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February 7, 2018 02:32
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Galaxy 17.09 run.sh log
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| Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample | |
| Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample | |
| Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample | |
| Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample | |
| Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample | |
| Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample | |
| Initializing static/welcome.html from welcome.html.sample | |
| Running virtualenv with interpreter /usr/bin/python2.7 | |
| New python executable in .venv/bin/python2.7 | |
| Also creating executable in .venv/bin/python | |
| Installing setuptools, pip...done. | |
| Activating virtualenv at .venv | |
| Downloading/unpacking pip>=8.1 | |
| Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB): 1.3MB downloaded | |
| Installing collected packages: pip | |
| Found existing installation: pip 1.5.4 | |
| Uninstalling pip: | |
| Successfully uninstalled pip | |
| Successfully installed pip | |
| Cleaning up... | |
| Collecting bx-python==0.7.3 (from -r requirements.txt (line 2)) | |
| /mnt/sda1/sdc1/Project/ML/trunk/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:318: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#snimissingwarning. | |
| SNIMissingWarning | |
| /mnt/sda1/sdc1/Project/ML/trunk/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning. | |
| InsecurePlatformWarning | |
| /mnt/sda1/sdc1/Project/ML/trunk/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning. | |
| InsecurePlatformWarning | |
| Downloading https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27mu-manylinux1_x86_64.whl (2.1MB) | |
| 100% |████████████████████████████████| 2.2MB 12.2MB/s | |
| Collecting MarkupSafe==0.23 (from -r requirements.txt (line 3)) | |
| Downloading https://wheels.galaxyproject.org/packages/MarkupSafe-0.23-cp27-cp27mu-manylinux1_x86_64.whl | |
| Collecting PyYAML==3.11 (from -r requirements.txt (line 4)) | |
| Downloading https://wheels.galaxyproject.org/packages/PyYAML-3.11-cp27-cp27mu-manylinux1_x86_64.whl (367kB) | |
| 100% |████████████████████████████████| 368kB 14.5MB/s | |
| Collecting SQLAlchemy==1.0.15 (from -r requirements.txt (line 5)) | |
| Downloading https://wheels.galaxyproject.org/packages/SQLAlchemy-1.0.15-cp27-cp27mu-manylinux1_x86_64.whl (1.0MB) | |
| 100% |████████████████████████████████| 1.0MB 476kB/s | |
| Collecting mercurial==3.7.3 (from -r requirements.txt (line 6)) | |
| Downloading https://wheels.galaxyproject.org/packages/mercurial-3.7.3-cp27-cp27mu-manylinux1_x86_64.whl (1.5MB) | |
| 100% |████████████████████████████████| 1.5MB 14.4MB/s | |
| Collecting numpy==1.9.2 (from -r requirements.txt (line 7)) | |
| Downloading https://wheels.galaxyproject.org/packages/numpy-1.9.2-cp27-cp27mu-manylinux1_x86_64.whl (10.2MB) | |
| 100% |████████████████████████████████| 10.2MB 1.6MB/s | |
| Collecting pycrypto==2.6.1 (from -r requirements.txt (line 8)) | |
| Downloading https://wheels.galaxyproject.org/packages/pycrypto-2.6.1-cp27-cp27mu-manylinux1_x86_64.whl (492kB) | |
| 100% |████████████████████████████████| 501kB 51.2MB/s | |
| Collecting uWSGI==2.0.15 (from -r requirements.txt (line 9)) | |
| Downloading https://wheels.galaxyproject.org/packages/uWSGI-2.0.15-cp27-cp27mu-manylinux1_x86_64.whl (494kB) | |
| 100% |████████████████████████████████| 501kB 38.2MB/s | |
| Collecting bz2file==0.98 (from -r requirements.txt (line 16)) | |
| Downloading https://wheels.galaxyproject.org/packages/bz2file-0.98-py2-none-any.whl | |
| Collecting ipaddress==1.0.18 (from -r requirements.txt (line 17)) | |
| Downloading https://wheels.galaxyproject.org/packages/ipaddress-1.0.18-py2-none-any.whl | |
| Collecting Paste==2.0.2 (from -r requirements.txt (line 18)) | |
| Downloading https://wheels.galaxyproject.org/packages/Paste-2.0.2-py2-none-any.whl (610kB) | |
| 100% |████████████████████████████████| 614kB 71.5MB/s | |
| Collecting PasteDeploy==1.5.2 (from -r requirements.txt (line 19)) | |
| Downloading https://wheels.galaxyproject.org/packages/PasteDeploy-1.5.2-py2.py3-none-any.whl | |
| Collecting docutils==0.14 (from -r requirements.txt (line 20)) | |
| Downloading docutils-0.14-py2-none-any.whl (543kB) | |
| 100% |████████████████████████████████| 552kB 1.0MB/s | |
| Collecting wchartype==0.1 (from -r requirements.txt (line 21)) | |
| Downloading https://wheels.galaxyproject.org/packages/wchartype-0.1-py2-none-any.whl | |
| Collecting repoze.lru==0.6 (from -r requirements.txt (line 22)) | |
| Downloading repoze.lru-0.6.tar.gz | |
| Collecting Routes==2.4.1 (from -r requirements.txt (line 23)) | |
| Downloading https://wheels.galaxyproject.org/packages/Routes-2.4.1-py2.py3-none-any.whl (48kB) | |
| 100% |████████████████████████████████| 51kB 24.6MB/s | |
| Collecting WebOb==1.4.1 (from -r requirements.txt (line 24)) | |
| Downloading https://wheels.galaxyproject.org/packages/WebOb-1.4.1-py2.py3-none-any.whl (73kB) | |
| 100% |████████████████████████████████| 81kB 330kB/s | |
| Collecting WebHelpers==1.3 (from -r requirements.txt (line 25)) | |
| Downloading https://wheels.galaxyproject.org/packages/WebHelpers-1.3-py2-none-any.whl (149kB) | |
| 100% |████████████████████████████████| 153kB 395kB/s | |
| Collecting Mako==1.0.2 (from -r requirements.txt (line 26)) | |
| Downloading https://wheels.galaxyproject.org/packages/Mako-1.0.2-py2-none-any.whl (76kB) | |
| 100% |████████████████████████████████| 81kB 15.4MB/s | |
| Collecting pytz==2015.4 (from -r requirements.txt (line 27)) | |
| Downloading https://wheels.galaxyproject.org/packages/pytz-2015.4-py2-none-any.whl (475kB) | |
| 100% |████████████████████████████████| 481kB 478kB/s | |
| Collecting Babel==2.4.0 (from -r requirements.txt (line 28)) | |
| Downloading https://wheels.galaxyproject.org/packages/Babel-2.4.0-py2.py3-none-any.whl (6.8MB) | |
| 100% |████████████████████████████████| 6.8MB 2.6MB/s | |
| Collecting Beaker==1.7.0 (from -r requirements.txt (line 29)) | |
| Downloading https://wheels.galaxyproject.org/packages/Beaker-1.7.0-py2-none-any.whl (44kB) | |
| 100% |████████████████████████████████| 51kB 26.7MB/s | |
| Collecting dictobj==0.3.1 (from -r requirements.txt (line 30)) | |
| Downloading https://wheels.galaxyproject.org/packages/dictobj-0.3.1-py2-none-any.whl | |
| Collecting nose==1.3.7 (from -r requirements.txt (line 31)) | |
| Downloading https://wheels.galaxyproject.org/packages/nose-1.3.7-py2-none-any.whl (154kB) | |
| 100% |████████████████████████████████| 163kB 78.6MB/s | |
| Collecting Parsley==1.3 (from -r requirements.txt (line 32)) | |
| Downloading https://wheels.galaxyproject.org/packages/Parsley-1.3-py2-none-any.whl (88kB) | |
| 100% |████████████████████████████████| 92kB 8.9MB/s | |
| Collecting six==1.10.0 (from -r requirements.txt (line 33)) | |
| Downloading https://wheels.galaxyproject.org/packages/six-1.10.0-py2.py3-none-any.whl | |
| Collecting Whoosh==2.7.4 (from -r requirements.txt (line 34)) | |
| Downloading https://wheels.galaxyproject.org/packages/Whoosh-2.7.4-py2.py3-none-any.whl (468kB) | |
| 100% |████████████████████████████████| 471kB 70.2MB/s | |
| Collecting galaxy_sequence_utils==1.0.2 (from -r requirements.txt (line 35)) | |
| Downloading https://wheels.galaxyproject.org/packages/galaxy_sequence_utils-1.0.2-py2.py3-none-any.whl | |
| Collecting h5py==2.7.1 (from -r requirements.txt (line 36)) | |
| Downloading h5py-2.7.1-cp27-cp27mu-manylinux1_x86_64.whl (4.8MB) | |
| 100% |████████████████████████████████| 4.8MB 335kB/s | |
| Collecting pykwalify==1.5.1 (from -r requirements.txt (line 39)) | |
| Downloading pykwalify-1.5.1.tar.gz (40kB) | |
| 100% |████████████████████████████████| 40kB 6.9MB/s | |
| Collecting python-dateutil==2.5.3 (from -r requirements.txt (line 40)) | |
| Downloading python_dateutil-2.5.3-py2.py3-none-any.whl (201kB) | |
| 100% |████████████████████████████████| 204kB 3.4MB/s | |
| Collecting docopt==0.6.2 (from -r requirements.txt (line 41)) | |
| Downloading docopt-0.6.2.tar.gz | |
| Collecting Cheetah==2.4.4 (from -r requirements.txt (line 44)) | |
| Downloading https://wheels.galaxyproject.org/packages/Cheetah-2.4.4-cp27-cp27mu-manylinux1_x86_64.whl (193kB) | |
| 100% |████████████████████████████████| 194kB 465kB/s | |
| Collecting Markdown==2.6.3 (from -r requirements.txt (line 45)) | |
| Downloading https://wheels.galaxyproject.org/packages/Markdown-2.6.3-py2-none-any.whl (158kB) | |
| 100% |████████████████████████████████| 163kB 468kB/s | |
| Collecting bioblend==0.7.0 (from -r requirements.txt (line 48)) | |
| Downloading https://wheels.galaxyproject.org/packages/bioblend-0.7.0-py2.py3-none-any.whl (82kB) | |
| 100% |████████████████████████████████| 92kB 72.4MB/s | |
| Collecting boto==2.38.0 (from -r requirements.txt (line 49)) | |
| Downloading https://wheels.galaxyproject.org/packages/boto-2.38.0-py2.py3-none-any.whl (1.3MB) | |
| 100% |████████████████████████████████| 1.3MB 10.8MB/s | |
| Collecting requests==2.10.0 (from -r requirements.txt (line 50)) | |
| Downloading https://wheels.galaxyproject.org/packages/requests-2.10.0-py2-none-any.whl (506kB) | |
| 100% |████████████████████████████████| 512kB 15.4MB/s | |
| Collecting requests-toolbelt==0.4.0 (from -r requirements.txt (line 51)) | |
| Downloading https://wheels.galaxyproject.org/packages/requests_toolbelt-0.4.0-py2.py3-none-any.whl | |
| Collecting kombu==3.0.30 (from -r requirements.txt (line 54)) | |
| Downloading https://wheels.galaxyproject.org/packages/kombu-3.0.30-py2.py3-none-any.whl (241kB) | |
| 100% |████████████████████████████████| 245kB 13.8MB/s | |
| Collecting amqp==1.4.8 (from -r requirements.txt (line 55)) | |
| Downloading https://wheels.galaxyproject.org/packages/amqp-1.4.8-py2.py3-none-any.whl (51kB) | |
| 100% |████████████████████████████████| 61kB 64.3MB/s | |
| Collecting anyjson==0.3.3 (from -r requirements.txt (line 56)) | |
| Downloading https://wheels.galaxyproject.org/packages/anyjson-0.3.3-py2-none-any.whl | |
| Collecting psutil==4.1.0 (from -r requirements.txt (line 59)) | |
| Downloading https://wheels.galaxyproject.org/packages/psutil-4.1.0-cp27-cp27mu-manylinux1_x86_64.whl (168kB) | |
| 100% |████████████████████████████████| 174kB 14.9MB/s | |
| Collecting pulsar-galaxy-lib==0.8.0 (from -r requirements.txt (line 60)) | |
| Downloading pulsar_galaxy_lib-0.8.0-py2-none-any.whl (163kB) | |
| 100% |████████████████████████████████| 174kB 3.7MB/s | |
| Collecting sqlalchemy-migrate==0.10.0 (from -r requirements.txt (line 63)) | |
| Downloading https://wheels.galaxyproject.org/packages/sqlalchemy_migrate-0.10.0-py2-none-any.whl (108kB) | |
| 100% |████████████████████████████████| 112kB 71.9MB/s | |
| Collecting decorator==4.0.2 (from -r requirements.txt (line 64)) | |
| Downloading https://wheels.galaxyproject.org/packages/decorator-4.0.2-py2.py3-none-any.whl | |
| Collecting Tempita==0.5.3dev (from -r requirements.txt (line 65)) | |
| Downloading https://wheels.galaxyproject.org/packages/Tempita-0.5.3.dev0-py2-none-any.whl | |
| Collecting sqlparse==0.1.16 (from -r requirements.txt (line 66)) | |
| Downloading https://wheels.galaxyproject.org/packages/sqlparse-0.1.16-py2-none-any.whl | |
| Collecting pbr==1.8.0 (from -r requirements.txt (line 67)) | |
| Downloading https://wheels.galaxyproject.org/packages/pbr-1.8.0-py2.py3-none-any.whl (87kB) | |
| 100% |████████████████████████████████| 92kB 74.0MB/s | |
| Collecting svgwrite==1.1.6 (from -r requirements.txt (line 70)) | |
| Downloading https://wheels.galaxyproject.org/packages/svgwrite-1.1.6-py2-none-any.whl (62kB) | |
| 100% |████████████████████████████████| 71kB 78.5MB/s | |
| Collecting pyparsing==2.1.1 (from -r requirements.txt (line 71)) | |
| Downloading https://wheels.galaxyproject.org/packages/pyparsing-2.1.1-py2.py3-none-any.whl | |
| Collecting Fabric==1.13.2 (from -r requirements.txt (line 74)) | |
| Downloading https://wheels.galaxyproject.org/packages/Fabric-1.13.2-py2-none-any.whl (92kB) | |
| 100% |████████████████████████████████| 102kB 36.1MB/s | |
| Collecting paramiko==2.2.1 (from -r requirements.txt (line 75)) | |
| Downloading https://wheels.galaxyproject.org/packages/paramiko-2.2.1-py2.py3-none-any.whl (176kB) | |
| 100% |████████████████████████████████| 184kB 466kB/s | |
| Collecting ecdsa==0.13 (from -r requirements.txt (line 76)) | |
| Downloading https://wheels.galaxyproject.org/packages/ecdsa-0.13-py2.py3-none-any.whl (44kB) | |
| 100% |████████████████████████████████| 51kB 64.7MB/s | |
| Collecting pysam==0.8.4+gx5 (from -r requirements.txt (line 79)) | |
| /mnt/sda1/sdc1/Project/ML/trunk/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning. | |
| InsecurePlatformWarning | |
| Downloading https://wheels.galaxyproject.org/packages/pysam-0.8.4+gx5-cp27-cp27mu-manylinux1_x86_64.whl (11.8MB) | |
| 100% |████████████████████████████████| 11.8MB 1.2MB/s | |
| Collecting python-genomespaceclient==0.1.8 (from -r requirements.txt (line 82)) | |
| Downloading python-genomespaceclient-0.1.8.tar.gz | |
| Collecting PasteScript (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) | |
| Downloading PasteScript-2.0.2-py2.py3-none-any.whl (74kB) | |
| 100% |████████████████████████████████| 81kB 6.3MB/s | |
| Collecting pynacl>=1.0.1 (from paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Downloading PyNaCl-1.2.1-cp27-cp27mu-manylinux1_x86_64.whl (696kB) | |
| 100% |████████████████████████████████| 706kB 1.5MB/s | |
| Collecting bcrypt>=3.1.3 (from paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Downloading bcrypt-3.1.4-cp27-cp27mu-manylinux1_x86_64.whl (57kB) | |
| 100% |████████████████████████████████| 61kB 7.6MB/s | |
| Collecting cryptography>=1.1 (from paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Downloading cryptography-2.1.4-cp27-cp27mu-manylinux1_x86_64.whl (2.2MB) | |
| 100% |████████████████████████████████| 2.2MB 660kB/s | |
| Collecting pyasn1>=0.1.7 (from paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Downloading pyasn1-0.4.2-py2.py3-none-any.whl (71kB) | |
| 100% |████████████████████████████████| 71kB 4.1MB/s | |
| Collecting boto3 (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) | |
| Downloading boto3-1.5.24-py2.py3-none-any.whl (128kB) | |
| 100% |████████████████████████████████| 133kB 5.4MB/s | |
| Collecting python-swiftclient (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) | |
| Downloading python_swiftclient-3.5.0-py2.py3-none-any.whl (77kB) | |
| 100% |████████████████████████████████| 81kB 8.4MB/s | |
| Collecting cffi>=1.4.1 (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Downloading cffi-1.11.4-cp27-cp27mu-manylinux1_x86_64.whl (406kB) | |
| 100% |████████████████████████████████| 409kB 3.1MB/s | |
| Collecting enum34; python_version < "3" (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Downloading enum34-1.1.6-py2-none-any.whl | |
| Collecting idna>=2.1 (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Downloading https://wheels.galaxyproject.org/packages/idna-2.6-py2.py3-none-any.whl (56kB) | |
| 100% |████████████████████████████████| 61kB 304kB/s | |
| Collecting asn1crypto>=0.21.0 (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Downloading asn1crypto-0.24.0-py2.py3-none-any.whl (101kB) | |
| 100% |████████████████████████████████| 102kB 8.0MB/s | |
| Collecting jmespath<1.0.0,>=0.7.1 (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) | |
| Downloading jmespath-0.9.3-py2.py3-none-any.whl | |
| Collecting botocore<1.9.0,>=1.8.38 (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) | |
| Downloading botocore-1.8.38-py2.py3-none-any.whl (4.1MB) | |
| 100% |████████████████████████████████| 4.1MB 408kB/s | |
| Collecting s3transfer<0.2.0,>=0.1.10 (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) | |
| Downloading s3transfer-0.1.12-py2.py3-none-any.whl (59kB) | |
| 100% |████████████████████████████████| 61kB 6.3MB/s | |
| Collecting futures>=3.0; python_version == "2.7" or python_version == "2.6" (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) | |
| Downloading futures-3.2.0-py2-none-any.whl | |
| Collecting pycparser (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Downloading pycparser-2.18.tar.gz (245kB) | |
| 100% |████████████████████████████████| 256kB 7.2MB/s | |
| Installing collected packages: bx-python, MarkupSafe, PyYAML, SQLAlchemy, mercurial, numpy, pycrypto, uWSGI, bz2file, ipaddress, six, Paste, PasteDeploy, docutils, wchartype, repoze.lru, Routes, WebOb, WebHelpers, Mako, pytz, Babel, Beaker, dictobj, nose, Parsley, Whoosh, galaxy-sequence-utils, h5py, docopt, python-dateutil, pykwalify, Markdown, Cheetah, boto, requests, requests-toolbelt, bioblend, amqp, anyjson, kombu, psutil, PasteScript, pulsar-galaxy-lib, Tempita, decorator, sqlparse, pbr, sqlalchemy-migrate, pyparsing, svgwrite, pycparser, cffi, pynacl, bcrypt, enum34, idna, asn1crypto, cryptography, pyasn1, paramiko, Fabric, ecdsa, pysam, jmespath, botocore, futures, s3transfer, boto3, python-swiftclient, python-genomespaceclient | |
| Running setup.py install for repoze.lru ... done | |
| Running setup.py install for docopt ... done | |
| Running setup.py install for pykwalify ... done | |
| Running setup.py install for pycparser ... done | |
| Running setup.py install for python-genomespaceclient ... done | |
| Successfully installed Babel-2.4.0 Beaker-1.7.0 Cheetah-2.4.4 Fabric-1.13.2 Mako-1.0.2 Markdown-2.6.3 MarkupSafe-0.23 Parsley-1.3 Paste-2.0.2 PasteDeploy-1.5.2 PasteScript-2.0.2 PyYAML-3.11 Routes-2.4.1 SQLAlchemy-1.0.15 Tempita-0.5.3.dev0 WebHelpers-1.3 WebOb-1.4.1 Whoosh-2.7.4 amqp-1.4.8 anyjson-0.3.3 asn1crypto-0.24.0 bcrypt-3.1.4 bioblend-0.7.0 boto-2.38.0 boto3-1.5.24 botocore-1.8.38 bx-python-0.7.3 bz2file-0.98 cffi-1.11.4 cryptography-2.1.4 decorator-4.0.2 dictobj-0.3.1 docopt-0.6.2 docutils-0.14 ecdsa-0.13 enum34-1.1.6 futures-3.2.0 galaxy-sequence-utils-1.0.2 h5py-2.7.1 idna-2.6 ipaddress-1.0.18 jmespath-0.9.3 kombu-3.0.30 mercurial-3.7.3 nose-1.3.7 numpy-1.9.2 paramiko-2.2.1 pbr-1.8.0 psutil-4.1.0 pulsar-galaxy-lib-0.8.0 pyasn1-0.4.2 pycparser-2.18 pycrypto-2.6.1 pykwalify-1.5.1 pynacl-1.2.1 pyparsing-2.1.1 pysam-0.8.4+gx5 python-dateutil-2.5.3 python-genomespaceclient-0.1.8 python-swiftclient-3.5.0 pytz-2015.4 repoze.lru-0.6 requests-2.10.0 requests-toolbelt-0.4.0 s3transfer-0.1.12 six-1.10.0 sqlalchemy-migrate-0.10.0 sqlparse-0.1.16 svgwrite-1.1.6 uWSGI-2.0.15 wchartype-0.1 | |
| /mnt/sda1/sdc1/Project/ML/trunk/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.io/en/latest/security.html#insecureplatformwarning. | |
| InsecurePlatformWarning | |
| Activating virtualenv at .venv | |
| Requirement already satisfied: pip>=8.1 in ./.venv/lib/python2.7/site-packages | |
| Requirement already satisfied: bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) | |
| Requirement already satisfied: MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) | |
| Requirement already satisfied: PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) | |
| Requirement already satisfied: SQLAlchemy==1.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) | |
| Requirement already satisfied: mercurial==3.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6)) | |
| Requirement already satisfied: numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) | |
| Requirement already satisfied: pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) | |
| Requirement already satisfied: uWSGI==2.0.15 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) | |
| Requirement already satisfied: bz2file==0.98 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) | |
| Requirement already satisfied: ipaddress==1.0.18 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) | |
| Requirement already satisfied: Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) | |
| Requirement already satisfied: PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) | |
| Requirement already satisfied: docutils==0.14 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) | |
| Requirement already satisfied: wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) | |
| Requirement already satisfied: repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) | |
| Requirement already satisfied: Routes==2.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) | |
| Requirement already satisfied: WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) | |
| Requirement already satisfied: WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) | |
| Requirement already satisfied: Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) | |
| Requirement already satisfied: pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) | |
| Requirement already satisfied: Babel==2.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 28)) | |
| Requirement already satisfied: Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 29)) | |
| Requirement already satisfied: dictobj==0.3.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) | |
| Requirement already satisfied: nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) | |
| Requirement already satisfied: Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32)) | |
| Requirement already satisfied: six==1.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 33)) | |
| Requirement already satisfied: Whoosh==2.7.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) | |
