRgY4O,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_GAZWhy,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_m7Y7NX,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_F8IJMS,/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_2.dat,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_be9LgQ" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2016-04-11 15:38:03,625 (2) executing job script: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/galaxy_2.sh galaxy.jobs DEBUG 2016-04-11 15:38:03,634 (2) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:03,652 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:06,835 Starting new HTTP connection (1): localhost galaxy.jobs.runners.local DEBUG 2016-04-11 15:38:06,835 execution finished: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/2/galaxy_2.sh requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:07,054 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:07,057 Starting new HTTP connection (1): localhost galaxy.datatypes.metadata DEBUG 2016-04-11 15:38:07,115 loading metadata from file for: HistoryDatasetAssociation 2 requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:07,219 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:07,221 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:07,491 "GET /api/histories/2891970512fa2d5a?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:07,493 Starting new HTTP connection (1): localhost galaxy.tools DEBUG 2016-04-11 15:38:07,715 Validated and populated state for tool request (166.265 ms) galaxy.jobs DEBUG 2016-04-11 15:38:07,785 job 2 ended (finish() executed in (949.551 ms)) galaxy.tools.actions INFO 2016-04-11 15:38:07,880 Handled output (128.083 ms) galaxy.tools.actions INFO 2016-04-11 15:38:07,988 Verified access to datasets (18.086 ms) galaxy.tools.execute DEBUG 2016-04-11 15:38:08,088 Tool [testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3] created job [3] (343.920 ms) galaxy.tools.execute DEBUG 2016-04-11 15:38:08,105 Executed all jobs for tool request: (390.169 ms) requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:08,147 "POST /api/tools HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:08,150 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:08,302 "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:08,504 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:08,668 "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None galaxy.jobs DEBUG 2016-04-11 15:38:08,757 (3) Working directory for job is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3 galaxy.jobs.handler DEBUG 2016-04-11 15:38:08,771 (3) Dispatching to local runner galaxy.jobs DEBUG 2016-04-11 15:38:08,815 (3) Persisting job destination (destination id: local:///) galaxy.jobs.runners DEBUG 2016-04-11 15:38:08,880 Job [3] queued (108.709 ms) galaxy.jobs.handler INFO 2016-04-11 15:38:08,914 (3) Job dispatched requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:09,077 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:09,441 "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None galaxy.tools.deps DEBUG 2016-04-11 15:38:09,567 Building dependency shell command for dependency 'R' galaxy.tools.deps DEBUG 2016-04-11 15:38:09,567 Find dependency R version 3.1.2 galaxy.tools.deps DEBUG 2016-04-11 15:38:09,575 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2aebec36b910> (isnull? False) galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Building dependency shell command for dependency 'r-snow' galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Find dependency r-snow version 0.4_1 galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps WARNING 2016-04-11 15:38:09,576 Failed to resolve dependency on 'r-snow', ignoring galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Building dependency shell command for dependency 'bioconductor-camera' galaxy.tools.deps DEBUG 2016-04-11 15:38:09,576 Find dependency bioconductor-camera version 1.44.0 galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps WARNING 2016-04-11 15:38:09,577 Failed to resolve dependency on 'bioconductor-camera', ignoring galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Building dependency shell command for dependency 'r-batch' galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Find dependency r-batch version 1.1_4 galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:09,577 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:09,578 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:09,578 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps DEBUG 2016-04-11 15:38:09,578 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x48bd090> (isnull? True) galaxy.tools.deps WARNING 2016-04-11 15:38:09,578 Failed to resolve dependency on 'r-batch', ignoring galaxy.tools.deps DEBUG 2016-04-11 15:38:09,578 Building dependency shell command for dependency 'graphicsmagick' galaxy.tools.deps DEBUG 2016-04-11 15:38:09,578 Find dependency graphicsmagick version 1.3.20 galaxy.tools.deps DEBUG 2016-04-11 15:38:09,578 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x2aebec1cd390> (isnull? False) galaxy.jobs.command_factory INFO 2016-04-11 15:38:09,656 Built script [/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/tool_script.sh] for tool command[PACKAGE_BASE=/tmp/713334.1.short.q/tmpsEEpi3/deps/R/3.1.2/mmonsoor/camera_combinexsannos/2591056df814; export PACKAGE_BASE; . /tmp/713334.1.short.q/tmpsEEpi3/deps/R/3.1.2/mmonsoor/camera_combinexsannos/2591056df814/env.sh; PACKAGE_BASE=/tmp/713334.1.short.q/tmpsEEpi3/deps/graphicsmagick/1.3.20/mmonsoor/camera_combinexsannos/2591056df814; export