| Requirement already satisfied: galaxy_sequence_utils==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) | |
| Requirement already satisfied: h5py==2.7.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) | |
| Requirement already satisfied: pykwalify==1.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39)) | |
| Requirement already satisfied: python-dateutil==2.5.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) | |
| Requirement already satisfied: docopt==0.6.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) | |
| Requirement already satisfied: Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44)) | |
| Requirement already satisfied: Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) | |
| Requirement already satisfied: bioblend==0.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) | |
| Requirement already satisfied: boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) | |
| Requirement already satisfied: requests==2.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50)) | |
| Requirement already satisfied: requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) | |
| Requirement already satisfied: kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) | |
| Requirement already satisfied: amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55)) | |
| Requirement already satisfied: anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56)) | |
| Requirement already satisfied: psutil==4.1.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) | |
| Requirement already satisfied: pulsar-galaxy-lib==0.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 60)) | |
| Requirement already satisfied: sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 63)) | |
| Requirement already satisfied: decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64)) | |
| Requirement already satisfied: Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 65)) | |
| Requirement already satisfied: sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) | |
| Requirement already satisfied: pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 67)) | |
| Requirement already satisfied: svgwrite==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70)) | |
| Requirement already satisfied: pyparsing==2.1.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 71)) | |
| Requirement already satisfied: Fabric==1.13.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 74)) | |
| Requirement already satisfied: paramiko==2.2.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 75)) | |
| Requirement already satisfied: ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 76)) | |
| Requirement already satisfied: pysam==0.8.4+gx5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 79)) | |
| Requirement already satisfied: python-genomespaceclient==0.1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 82)) | |
| Requirement already satisfied: PasteScript in ./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.8.0->-r requirements.txt (line 60)) | |
| Requirement already satisfied: pynacl>=1.0.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Requirement already satisfied: bcrypt>=3.1.3 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Requirement already satisfied: cryptography>=1.1 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Requirement already satisfied: pyasn1>=0.1.7 in ./.venv/lib/python2.7/site-packages (from paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Requirement already satisfied: boto3 in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) | |
| Requirement already satisfied: python-swiftclient in ./.venv/lib/python2.7/site-packages (from python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) | |
| Requirement already satisfied: cffi>=1.4.1 in ./.venv/lib/python2.7/site-packages (from pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Requirement already satisfied: enum34; python_version < "3" in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Requirement already satisfied: idna>=2.1 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Requirement already satisfied: asn1crypto>=0.21.0 in ./.venv/lib/python2.7/site-packages (from cryptography>=1.1->paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) | |
| Requirement already satisfied: botocore<1.9.0,>=1.8.38 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) | |
| Requirement already satisfied: s3transfer<0.2.0,>=0.1.10 in ./.venv/lib/python2.7/site-packages (from boto3->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) | |
| Requirement already satisfied: futures>=3.0; python_version == "2.7" or python_version == "2.6" in ./.venv/lib/python2.7/site-packages (from python-swiftclient->python-genomespaceclient==0.1.8->-r requirements.txt (line 82)) | |
| Requirement already satisfied: pycparser in ./.venv/lib/python2.7/site-packages (from cffi>=1.4.1->pynacl>=1.0.1->paramiko==2.2.1->-r requirements.txt (line 75)) | |
| Activating virtualenv at .venv | |
| galaxy.tools.deps WARNING 2018-02-07 10:06:58,333 Path './database/dependencies' does not exist, ignoring | |
| galaxy.tools.deps WARNING 2018-02-07 10:06:58,333 Path './database/dependencies' is not directory, ignoring | |
| galaxy.tools.deps DEBUG 2018-02-07 10:06:58,337 Unable to find config file './dependency_resolvers_conf.xml' | |
| galaxy.tools.deps.conda_util INFO 2018-02-07 10:06:58,337 Installing Conda, this may take several minutes. | |
| PREFIX=/mnt/sda1/sdc1/Project/ML/trunk/galaxy/database/dependencies/_conda | |
| installing: python-3.5.2-0 ... | |
| installing: conda-env-2.6.0-0 ... | |
| installing: openssl-1.0.2j-0 ... | |
| installing: pycosat-0.6.1-py35_1 ... | |
| installing: readline-6.2-2 ... | |
| installing: requests-2.11.1-py35_0 ... | |
| installing: ruamel_yaml-0.11.14-py35_0 ... | |
| installing: sqlite-3.13.0-0 ... | |
| installing: tk-8.5.18-0 ... | |
| installing: xz-5.2.2-0 ... | |
| installing: yaml-0.1.6-0 ... | |
| installing: zlib-1.2.8-3 ... | |
| installing: conda-4.2.12-py35_0 ... | |
| installing: pycrypto-2.6.1-py35_4 ... | |
| installing: pip-8.1.2-py35_0 ... | |
| installing: wheel-0.29.0-py35_0 ... | |
| installing: setuptools-27.2.0-py35_0 ... | |
| Python 3.5.2 :: Continuum Analytics, Inc. | |
| creating default environment... | |
| installation finished. | |
| Fetching package metadata ....... | |
| Solving package specifications: .......... | |
| Package plan for installation in environment /mnt/sda1/sdc1/Project/ML/trunk/galaxy/database/dependencies/_conda: | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| libffi-3.2.1 | 1 38 KB | |
| asn1crypto-0.22.0 | py35_0 149 KB | |
| idna-2.6 | py35_0 123 KB | |
| pycparser-2.18 | py35_0 168 KB | |
| pyparsing-2.2.0 | py35_0 96 KB | |
| requests-2.14.2 | py35_0 723 KB | |
| six-1.10.0 | py35_0 17 KB | |
| cffi-1.10.0 | py35_0 342 KB | |
| packaging-16.8 | py35_0 31 KB | |
| cryptography-1.8.1 | py35_0 846 KB | |
| pyopenssl-17.0.0 | py35_0 76 KB | |
| conda-4.3.24 | py35_0 516 KB | |
| ------------------------------------------------------------ | |
| Total: 3.1 MB | |
| The following NEW packages will be INSTALLED: | |
| asn1crypto: 0.22.0-py35_0 | |
| cffi: 1.10.0-py35_0 | |
| cryptography: 1.8.1-py35_0 | |
| idna: 2.6-py35_0 | |
| libffi: 3.2.1-1 | |
| packaging: 16.8-py35_0 | |
| pycparser: 2.18-py35_0 | |
| pyopenssl: 17.0.0-py35_0 | |
| pyparsing: 2.2.0-py35_0 | |
| six: 1.10.0-py35_0 | |
| The following packages will be UPDATED: | |
| conda: 4.2.12-py35_0 --> 4.3.24-py35_0 | |
| requests: 2.11.1-py35_0 --> 2.14.2-py35_0 | |
| DEBUG:galaxy.app:python path is: /mnt/sda1/sdc1/Project/ML/trunk/galaxy/scripts, /mnt/sda1/sdc1/Project/ML/trunk/galaxy/lib, /mnt/sda1/sdc1/Project/ML/trunk/galaxy/.venv/lib/python2.7, /mnt/sda1/sdc1/Project/ML/trunk/galaxy/.venv/lib/python2.7/plat-x86_64-linux-gnu, /mnt/sda1/sdc1/Project/ML/trunk/galaxy/.venv/lib/python2.7/lib-tk, /mnt/sda1/sdc1/Project/ML/trunk/galaxy/.venv/lib/python2.7/lib-old, /mnt/sda1/sdc1/Project/ML/trunk/galaxy/.venv/lib/python2.7/lib-dynload, /usr/lib/python2.7, /usr/lib/python2.7/plat-x86_64-linux-gnu, /usr/lib/python2.7/lib-tk, /mnt/sda1/sdc1/Project/ML/trunk/galaxy/.venv/local/lib/python2.7/site-packages | |
| DEBUG:galaxy.containers:config file './config/containers_conf.yml' does not exist, running with default config | |
| INFO:galaxy.config:Logging at '10' level to 'stdout' | |
| galaxy.queue_worker INFO 2018-02-07 10:07:23,463 Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE | |
| tool_shed.tool_shed_registry DEBUG 2018-02-07 10:07:23,480 Loading references to tool sheds from ./config/tool_sheds_conf.xml.sample | |
| tool_shed.tool_shed_registry DEBUG 2018-02-07 10:07:23,480 Loaded reference to tool shed: Galaxy Main Tool Shed | |
| galaxy.app DEBUG 2018-02-07 10:07:23,483 Using "galaxy.ini" config file: /mnt/sda1/sdc1/Project/ML/trunk/galaxy/config/galaxy.ini.sample | |
| migrate.versioning.repository DEBUG 2018-02-07 10:07:23,508 Loading repository lib/galaxy/model/migrate... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,508 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,508 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,508 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,508 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,508 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,508 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,508 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,509 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,510 Loading script lib/galaxy/model/migrate/versions/0014_pages.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,510 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,510 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,510 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,510 Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,510 Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,510 Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,510 Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,510 Loading script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,510 Script lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,510 Loading script lib/galaxy/model/migrate/versions/0019_request_library_folder.py... | |
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| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Loading script lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Script lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Loading script lib/galaxy/model/migrate/versions/0095_hda_subsets.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Script lib/galaxy/model/migrate/versions/0095_hda_subsets.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Loading script lib/galaxy/model/migrate/versions/0096_openid_provider.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Script lib/galaxy/model/migrate/versions/0096_openid_provider.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Loading script lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Script lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Loading script lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Script lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Loading script lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Script lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Loading script lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Script lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Loading script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Loading script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Loading script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,519 Script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Loading script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Loading script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Loading script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Loading script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Loading script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Loading script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Loading script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Loading script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Loading script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,520 Loading script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Loading script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Loading script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Loading script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Loading script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Loading script lib/galaxy/model/migrate/versions/0119_job_metrics.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Script lib/galaxy/model/migrate/versions/0119_job_metrics.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Loading script lib/galaxy/model/migrate/versions/0120_dataset_collections.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Script lib/galaxy/model/migrate/versions/0120_dataset_collections.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Loading script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Loading script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,521 Script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Loading script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Loading script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Script lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,522 Loading script lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,523 Script lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,523 Loading script lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,523 Script lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,523 Loading script lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,523 Script lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,523 Loading script lib/galaxy/model/migrate/versions/0135_add_library_tags.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:07:23,523 Script lib/galaxy/model/migrate/versions/0135_add_library_tags.py loaded successfully | |
| migrate.versioning.repository DEBUG 2018-02-07 10:07:23,523 Repository lib/galaxy/model/migrate loaded successfully | |
| migrate.versioning.repository DEBUG 2018-02-07 10:07:23,523 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:23,525 No database, initializing | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:23,787 Migrating 0 -> 1... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:30,146 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:30,146 Migrating 1 -> 2... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:30,814 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:30,814 Migrating 2 -> 3... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:44,384 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:44,384 Migrating 3 -> 4... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:44,922 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:44,922 Migrating 4 -> 5... | |
| 0005_cleanup_datasets_fix DEBUG 2018-02-07 10:07:44,952 Fixing a discrepancy concerning deleted shared history items. | |
| /mnt/sda1/sdc1/Project/ML/trunk/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/relationships.py:2408: SAWarning: Non-simple column elements in primary join condition for property HistoryDatasetAssociation.visible_children - consider using remote() annotations to mark the remote side. | |
| % self.prop | |
| /mnt/sda1/sdc1/Project/ML/trunk/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/relationships.py:2408: SAWarning: Non-simple column elements in primary join condition for property LibraryDatasetDatasetAssociation.visible_children - consider using remote() annotations to mark the remote side. | |
| % self.prop | |
| /mnt/sda1/sdc1/Project/ML/trunk/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:562: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage. | |
| 'storage.' % (dialect.name, dialect.driver)) | |
| 0005_cleanup_datasets_fix DEBUG 2018-02-07 10:07:44,995 0 items affected, and restored. | |
| 0005_cleanup_datasets_fix DEBUG 2018-02-07 10:07:44,996 Time elapsed: 0.043848991394 | |
| 0005_cleanup_datasets_fix DEBUG 2018-02-07 10:07:44,996 Fixing a discrepancy concerning cleaning up deleted history items shared before HDAs. | |
| 0005_cleanup_datasets_fix DEBUG 2018-02-07 10:07:44,998 0 items affected, and restored. | |
| 0005_cleanup_datasets_fix DEBUG 2018-02-07 10:07:44,998 Time elapsed: 0.00210404396057 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:45,096 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:45,096 Migrating 5 -> 6... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:45,518 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:45,518 This migration script changes certain values in the history_dataset_association.extension | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:45,518 column, specifically 'qual' is changed to be 'qual454'. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:45,518 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:45,518 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:45,518 Migrating 6 -> 7... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:46,272 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:46,272 This migration script creates the new history_user_share_association table, and adds | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:46,272 a new boolean type column to the history table. This provides support for sharing | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:46,272 histories in the same way that workflows are shared. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:46,272 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:46,272 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:46,272 Migrating 7 -> 8... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,033 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,033 This migration script adds the following new tables for supporting Galaxy forms: | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,033 1) form_definition_current | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,033 2) form_definition | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,033 3) form_values | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,033 4) request_type | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,033 5) request | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,033 6) sample | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,033 7) sample_state | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,033 8) sample_event | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,033 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,033 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,033 Migrating 8 -> 9... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,787 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,787 This migration script adds a new column to 2 tables: | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,787 1) a new boolean type column named 'submitted' to the 'request' table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,787 2) a new string type column named 'bar_code' to the 'sample' table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,787 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,788 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:51,788 Migrating 9 -> 10... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,733 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,733 This migration script adds the history_dataset_association_display_at_authorization table, | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,733 which allows 'private' datasets to be displayed at external sites without making them public. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,733 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,733 If using mysql, this script will display the following error, which is corrected in the next | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,733 migration script: | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,733 history_dataset_association_display_at_authorization table failed: (OperationalError) | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,733 (1059, "Identifier name 'ix_history_dataset_association_display_at_authorization_update_time' | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,733 is too long | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,733 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,733 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,733 Migrating 10 -> 11... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,932 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,932 This script fixes a problem introduced in the previous migration script | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,932 0010_hda_display_at_atuhz_table.py . MySQL has a name length limit and | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,932 thus the index "ix_hdadaa_history_dataset_association_id" has to be | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,932 manually created. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,933 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,933 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:52,933 Migrating 11 -> 12... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:54,975 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:54,975 This script adds a new user_address table that is currently only used with sample requests, where | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:54,975 a user can select from a list of his addresses to associate with the request. This script also | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:54,975 drops the request.submitted column which was boolean and replaces it with a request.state column | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:54,975 which is a string, allowing for more flexibility with request states. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:54,975 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:54,975 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:54,975 Migrating 12 -> 13... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 This migration script eliminates all of the tables that were used for the 1st version of the | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 library templates where template fields and contents were each stored as a separate table row | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 in various library item tables. All of these tables are dropped in this script, eliminating all | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 existing template data. A total of 14 existing tables are dropped. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 We're now basing library templates on forms, so field contents are | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 stored as a jsonified list in the form_values table. This script introduces the following 3 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 new association tables: | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 1) library_info_association | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 2) library_folder_info_association | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 3) library_dataset_dataset_info_association | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 If using mysql, this script will throw an (OperationalError) exception due to a long index name on | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 the library_dataset_dataset_info_association table, which is OK because the script creates an index | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,687 with a shortened name. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,688 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,688 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:07:59,688 Migrating 13 -> 14... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:01,064 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:01,064 Migration script to add support for "Pages". | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:01,065 1) Creates Page and PageRevision tables | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:01,065 2) Adds username column to User table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:01,065 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:01,065 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:01,065 Migrating 14 -> 15... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,059 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,059 This migration script adds the tables necessary to support tagging of histories, | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,059 datasets, and history-dataset associations (user views of datasets). | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,059 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,059 If using mysql, this script will display the following error, which is corrected in the next | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,059 migration script: | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,059 history_dataset_association_tag_association table failed: (OperationalError) | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,059 (1059, "Identifier name 'ix_history_dataset_association_tag_association_history_dataset_association_id' | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,059 is too long) | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,059 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,059 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,059 Migrating 15 -> 16... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,505 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,506 This script fixes a problem introduced in 0015_tagging.py. MySQL has a name length | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,506 limit and thus the index "ix_hda_ta_history_dataset_association_id" has to be | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,506 manually created. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,506 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,506 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:04,506 Migrating 16 -> 17... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:05,432 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:05,432 This script adds 3 indexes to table columns: library_folder.name, | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:05,432 library_dataset.name, library_dataset_dataset_association.name. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:05,432 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:05,432 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:05,433 Migrating 17 -> 18... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:09,894 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:09,894 This migration script provides support for (a) ordering tags by recency and | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:09,894 (b) tagging pages. This script deletes all existing tags. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:09,894 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:09,894 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:09,894 Migrating 18 -> 19... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:11,014 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:11,014 This script creates a request.folder_id column which is a foreign | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:11,014 key to the library_folder table. This also adds a 'type' and 'layout' column | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:11,014 to the form_definition table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:11,014 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:11,014 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:11,014 Migrating 19 -> 20... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:12,293 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:12,293 This script creates a job_to_output_library_dataset table for allowing library | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:12,293 uploads to run as regular jobs. To support this, a library_folder_id column is | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:12,293 added to the job table, and library_folder/output_library_datasets relations | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:12,293 are added to the Job object. An index is also added to the dataset.state | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:12,293 column. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:12,293 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:12,293 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:12,293 Migrating 20 -> 21... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:13,064 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:13,064 This migration script adds a user preferences table to Galaxy. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:13,065 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:13,065 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:13,065 Migrating 21 -> 22... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:14,084 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:14,084 Migration script to add support for storing visualizations. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:14,084 1) Creates Visualization and VisualizationRevision tables | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:14,085 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:14,085 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:14,085 Migrating 22 -> 23... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:15,018 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:15,018 Migration script to add columns for tracking whether pages are deleted and | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:15,018 publicly accessible. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:15,018 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:15,018 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:15,019 Migrating 23 -> 24... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:15,686 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:15,686 Remove unique constraint from page slugs to allow creating a page with | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:15,686 the same slug as a deleted page. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:15,686 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:15,686 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:15,686 Migrating 24 -> 25... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:16,326 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:16,326 This script adds a foreign key to the form_values table in the galaxy_user table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:16,326 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:16,326 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:16,326 Migrating 25 -> 26... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:19,505 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:19,505 This script adds tables needed for Galaxy cloud functionality. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:19,505 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:19,505 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:19,505 Migrating 26 -> 27... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:20,337 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:20,337 This migration script adds the request_event table and | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:20,337 removes the state field in the request table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:20,337 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:20,337 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:20,337 Migrating 27 -> 28... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:20,909 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:20,909 This script adds the filename_override_metadata column to the JobExternalOutputMetadata table, | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:20,909 allowing existing metadata files to be written when using external metadata and a cluster | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:20,909 set up with read-only access to database/files | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:20,909 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:20,909 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:20,909 Migrating 28 -> 29... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:21,681 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:21,681 This migration script adds a user actions table to Galaxy. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:21,681 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:21,682 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:21,682 Migrating 29 -> 30... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:22,226 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:22,227 Migration script to add column for a history slug. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:22,227 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:22,227 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:22,227 Migrating 30 -> 31... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:25,087 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:25,087 Migration script to (a) add and populate necessary columns for doing community tagging of histories, datasets, and pages and (b) add table for doing individual and community tagging of workflows. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:25,087 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:25,087 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:25,087 Migrating 31 -> 32... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:25,610 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:25,610 Migration script to add slug column for stored workflow. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:25,610 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:25,610 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:25,610 Migrating 32 -> 33... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:26,847 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:26,847 Migration script to add necessary columns for distinguishing between viewing/importing and publishing histories, workflows, and pages. Script adds published column to histories and workflows and importable column to pages. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:26,847 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:26,847 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:26,847 Migrating 33 -> 34... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:27,685 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:27,685 Migration script to create a table for page-user share association. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:27,685 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:27,685 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:27,685 Migrating 34 -> 35... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:31,493 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:31,493 Migration script to (a) create tables for annotating objects and (b) create tags for workflow steps. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:31,493 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:31,493 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:31,493 Migrating 35 -> 36... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:32,872 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:32,872 Migration script to add a deleted column to the following tables: | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:32,872 library_info_association, library_folder_info_association, library_dataset_dataset_info_association. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:32,872 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:32,872 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:32,872 Migrating 36 -> 37... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:35,454 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:35,454 This migration script removes the library_id & folder_id fields in the 'request' table and | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:35,454 adds the same to the 'sample' table. This also adds a 'datatx' column to request_type table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:35,454 to store the sequencer login information. Finally, this adds a 'dataset_files' column to | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:35,454 the sample table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:35,454 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:35,454 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:35,455 Migrating 37 -> 38... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:36,432 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:36,433 Migration script to add an inheritable column to the following tables: | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:36,433 library_info_association, library_folder_info_association. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:36,433 Also, in case of sqlite check if the previous migration script deleted the | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:36,433 request table and if so, restore the table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:36,433 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:36,433 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:36,433 Migrating 38 -> 39... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:36,966 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:36,966 Migration script to add a synopsis column to the library table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:36,966 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:36,966 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:36,966 Migrating 39 -> 40... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:38,862 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:38,862 Migration script to (a) create tables for annotating pages. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:38,862 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:38,862 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:38,862 Migrating 40 -> 41... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:40,040 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:40,040 Migration script to create tables for tracking workflow invocations. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:40,040 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:40,040 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:40,040 Migrating 41 -> 42... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:41,552 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:41,552 Drop and readd workflow invocation tables, allowing null jobs | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:41,552 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:41,553 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:41,553 Migrating 42 -> 43... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:45,174 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:45,174 Migration script to create tables and columns for sharing visualizations. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:45,174 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:45,174 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:45,174 Migrating 43 -> 44... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:45,683 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:45,683 Migration script to add a notify column to the request table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:45,683 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:45,683 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:45,683 Migrating 44 -> 45... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:46,510 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:46,510 Migration script to add the request_type_permissions table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:46,510 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:46,510 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:46,510 Migrating 45 -> 46... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,154 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,154 Migration script to create tables for handling post-job actions. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,154 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,154 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,154 Migrating 46 -> 47... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,880 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,880 Add a user_id column to the job table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,880 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,880 Updating user_id column in job table for 0 rows... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,880 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,881 Updated the user_id column for 0 rows in the job table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,881 0 rows have no user_id since the value was NULL in the galaxy_session table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,881 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,881 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:47,881 Migrating 47 -> 48... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:48,925 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:48,925 Add a state column to the history_dataset_association and library_dataset_dataset_association table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:48,925 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:48,925 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:48,926 Migrating 48 -> 49... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:49,735 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:49,735 Migration script to add the api_keys table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:49,735 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:49,735 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:49,735 Migrating 49 -> 50... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:51,406 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:51,406 This script drops tables that were associated with the old Galaxy Cloud functionality. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:51,406 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:51,406 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:51,406 Migrating 50 -> 51... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:52,116 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:52,116 Migration script to add imported column for jobs table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:52,116 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:52,116 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:52,116 Migrating 51 -> 52... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:55,234 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:55,234 Migration script to add the sample_dataset table and remove the 'dataset_files' column | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:55,235 from the 'sample' table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:55,235 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:55,235 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:55,235 Migrating 52 -> 53... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:58,869 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:58,870 Migration script to create tables for rating histories, datasets, workflows, pages, and visualizations. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:58,870 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:58,870 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:58,870 Migrating 53 -> 54... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:59,789 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:59,789 Migration script to add dbkey column for visualization. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:59,789 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:59,789 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:08:59,789 Migrating 54 -> 55... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:00,567 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:00,567 Migration script to add the post_job_action_association table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:00,567 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:00,567 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:00,567 Migrating 55 -> 56... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:01,169 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:01,169 Migration script to create tables for adding explicit workflow outputs. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:01,169 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:01,169 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:01,169 Migrating 56 -> 57... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:01,661 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:01,661 Migration script to modify the 'notify' field in the 'request' table from a boolean | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:01,661 to a JSONType | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:01,661 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:01,661 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:01,661 Migrating 57 -> 58... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:03,122 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:03,122 Migration script to create table for exporting histories to archives. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:03,123 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:03,123 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:03,123 Migrating 58 -> 59... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:05,543 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:05,543 Migration script to modify the 'file_path' field type in 'sample_dataset' table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:05,543 to 'TEXT' so that it can support large file paths exceeding 255 characters | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:05,543 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:05,543 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:05,544 Migrating 59 -> 60... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:06,613 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:06,613 Migration script to create column and table for importing histories from | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:06,613 file archives. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:06,613 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:06,613 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:06,613 Migrating 60 -> 61... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:07,441 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:07,441 Migration script to create tables task management. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:07,441 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:07,441 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:07,441 Migrating 61 -> 62... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:08,610 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:08,611 Migration script to create table for associating sessions and users with | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:08,611 OpenIDs. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:08,611 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:08,611 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:08,611 Migrating 62 -> 63... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:09,521 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:09,522 Migration script to create a new 'sequencer' table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:09,522 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:09,522 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:09,522 Migrating 63 -> 64... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:11,478 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:11,478 Migration script to add the run and sample_run_association tables. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:11,478 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:11,478 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:11,478 Migrating 64 -> 65... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:11,904 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:11,904 Migration script to add 'name' attribute to the JSON dict which describes | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:11,904 a form definition field and the form values in the database. In the 'form_values' | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:11,905 table, the 'content' column is now a JSON dict instead of a list. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:11,905 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:11,905 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:11,905 Migrating 65 -> 66... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:13,040 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:13,040 Migration script to create table for storing deferred job and managed transfer | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:13,040 information. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:13,040 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:13,040 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:13,040 Migrating 66 -> 67... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:16,217 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:16,217 Migration script to populate the 'sequencer' table and it is populated using unique | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:16,217 entries in the 'datatx_info' column in the 'request_type' table. It also deletes the 'datatx_info' | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:16,217 column in the 'request_type' table and adds a foreign key to the 'sequencer' table. The | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:16,217 actual contents of the datatx_info column are stored as form_values. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:16,217 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:16,218 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:16,218 Migrating 67 -> 68... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,314 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,315 This migration script renames the sequencer table to 'external_service' table and | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,315 creates a association table, 'request_type_external_service_association' and | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,315 populates it. The 'sequencer_id' foreign_key from the 'request_type' table is removed. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,315 The 'sequencer_type_id' column is renamed to 'external_service_type_id' in the renamed | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,315 table 'external_service'. Finally, adds a foreign key to the external_service table in the | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,315 sample_dataset table and populates it. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,315 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,315 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,315 Migrating 68 -> 69... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,714 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,714 Migration script to rename the sequencer information form type to external service information form | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,715 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,715 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:20,715 Migrating 69 -> 70... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:21,207 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:21,207 Migration script to add 'info' column to the transfer_job table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:21,207 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:21,207 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:21,207 Migrating 70 -> 71... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:23,991 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:23,991 Migration script to add 'workflow' and 'history' columns for a sample. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:23,991 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:23,991 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:23,991 Migrating 71 -> 72... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:25,184 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:25,184 Migration script to add 'pid' and 'socket' columns to the transfer_job table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:25,184 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:25,184 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:25,184 Migrating 72 -> 73... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:25,869 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:25,869 Migration script to add 'ldda_parent_id' column to the implicitly_converted_dataset_association table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:25,869 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:25,869 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:25,869 Migrating 73 -> 74... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:26,571 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:26,572 Migration script to add 'purged' column to the library_dataset table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:26,572 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:26,572 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:26,572 Migrating 74 -> 75... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:27,322 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:27,322 Migration script to add a 'subindex' column to the run table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:27,322 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:27,322 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:27,322 Migrating 75 -> 76... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:27,739 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:27,740 This migration script fixes the data corruption caused in the form_values | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:27,740 table (content json field) by migrate script 65. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:27,740 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:27,740 No corrupted rows found. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:27,740 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:27,740 Migrating 76 -> 77... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:29,111 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:29,111 Migration script to create table for storing tool tag associations. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:29,111 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:29,111 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:29,111 Migrating 77 -> 78... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:30,657 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:30,657 Migration script to add 'total_size' column to the dataset table, 'purged' | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:30,657 column to the HDA table, and 'disk_usage' column to the User and GalaxySession | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:30,657 tables. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:30,657 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:30,657 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:30,657 Migrating 78 -> 79... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:31,709 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:31,710 Migration script to add the job_to_input_library_dataset table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:31,710 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:31,710 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:31,710 Migrating 79 -> 80... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:34,150 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:34,150 Migration script to create tables for disk quotas. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:34,150 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:34,150 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:34,150 Migrating 80 -> 81... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:34,818 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:34,818 Migration script to add a 'tool_version' column to the hda/ldda tables. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:34,818 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:34,818 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:34,819 Migrating 81 -> 82... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:36,289 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:36,289 Migration script to add the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:36,289 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:36,289 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:36,289 Migrating 82 -> 83... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:38,036 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:38,036 Migration script to add 'prepare_input_files_cmd' column to the task table and to rename a column. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:38,036 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:38,036 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:38,036 Migrating 83 -> 84... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:38,829 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:38,829 Migration script to add 'ldda_id' column to the implicitly_converted_dataset_association table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:38,829 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:38,829 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:38,829 Migrating 84 -> 85... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:39,447 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:39,447 Migration script to add 'info' column to the task table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:39,447 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:39,447 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:39,447 Migrating 85 -> 86... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:40,516 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:40,516 Migration script to add the metadata, update_available and includes_datatypes columns to the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:40,516 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:40,516 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:40,516 Migrating 86 -> 87... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:41,634 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:41,635 Migration script to create the tool_id_guid_map table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:41,635 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:41,635 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:41,635 Migrating 87 -> 88... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:42,194 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:42,194 Migration script to add the installed_changeset_revision column to the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:42,194 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:42,195 Updated the installed_changeset_revision column for 0 rows in the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:42,195 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:42,195 Migrating 88 -> 89... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:43,540 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:43,540 Migration script to add 'object_store_id' column to various tables | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:43,540 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:43,540 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:43,540 Migrating 89 -> 90... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:44,308 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:44,308 Migration script to add the uninstalled and dist_to_shed columns to the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:44,308 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:44,308 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:44,308 Migrating 90 -> 91... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:45,654 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:45,654 Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:45,654 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:45,654 Added 0 rows to the new tool_version table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:45,654 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:45,654 Migrating 91 -> 92... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:46,330 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:46,330 Migration script to create the migrate_tools table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:46,331 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:46,331 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:46,331 Migrating 92 -> 93... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:47,115 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:47,115 Migration script to add a 'params' column to the 'job' table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:47,115 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:47,115 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:47,116 Migrating 93 -> 94... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:47,792 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:47,792 Migration script to add a 'handler' column to the 'job' table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:47,792 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:47,792 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:47,792 Migrating 94 -> 95... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:48,886 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:48,886 Migration script to create table for tracking history_dataset_association subsets. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:48,886 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:48,886 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:48,886 Migrating 95 -> 96... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:49,522 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:49,522 Migration script to add column to openid table for provider. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:49,522 Remove any OpenID entries with nonunique GenomeSpace Identifier | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:49,522 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:49,522 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:49,522 Migrating 96 -> 97... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:50,097 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:50,097 Migration script to add the ctx_rev column to the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:50,097 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:50,098 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:50,098 Migrating 97 -> 98... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:51,409 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:51,409 Migration script to create the genome_index_tool_data table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:51,409 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:51,409 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:51,409 Migrating 98 -> 99... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:52,128 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:52,129 Migration script to add the tool_dependency table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:52,129 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:52,129 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:52,129 Migrating 99 -> 100... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:52,577 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:52,578 Migration script to alter the type of the tool_dependency.version column from TrimmedString(40) to Text. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:52,578 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:52,578 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:52,578 Migrating 100 -> 101... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:53,766 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:53,766 Migration script to drop the installed_changeset_revision column from the tool_dependency table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:53,766 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:53,766 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:53,766 Migrating 101 -> 102... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:54,491 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:54,492 Migration script to add status and error_message columns to the tool_dependency table and drop the uninstalled column from the tool_dependency table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:54,492 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:54,492 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:54,492 Migrating 102 -> 103... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:55,343 Migration script to add status and error_message columns to the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:55,343 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:55,343 Migrating 103 -> 104... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:55,485 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:09:55,486 Migrating 104 -> 105... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:00,435 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:00,435 Migration script to add the cleanup_event* tables. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:00,435 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:00,435 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:00,435 Migrating 105 -> 106... | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:00,715 Creating index 'ix_metadata_file_lda_id' on column 'lda_id' in table 'metadata_file' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:00,737 Creating index 'ix_history_importable' on column 'importable' in table 'history' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:00,764 Creating index 'ix_sample_bar_code' on column 'bar_code' in table 'sample' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:00,785 Creating index 'ix_request_type_deleted' on column 'deleted' in table 'request_type' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:00,797 Creating index 'ix_galaxy_user_username' on column 'username' in table 'galaxy_user' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:01,043 Creating index 'ix_form_definition_type' on column 'type' in table 'form_definition' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:01,052 Creating index 'ix_form_definition_layout' on column 'layout' in table 'form_definition' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:01,199 Creating index 'ix_job_library_folder_id' on column 'library_folder_id' in table 'job' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:01,227 Creating index 'ix_page_published' on column 'published' in table 'page' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:01,248 Creating index 'ix_page_deleted' on column 'deleted' in table 'page' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:01,248 Creating index 'ix_galaxy_user_form_values_id' on column 'form_values_id' in table 'galaxy_user' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:01,416 Creating index 'ix_lia_deleted' on column 'deleted' in table 'library_info_association' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:01,575 Creating index 'ix_lfia_deleted' on column 'deleted' in table 'library_folder_info_association' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:01,743 Creating index 'ix_lddia_deleted' on column 'deleted' in table 'library_dataset_dataset_info_association' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:01,901 Creating index 'ix_sample_library_id' on column 'library_id' in table 'sample' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:01,901 Creating index 'ix_sample_folder_id' on column 'folder_id' in table 'sample' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:02,060 Creating index 'ix_lia_inheritable' on column 'inheritable' in table 'library_info_association' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:02,228 Creating index 'ix_lfia_inheritable' on column 'inheritable' in table 'library_folder_info_association' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:02,369 Creating index 'ix_job_imported' on column 'imported' in table 'job' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:02,370 Creating index 'ix_request_notification' on column 'notification' in table 'request' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:02,545 Creating index 'ix_sd_external_service_id' on column 'external_service_id' in table 'sample_dataset' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:02,688 Creating index 'ix_icda_ldda_parent_id' on column 'ldda_parent_id' in table 'implicitly_converted_dataset_association' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:02,855 Creating index 'ix_library_dataset_purged' on column 'purged' in table 'library_dataset' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:02,874 Creating index 'ix_run_subindex' on column 'subindex' in table 'run' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:02,889 Creating index 'ix_history_dataset_association_purged' on column 'purged' in table 'history_dataset_association' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:02,910 Creating index 'ix_galaxy_user_disk_usage' on column 'disk_usage' in table 'galaxy_user' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:02,911 Creating index 'ix_galaxy_session_disk_usage' on column 'disk_usage' in table 'galaxy_session' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:02,923 Creating index 'ix_icda_ldda_id' on column 'ldda_id' in table 'implicitly_converted_dataset_association' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:03,097 Creating index 'ix_tsr_includes_datatypes' on column 'includes_datatypes' in table 'tool_shed_repository' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:03,281 Creating index 'ix_dataset_object_store_id' on column 'object_store_id' in table 'dataset' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:03,300 Creating index 'ix_job_object_store_id' on column 'object_store_id' in table 'job' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:03,300 Creating index 'ix_metadata_file_object_store_id' on column 'object_store_id' in table 'metadata_file' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:03,300 Creating index 'ix_job_handler' on column 'handler' in table 'job' | |
| 0106_add_missing_indexes DEBUG 2018-02-07 10:10:03,300 Creating index 'ix_galaxy_user_email' on column 'email' in table 'galaxy_user' | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:04,144 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:04,144 Migration script to create missing indexes. Adding new columns to existing tables via SQLAlchemy does not create the index, even if the column definition includes index=True. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:04,144 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:04,144 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:04,144 Migrating 106 -> 107... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:04,995 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:04,996 Add the exit_code column to the Job and Task tables. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:04,996 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:04,996 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:04,996 Migrating 107 -> 108... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:08,197 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:08,197 Add the ExtendedMetadata and ExtendedMetadataIndex tables | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:08,197 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:08,197 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:08,197 Migrating 108 -> 109... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:09,467 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:09,467 Migration script to add the repository_dependency and repository_repository_dependency_association tables. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:09,467 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:09,467 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:09,467 Migrating 109 -> 110... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:10,177 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:10,177 Add UUID column to dataset table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:10,177 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:10,177 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:10,177 Migrating 110 -> 111... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:10,953 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:10,954 Add support for job destinations to the job table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:10,954 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:10,954 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:10,954 Migrating 111 -> 112... | |
| 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2018-02-07 10:10:11,860 Created data_manager_history_association table | |
| 0112_add_data_manager_history_association_and_data_manager_job_association_tables DEBUG 2018-02-07 10:10:12,429 Created data_manager_job_association table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:12,559 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:12,559 Migration script to add the data_manager_history_association table and data_manager_job_association. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:12,559 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:12,560 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:12,560 Migrating 112 -> 113... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:12,834 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:12,834 Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:12,834 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:12,834 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:12,835 Migrating 113 -> 114... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:13,086 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:13,086 Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:13,086 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:13,086 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:13,086 Migrating 114 -> 115... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:17,390 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:17,390 Migrating 115 -> 116... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:18,008 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:18,008 Migration script to drop the update_available Boolean column and replace it with the tool_shed_status JSONType column in the tool_shed_repository table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:18,008 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:18,008 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:18,008 Migrating 116 -> 117... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:18,810 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:18,810 Adds 'active' and 'activation_token' columns to the galaxy_user table. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:18,811 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:18,811 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:18,811 Migrating 117 -> 118... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:21,934 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:21,934 Add link from history_dataset_association to the extended_metadata table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:21,934 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:21,935 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:21,935 Migrating 118 -> 119... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:23,514 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:23,515 Migration script for job metric plugins. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:23,515 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:23,515 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:23,515 Migrating 119 -> 120... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:34,625 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:34,625 Migration script for tables related to dataset collections. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:34,625 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:34,625 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:34,626 Migrating 120 -> 121... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:35,343 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:35,343 Add UUIDs to workflows | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:35,343 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:35,343 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:35,343 Migrating 121 -> 122... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:35,880 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:35,880 Migration script to grow MySQL blobs. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:35,880 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:35,880 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:35,880 Migrating 122 -> 123... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:39,221 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:39,221 Migration script for workflow request tables. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:39,221 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:39,221 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:39,221 Migrating 123 -> 124... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:40,265 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:40,265 Migration script for the job state history table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:40,265 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:40,265 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:40,265 Migrating 124 -> 125... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:41,116 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:41,116 Migration script to enhance workflow step usability by adding labels and UUIDs. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:41,117 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:41,117 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:41,117 Migrating 125 -> 126... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:42,161 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:42,161 Migration script for the password reset table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:42,161 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:42,161 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:42,161 Migrating 126 -> 127... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:44,073 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:44,073 Migration script updating collections tables for output collections. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:44,073 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:44,073 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:44,073 Migrating 127 -> 128... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:44,798 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:44,798 Migration script to add session update time (used for timeouts) | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:44,798 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:44,799 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:44,799 Migrating 128 -> 129... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:45,591 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:45,591 Migration script to allow invalidation of job external output metadata temp files | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:45,591 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:45,591 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:45,591 Migrating 129 -> 130... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:47,221 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:47,221 Migration script to change the 'value' column of 'user_preference' table from varchar to text. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:47,221 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:47,221 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:47,221 Migrating 130 -> 131... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:50,146 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:50,147 Migration script to support subworkflows and workflow request input parameters | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:50,147 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:50,147 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:50,147 Migrating 131 -> 132... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:50,430 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:50,431 Migrating 132 -> 133... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:51,156 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:51,157 Add dependencies column to jobs table | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:51,157 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:51,157 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:51,157 Migrating 133 -> 134... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:51,299 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:51,299 Migration script to set the 'deleted' column of the | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:51,299 'history_dataset_association' table to True if 'purged' is True. | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:51,299 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:51,299 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:51,299 Migrating 134 -> 135... | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:53,003 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:53,003 This migration script adds support for storing tags in the context of a dataset in a library | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:53,003 | |
| galaxy.model.migrate.check INFO 2018-02-07 10:10:53,003 | |
| migrate.versioning.repository DEBUG 2018-02-07 10:10:53,004 Loading repository lib/tool_shed/galaxy_install/migrate... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Loading script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Loading script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Loading script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Script lib/tool_shed/galaxy_install/migrate/versions/0003_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Loading script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Script lib/tool_shed/galaxy_install/migrate/versions/0004_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Loading script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Script lib/tool_shed/galaxy_install/migrate/versions/0005_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Loading script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Script lib/tool_shed/galaxy_install/migrate/versions/0006_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Loading script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Script lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Loading script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,005 Script lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,006 Loading script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,006 Script lib/tool_shed/galaxy_install/migrate/versions/0009_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,006 Loading script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,006 Script lib/tool_shed/galaxy_install/migrate/versions/0010_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,006 Loading script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,006 Script lib/tool_shed/galaxy_install/migrate/versions/0011_tools.py loaded successfully | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,006 Loading script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py... | |