PACKAGE_BASE; . /tmp/713334.1.short.q/tmpsEEpi3/deps/graphicsmagick/1.3.20/mmonsoor/camera_combinexsannos/2591056df814/env.sh; LANG=C Rscript /tmp/713334.1.short.q/tmpsEEpi3/shed_tools/testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/2591056df814/camera_combinexsannos/CAMERA.r xfunction combinexsAnnos image_pos /tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_1.dat image_neg /tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_2.dat variableMetadataOutput /tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_3.dat pos TRUE tol 2 ruleset 1,1 convert_param FALSE keep_meta TRUE] galaxy.jobs.runners DEBUG 2016-04-11 15:38:09,912 (3) command is: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/tool_script.sh; return_code=$?; python "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/set_metadata_3_tNOM.py" "/tmp/713334.1.short.q/tmpsEEpi3/tmp/tmp8QRaEb" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/galaxy.json" "/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_in_HistoryDatasetAssociation_3_58fsJC,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_kwds_HistoryDatasetAssociation_3_y6cHAM,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_out_HistoryDatasetAssociation_3_K7CNlc,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_results_HistoryDatasetAssociation_3_EMb9Bo,/tmp/713334.1.short.q/tmpsEEpi3/files/000/dataset_3.dat,/tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/metadata_override_HistoryDatasetAssociation_3_fy9km1" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.local DEBUG 2016-04-11 15:38:09,929 (3) executing job script: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/galaxy_3.sh galaxy.jobs DEBUG 2016-04-11 15:38:09,940 (3) Persisting job destination (destination id: local:///) requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:10,244 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:10,411 "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:12,015 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:12,198 "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None galaxy.jobs.runners.local DEBUG 2016-04-11 15:38:12,523 execution finished: /tmp/713334.1.short.q/tmpsEEpi3/job_working_directory/000/3/galaxy_3.sh galaxy.jobs.output_checker INFO 2016-04-11 15:38:12,566 Job 3: Fatal error: Exit code 1 () galaxy.jobs.output_checker DEBUG 2016-04-11 15:38:12,566 Tool exit code indicates an error, failing job. galaxy.jobs DEBUG 2016-04-11 15:38:12,633 (3) setting dataset 3 state to ERROR galaxy.jobs DEBUG 2016-04-11 15:38:13,010 job 3 ended (finish() executed in (486.830 ms)) requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:15,404 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:15,554 "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:15,556 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:15,612 "GET /api/histories/2891970512fa2d5a/contents?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:15,614 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:15,781 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:15,783 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:15,896 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:15,898 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:16,277 "GET /api/jobs/54f2a3a23292eb07?full=true&key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:16,279 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:16,432 "GET /api/jobs/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:16,434 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:16,485 "GET /api/histories/2891970512fa2d5a/contents?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:16,487 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:16,647 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool INFO 2016-04-11 15:38:16,649 Starting new HTTP connection (1): localhost requests.packages.urllib3.connectionpool DEBUG 2016-04-11 15:38:16,760 "GET /api/histories/2891970512fa2d5a/contents/54f2a3a23292eb07/provenance?key=3e127c27dc9834f28705bc5836cf7cf2 HTTP/1.1" 200 None functional_tests.py INFO 2016-04-11 15:38:16,989 Shutting down functional_tests.py INFO 2016-04-11 15:38:16,989 Shutting down embedded web server functional_tests.py INFO 2016-04-11 15:38:16,992 Embedded web server stopped functional_tests.py INFO 2016-04-11 15:38:16,992 Shutting down app galaxy.jobs.handler INFO 2016-04-11 15:38:16,992 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-11 15:38:16,992 job handler queue stopped galaxy.jobs.runners INFO 2016-04-11 15:38:16,992 TaskRunner: Sending stop signal to 2 worker threads galaxy.jobs.runners INFO 2016-04-11 15:38:16,992 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2016-04-11 15:38:16,993 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-11 15:38:16,993 job handler stop queue stopped functional_tests.py INFO 2016-04-11 15:38:16,994 Embedded Universe application stopped functional_tests.py INFO 2016-04-11 15:38:16,994 Cleaning up temporary files in /tmp/713334.1.short.q/tmpi0htl5/tmpWnIGuv galaxy.jobs.handler INFO 2016-04-11 15:38:17,651 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-11 15:38:17,652 job handler queue stopped galaxy.jobs.runners INFO 2016-04-11 15:38:17,652 TaskRunner: Sending stop signal to 2 worker threads galaxy.jobs.runners INFO 2016-04-11 15:38:17,652 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2016-04-11 15:38:17,652 sending stop signal to worker thread galaxy.jobs.handler INFO 2016-04-11 15:38:17,652 job handler stop queue stopped testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3[0]: failed testtoolshed.g2.bx.psu.edu/repos/mmonsoor/camera_combinexsannos/abims_CAMERA_combinexsAnnos/2.0.3[0]: failed