| migrate.versioning.script.base DEBUG 2018-02-07 10:10:53,006 Script lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py loaded successfully | |
| migrate.versioning.repository DEBUG 2018-02-07 10:10:53,006 Repository lib/tool_shed/galaxy_install/migrate loaded successfully | |
| migrate.versioning.repository DEBUG 2018-02-07 10:10:53,006 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'GalaxyTools'), ('version_table', 'migrate_tools'), ('required_dbs', '[]')]))]) | |
| tool_shed.galaxy_install.migrate.check DEBUG 2018-02-07 10:10:53,021 The main Galaxy tool shed is not currently available, so skipped tool migration 1 until next server startup | |
| galaxy.config INFO 2018-02-07 10:10:53,034 Install database targetting Galaxy's database configuration. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,084 Loading datatypes from ./config/datatypes_conf.xml.sample | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,084 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,086 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,086 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,086 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,086 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,086 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,086 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,086 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,086 Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,087 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,087 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,087 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,087 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,087 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,087 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,087 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,087 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,088 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,088 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,088 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,088 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,088 Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,088 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,089 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,089 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,089 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,089 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,089 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,089 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,089 Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,089 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,090 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,090 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,090 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,090 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,090 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,090 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,090 Retrieved datatype module galaxy.datatypes.sequence:FastqGz from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,090 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerGz from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,090 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaGz from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,090 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerGz from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,090 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaGz from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,090 Retrieved datatype module galaxy.datatypes.sequence:FastqBz2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,091 Retrieved datatype module galaxy.datatypes.sequence:FastqSangerBz2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,091 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexaBz2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,091 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSangerBz2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,091 Retrieved datatype module galaxy.datatypes.sequence:FastqIlluminaBz2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,091 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,091 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,091 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,091 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,091 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,091 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,091 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,091 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,092 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,092 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,092 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,092 Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,092 Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,092 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,092 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,092 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,092 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,093 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,093 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,093 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,093 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,093 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,093 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,093 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,093 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,094 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,094 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,094 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,094 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,094 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,094 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,094 Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,094 Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,094 Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,094 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,095 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,095 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,095 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,095 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,095 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,095 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,095 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,095 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,095 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,095 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,095 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,095 Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,096 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,096 Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,096 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,099 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,100 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,100 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,100 Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,100 Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,100 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,100 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,100 Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,100 Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,100 Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,101 Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,101 Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,101 Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,101 Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,101 Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,101 Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,101 Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,101 Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,101 Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,101 Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,101 Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,101 Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,102 Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,102 Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,102 Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,102 Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,102 Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,102 Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,102 Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,102 Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,102 Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,102 Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,102 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,102 Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,103 Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,103 Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,103 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,103 Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,103 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,103 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,103 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,103 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,103 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,104 Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,104 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,104 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,104 Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,104 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,104 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,104 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,104 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,104 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,104 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,104 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,104 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,105 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,105 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,105 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,105 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,105 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,105 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,105 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,105 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,105 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,105 Roadmaps is not lower case, that could cause troubles in the future. Please change it to lower case | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,105 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,105 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,106 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,106 Sequences is not lower case, that could cause troubles in the future. Please change it to lower case | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,106 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,106 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,106 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,106 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,106 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,106 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,106 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,106 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,106 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,107 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,107 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,107 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,107 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,107 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,107 Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,107 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,107 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,107 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,107 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,107 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,107 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,107 Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,108 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,108 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,108 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,108 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,108 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,108 Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,108 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,108 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,108 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,113 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,113 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,113 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,114 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,114 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,114 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,114 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,114 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,114 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,114 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,114 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,114 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,114 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,115 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,115 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,115 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,115 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,115 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,115 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,115 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,117 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,117 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,118 Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,118 Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,118 Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,118 Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,118 Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,118 Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,118 Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,118 Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,118 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,119 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,119 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,119 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,119 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,119 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,119 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,119 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,119 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,120 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,120 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,120 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,120 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,120 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,120 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,120 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,120 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,120 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,121 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,121 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,121 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,121 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,121 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,121 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,121 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,121 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,122 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,122 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,122 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,122 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,122 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,122 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,122 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,122 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,122 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,123 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,123 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,123 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,123 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,123 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,123 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,123 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,123 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,124 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,124 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,124 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,124 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,124 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,124 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,124 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,124 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,124 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,125 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,125 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,125 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,125 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,125 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,125 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,125 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,125 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,126 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,126 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,126 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,126 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,126 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,126 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,126 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,126 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,126 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,127 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,127 Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,127 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,127 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,127 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,127 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,127 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,127 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,128 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,128 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,128 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,128 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,128 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,128 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,128 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,128 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,128 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,129 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,129 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,129 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,129 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,129 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,129 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,129 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,129 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,130 Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,130 Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,130 Retrieved datatype module galaxy.datatypes.binary:ICM from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,132 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,133 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,133 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,133 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,133 Retrieved datatype module galaxy.datatypes.binary:Cel from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,133 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,133 Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,133 Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,133 Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,133 Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,133 Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,133 Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,136 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,136 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,136 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,136 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,136 Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,136 Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,136 Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,136 Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,140 Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,140 Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,141 Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,141 Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,141 Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,141 Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,141 Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,141 Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,141 Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,141 Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,141 Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,141 Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,141 Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,142 Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,146 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,146 Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,146 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,147 Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,147 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,147 Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,147 Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,147 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,147 Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,147 Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,147 Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,147 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,147 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,148 Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,148 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,148 Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,148 Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,148 Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,148 Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,148 Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,148 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,148 Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,148 Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,149 Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,149 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,149 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,149 Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,149 Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,149 Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,149 Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,149 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,149 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,150 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,150 Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,150 Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,150 Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,150 Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,151 Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,151 Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,153 Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,153 Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,153 Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,153 Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,153 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,153 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,153 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,155 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,155 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,155 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,155 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,156 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,156 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,156 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,156 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrtho from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,156 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,156 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylip from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,156 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,156 Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,156 Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,156 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,156 Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,156 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,157 Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.binary:H5' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,158 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.binary:ICM' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,159 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,160 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,161 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,161 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,161 Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,161 Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,161 Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,161 Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,161 Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,161 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,161 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,161 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerGz' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,161 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSangerBz2' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,161 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,161 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqGz' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,161 Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqBz2' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,162 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,162 Loaded sniffer for datatype 'galaxy.datatypes.text:Html' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,162 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,162 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,162 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,162 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,162 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,162 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,162 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,162 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,162 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,162 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,162 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,162 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,163 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,163 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,163 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,163 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,163 Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,163 Loaded sniffer for datatype 'galaxy.datatypes.text:Json' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,163 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,163 Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,163 Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,163 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,163 Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,163 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,163 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,163 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,164 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,164 Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,164 Loaded sniffer for datatype 'galaxy.datatypes.binary:Cel' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,164 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,164 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,164 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,164 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,164 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,164 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,164 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,164 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,164 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,164 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,164 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,165 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,165 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,165 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,165 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,165 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,165 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,165 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,165 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,165 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,165 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,165 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,165 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,165 Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,169 Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample]. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,169 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla'] | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,169 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 2018-02-07 10:10:53,169 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,169 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,169 Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample]. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,169 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,169 Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample]. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:53,169 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample | |
| galaxy.tools.data INFO 2018-02-07 10:10:53,595 Could not find tool data tool-data/all_fasta.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,595 Loaded 0 lines from 'tool-data/all_fasta.loc.sample' for 'all_fasta' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,595 Loaded tool data table 'all_fasta' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:53,595 Could not find tool data tool-data/bfast_indexes.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,595 Loaded 0 lines from 'tool-data/bfast_indexes.loc.sample' for 'bfast_indexes' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,595 Loaded tool data table 'bfast_indexes' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:53,595 Could not find tool data tool-data/blastdb.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,596 Loaded 0 lines from 'tool-data/blastdb.loc.sample' for 'blastdb' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,596 Loaded tool data table 'blastdb' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:53,596 Could not find tool data tool-data/blastdb_p.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,596 Loaded 0 lines from 'tool-data/blastdb_p.loc.sample' for 'blastdb_p' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,596 Loaded tool data table 'blastdb_p' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:53,596 Could not find tool data tool-data/blastdb_d.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,596 Loaded 0 lines from 'tool-data/blastdb_d.loc.sample' for 'blastdb_d' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,596 Loaded tool data table 'blastdb_d' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data WARNING 2018-02-07 10:10:53,596 Cannot find index file 'tool-data/bwa_index.loc' for tool data table 'bwa_indexes' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,596 Loaded tool data table 'bwa_indexes' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data WARNING 2018-02-07 10:10:53,596 Cannot find index file 'tool-data/bwa_index_color.loc' for tool data table 'bwa_indexes_color' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,596 Loaded tool data table 'bwa_indexes_color' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:53,597 Could not find tool data tool-data/maf_index.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,597 Loaded 0 lines from 'tool-data/maf_index.loc.sample' for 'indexed_maf_files' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,597 Loaded tool data table 'indexed_maf_files' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:53,597 Could not find tool data tool-data/ngs_sim_fasta.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,597 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc.sample' for 'ngs_sim_fasta' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,597 Loaded tool data table 'ngs_sim_fasta' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:53,597 Could not find tool data tool-data/perm_base_index.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,597 Loaded 0 lines from 'tool-data/perm_base_index.loc.sample' for 'perm_base_indexes' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,597 Loaded tool data table 'perm_base_indexes' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:53,597 Could not find tool data tool-data/perm_color_index.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,597 Loaded 0 lines from 'tool-data/perm_color_index.loc.sample' for 'perm_color_indexes' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,597 Loaded tool data table 'perm_color_indexes' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:53,598 Could not find tool data tool-data/picard_index.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,598 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'picard_indexes' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,598 Loaded tool data table 'picard_indexes' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:53,598 Could not find tool data tool-data/picard_index.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,598 Loaded 0 lines from 'tool-data/picard_index.loc.sample' for 'srma_indexes' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,598 Loaded tool data table 'srma_indexes' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:53,598 Could not find tool data tool-data/mosaik_index.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,598 Loaded 0 lines from 'tool-data/mosaik_index.loc.sample' for 'mosaik_indexes' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,598 Loaded tool data table 'mosaik_indexes' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:53,598 Could not find tool data tool-data/twobit.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,598 Loaded 0 lines from 'tool-data/twobit.loc.sample' for 'twobit' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:53,598 Loaded tool data table 'twobit' from file './config/tool_data_table_conf.xml.sample' | |
| requests.packages.urllib3.connectionpool INFO 2018-02-07 10:10:53,603 Starting new HTTP connection (1): igv.broadinstitute.org | |
| requests.packages.urllib3.connectionpool DEBUG 2018-02-07 10:10:54,434 "GET /genomes/genomes.txt HTTP/1.1" 200 15681 | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:54,704 Loading Data Table URL "http://igv.broadinstitute.org/genomes/genomes.txt" as filename "/mnt/sda1/sdc1/Project/ML/trunk/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-QUUExD". | |
| galaxy.tools.data WARNING 2018-02-07 10:10:54,704 Line 1 in tool data table 'igv_broad_genomes' is invalid (HINT: '<TAB>' characters must be used to separate fields): | |
| <Server-Side Genome List> | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:54,705 Loaded 156 lines from '/mnt/sda1/sdc1/Project/ML/trunk/galaxy/database/tmp/TTDT_URL_igv_broad_genomes-QUUExD' for 'igv_broad_genomes' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:54,705 Loaded tool data table 'igv_broad_genomes' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:54,705 Could not find tool data tool-data/liftOver.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:54,705 Loaded 0 lines from 'tool-data/liftOver.loc.sample' for 'liftOver' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:54,705 Loaded tool data table 'liftOver' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:54,706 Could not find tool data tool-data/bam_iobio.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:54,706 Loaded 1 lines from 'tool-data/bam_iobio.loc.sample' for 'bam_iobio' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:54,706 Loaded tool data table 'bam_iobio' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:54,706 Could not find tool data tool-data/vcf_iobio.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:54,706 Loaded 1 lines from 'tool-data/vcf_iobio.loc.sample' for 'vcf_iobio' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:54,706 Loaded tool data table 'vcf_iobio' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.tools.data INFO 2018-02-07 10:10:54,706 Could not find tool data tool-data/biom_simple_display.loc, reading sample | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:54,706 Loaded 1 lines from 'tool-data/biom_simple_display.loc.sample' for 'biom_simple_display' | |
| galaxy.tools.data DEBUG 2018-02-07 10:10:54,706 Loaded tool data table 'biom_simple_display' from file './config/tool_data_table_conf.xml.sample' | |
| galaxy.jobs WARNING 2018-02-07 10:10:54,762 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/mnt/sda1/sdc1/Project/ML/trunk/galaxy/config/galaxy.ini.sample" instead | |
| galaxy.jobs DEBUG 2018-02-07 10:10:54,762 Loading job configuration from /mnt/sda1/sdc1/Project/ML/trunk/galaxy/config/galaxy.ini.sample | |
| galaxy.jobs DEBUG 2018-02-07 10:10:54,762 Done loading job configuration | |
| beaker.container DEBUG 2018-02-07 10:10:55,102 data file ./database/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache | |
| galaxy.tools.toolbox.base INFO 2018-02-07 10:10:55,103 Parsing the tool configuration ./config/tool_conf.xml.sample | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,116 Loaded tool id: upload1, version: 1.1.4 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,117 Loaded tool id: ucsc_table_direct1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,119 Loaded tool id: ucsc_table_direct_test1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,120 Loaded tool id: ucsc_table_direct_archaea1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,121 Loaded tool id: ebi_sra_main, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,124 Loaded tool id: microbial_import1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,125 Loaded tool id: biomart, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,126 Loaded tool id: cbi_rice_mart, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,128 Loaded tool id: gramenemart, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,129 Loaded tool id: modENCODEfly, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,130 Loaded tool id: flymine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,131 Loaded tool id: flymine_test, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,132 Loaded tool id: modmine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,133 Loaded tool id: mousemine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,134 Loaded tool id: ratmine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,135 Loaded tool id: yeastmine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,136 Loaded tool id: metabolicmine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,137 Loaded tool id: modENCODEworm, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,138 Loaded tool id: wormbase, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,139 Loaded tool id: wormbase_test, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,140 Loaded tool id: zebrafishmine, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,141 Loaded tool id: eupathdb, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,142 Loaded tool id: hbvar, version: 2.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,181 Loaded tool id: genomespace_importer, version: 0.0.5 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,182 Skipping tool panel addition of hidden tool: genomespace_push, version: 0.0.1 | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,183 Loaded tool id: genomespace_exporter, version: 0.0.5 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,184 Loaded tool id: __UNZIP_COLLECTION__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,185 Loaded tool id: __ZIP_COLLECTION__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,186 Loaded tool id: __FILTER_FAILED_DATASETS__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,187 Loaded tool id: __FLATTEN__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,202 Loaded tool id: __MERGE_COLLECTION__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,204 Loaded tool id: __RELABEL_FROM_FILE__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,206 Loaded tool id: __FILTER_FROM_FILE__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,207 Loaded tool id: __SORTLIST__, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base ERROR 2018-02-07 10:10:55,209 Error reading tool configuration file from path: extract/liftOver_wrapper.xml | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,210 Loaded tool id: addValue, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,211 Loaded tool id: cat1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,214 Loaded tool id: Cut1, version: 1.0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,215 Loaded tool id: mergeCols1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,216 Loaded tool id: Convert characters1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,218 Loaded tool id: createInterval, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,218 Loaded tool id: Cut1, version: 1.0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,219 Loaded tool id: ChangeCase, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,220 Loaded tool id: Paste1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,221 Loaded tool id: Remove beginning1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,222 Loaded tool id: random_lines1, version: 2.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,223 Loaded tool id: Show beginning1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,224 Loaded tool id: Show tail1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,226 Loaded tool id: trimmer, version: 0.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,227 Loaded tool id: wc_gnu, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,228 Loaded tool id: secure_hash_message_digest, version: 0.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,229 Loaded tool id: Filter1, version: 1.1.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,231 Loaded tool id: sort1, version: 1.0.3 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,232 Loaded tool id: Grep1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,234 Loaded tool id: Extract_features1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,235 Loaded tool id: gff_filter_by_attribute, version: 0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,236 Loaded tool id: gff_filter_by_feature_count, version: 0.1.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,237 Loaded tool id: gtf_filter_by_attribute_values_list, version: 0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,241 Loaded tool id: join1, version: 2.1.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,242 Loaded tool id: comp1, version: 1.0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,244 Loaded tool id: Grouping1, version: 2.1.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,246 Loaded tool id: axt_to_concat_fasta, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,247 Loaded tool id: axt_to_fasta, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,248 Loaded tool id: axt_to_lav_1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,249 Loaded tool id: bed2gff1, version: 2.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,250 Loaded tool id: gff2bed1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,251 Loaded tool id: lav_to_bed1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,253 Loaded tool id: MAF_To_BED1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,255 Loaded tool id: MAF_To_Interval1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,257 Loaded tool id: MAF_To_Fasta1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,258 Loaded tool id: wiggle2simple1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,259 Loaded tool id: Sff_extractor, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,260 Loaded tool id: gtf2bedgraph, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,262 Loaded tool id: wig_to_bigWig, version: 1.1.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,264 Loaded tool id: bed_to_bigBed, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,265 Loaded tool id: gene2exon1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,267 Loaded tool id: Extract genomic DNA 1, version: 2.2.3 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,268 Loaded tool id: Interval2Maf_pairwise1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,271 Loaded tool id: Interval2Maf1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,273 Loaded tool id: MAF_split_blocks_by_species1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,275 Loaded tool id: Interval_Maf_Merged_Fasta2, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,277 Loaded tool id: GeneBed_Maf_Fasta2, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,280 Loaded tool id: maf_stats1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,281 Loaded tool id: MAF_Thread_For_Species1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,283 Loaded tool id: MAF_Limit_To_Species1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,284 Loaded tool id: maf_limit_size1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,286 Loaded tool id: maf_by_block_number1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,287 Loaded tool id: MAF_Reverse_Complement_1, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,291 Loaded tool id: MAF_filter, version: 1.0.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,292 Loaded tool id: Summary_Statistics1, version: 1.1.1 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,293 Loaded tool id: Count1, version: 1.0.2 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,295 Loaded tool id: barchart_gnuplot, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,297 Loaded tool id: qual_stats_boxplot, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,299 Loaded tool id: vcf_to_maf_customtrack1, version: 1.0.0 into tool panel.. | |
| galaxy.tools.toolbox.base INFO 2018-02-07 10:10:55,299 Parsing the tool configuration ./config/shed_tool_conf.xml | |
| galaxy.tools.toolbox.base INFO 2018-02-07 10:10:55,299 Parsing the tool configuration ./config/migrated_tools_conf.xml | |
| galaxy.tools.toolbox.base DEBUG 2018-02-07 10:10:55,299 Reading tools from config files finshed (195.858 ms) | |
| galaxy.tools.deps DEBUG 2018-02-07 10:10:55,301 Unable to find config file './dependency_resolvers_conf.xml' | |
| galaxy.tools.search DEBUG 2018-02-07 10:10:55,313 Starting to build toolbox index. | |
| galaxy.tools.search DEBUG 2018-02-07 10:10:56,172 Toolbox index finished (858.923 ms) | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,174 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,176 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,201 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,202 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,202 Loaded display application 'iobio_bam' for datatype 'bam', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,202 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,203 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,204 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,204 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,205 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,206 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,207 Loaded display application 'igv_bigwig' for datatype 'bigwig', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,228 Loaded display application 'igv_fasta' for datatype 'fasta', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,231 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,252 Loaded display application 'igv_gff' for datatype 'gff', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,253 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,256 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,261 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,262 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,283 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,284 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,286 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,313 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,313 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,314 Loaded display application 'iobio_vcf' for datatype 'vcf', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,314 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,341 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,342 Loaded display application 'biom_simple' for datatype 'biom1', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,342 Loaded display application 'ucsc_trackhub' for datatype 'trackhub', inherit=False. | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,343 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,344 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,344 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,344 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,344 Adding inherited display application 'ensembl_interval' to datatype 'bed12' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,344 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,344 Adding inherited display application 'rviewer_interval' to datatype 'bed12' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,344 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,349 Adding inherited display application 'ensembl_gff' to datatype 'gtf' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,349 Adding inherited display application 'igv_gff' to datatype 'gtf' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,355 Adding inherited display application 'ensembl_interval' to datatype 'bed' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,355 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,355 Adding inherited display application 'rviewer_interval' to datatype 'bed' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,355 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,357 Adding inherited display application 'igv_fasta' to datatype 'sequences' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,357 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,357 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,357 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,357 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,358 Adding inherited display application 'igv_fasta' to datatype 'mothur.align' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,359 Adding inherited display application 'ensembl_gff' to datatype 'gff3' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,359 Adding inherited display application 'igv_gff' to datatype 'gff3' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,364 Adding inherited display application 'ensembl_interval' to datatype 'chrint' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,364 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,364 Adding inherited display application 'rviewer_interval' to datatype 'chrint' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,364 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,364 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,364 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,364 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,365 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,366 Adding inherited display application 'ensembl_interval' to datatype 'bed6' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,366 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,366 Adding inherited display application 'rviewer_interval' to datatype 'bed6' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,366 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6' | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,368 Loaded converter: CONVERTER_bam_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,369 Loaded converter: CONVERTER_bed_to_gff_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,370 Loaded converter: CONVERTER_bed_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,371 Loaded converter: CONVERTER_bed_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,371 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,372 Loaded converter: CONVERTER_bed_to_fli_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,373 Loaded converter: CONVERTER_bedgraph_to_bigwig | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,373 Loaded converter: CONVERTER_len_to_linecount | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,374 Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,375 Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,376 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,376 Loaded converter: CONVERTER_fasta_to_tabular | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,377 Loaded converter: CONVERTER_fasta_to_bowtie_base_index | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,378 Loaded converter: CONVERTER_fasta_to_bowtie_color_index | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,379 Loaded converter: CONVERTER_fasta_to_2bit | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,379 Loaded converter: CONVERTER_fasta_to_len | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,380 Loaded converter: CONVERTER_fasta_to_fai | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,381 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,381 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,382 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,383 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,383 Loaded converter: CONVERTER_fastq_to_fqtoc0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,384 Loaded converter: CONVERTER_fastqgz_to_fastq | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,385 Loaded converter: CONVERTER_fastqsangergz_to_fastqsanger | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,386 Loaded converter: CONVERTER_fastqsolexagz_to_fastqsolexa | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,386 Loaded converter: CONVERTER_fastqcssangergz_to_fastqcssanger | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,387 Loaded converter: CONVERTER_fastqilluminagz_to_fastqillumina | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,388 Loaded converter: CONVERTER_fastqbz2_to_fastq | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,389 Loaded converter: CONVERTER_fastqsangerbz2_to_fastqsanger | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,389 Loaded converter: CONVERTER_fastqsolexabz2_to_fastqsolexa | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,390 Loaded converter: CONVERTER_fastqcssangerbz2_to_fastqcssanger | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,391 Loaded converter: CONVERTER_fastqilluminabz2_to_fastqillumina | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,392 Loaded converter: CONVERTER_gff_to_bed_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,392 Loaded converter: CONVERTER_gff_to_interval_index_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,393 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,394 Loaded converter: CONVERTER_gff_to_fli_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,394 Loaded converter: CONVERTER_gff_to_interval_index_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,395 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,396 Loaded converter: CONVERTER_interval_to_bed_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,396 Loaded converter: CONVERTER_interval_to_bedstrict_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,397 Loaded converter: CONVERTER_interval_to_bed6_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,398 Loaded converter: CONVERTER_interval_to_bed12_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,399 Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,399 Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,400 Loaded converter: CONVERTER_interval_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,401 Loaded converter: CONVERTER_picard_interval_list_to_bed6 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,401 Loaded converter: CONVERTER_maf_to_fasta_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,402 Loaded converter: CONVERTER_maf_to_interval_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,403 Loaded converter: CONVERTER_encodepeak_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,404 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,404 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,405 Loaded converter: CONVERTER_interval_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,406 Loaded converter: CONVERTER_interval_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,407 Loaded converter: CONVERTER_sam_to_bam | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,407 Loaded converter: CONVERTER_sam_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,408 Loaded converter: tabular_to_dbnsfp | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,409 Loaded converter: CONVERTER_vcf_to_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,409 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,410 Loaded converter: CONVERTER_vcf_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,411 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,412 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,413 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,414 Loaded converter: CONVERTER_wig_to_bigwig | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,414 Loaded converter: CONVERTER_wiggle_to_interval_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,415 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,416 Loaded converter: lped2fpedconvert | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,416 Loaded converter: lped2pbedconvert | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,417 Loaded converter: pbed2lpedconvert | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,418 Loaded converter: pbed2ldindepconvert | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,419 Loaded converter: CONVERTER_biom1_to_biom2 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,419 Loaded converter: CONVERTER_biom2_to_biom1 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,420 Loaded converter: CONVERTER_SMILES_to_sdf | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,421 Loaded converter: CONVERTER_SMILES_to_inchi | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,423 Loaded converter: CONVERTER_SMILES_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,423 Loaded converter: CONVERTER_SMILES_to_MOL | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,424 Loaded converter: CONVERTER_SMILES_to_MOL2 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,426 Loaded converter: CONVERTER_smiles_to_smiles | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,426 Loaded converter: CONVERTER_sdf_to_smiles | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,427 Loaded converter: CONVERTER_sdf_to_inchi | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,428 Loaded converter: CONVERTER_sdf_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,429 Loaded converter: CONVERTER_sdf_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,430 Loaded converter: CONVERTER_inchi_to_smi | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,431 Loaded converter: CONVERTER_inchi_to_sdf | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,431 Loaded converter: CONVERTER_inchi_to_mol | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,432 Loaded converter: CONVERTER_inchi_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,433 Loaded converter: CONVERTER_inchi_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,434 Loaded converter: CONVERTER_mol_to_smi | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,435 Loaded converter: CONVERTER_mol_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,435 Loaded converter: CONVERTER_mol_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,436 Loaded converter: CONVERTER_mol_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,437 Loaded converter: CONVERTER_mol2_to_smi | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,438 Loaded converter: CONVERTER_mol2_to_sdf | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,439 Loaded converter: CONVERTER_mol2_to_inchi | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,439 Loaded converter: CONVERTER_mol2_to_mol | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,440 Loaded converter: CONVERTER_mol2_to_cml | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,441 Loaded converter: CONVERTER_cml_to_smiles | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,442 Loaded converter: CONVERTER_cml_to_inchi | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,443 Loaded converter: CONVERTER_cml_to_sdf | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,444 Loaded converter: CONVERTER_cml_to_mol2 | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,445 Loaded converter: CONVERTER_ref_to_seq_taxomony | |
| galaxy.datatypes.registry DEBUG 2018-02-07 10:10:56,447 Loaded external metadata tool: __SET_METADATA__ | |
| galaxy.tools.special_tools DEBUG 2018-02-07 10:10:56,451 Loaded history import tool: __IMPORT_HISTORY__ | |
| galaxy.tools.special_tools DEBUG 2018-02-07 10:10:56,451 Loaded history export tool: __EXPORT_HISTORY__ | |
| galaxy.web.base.pluginframework INFO 2018-02-07 10:10:56,452 VisualizationsRegistry, loaded plugin: charts | |
| galaxy.visualization.plugins.config_parser INFO 2018-02-07 10:10:56,453 Visualizations plugin disabled: Circster. Skipping... | |
| galaxy.visualization.plugins.config_parser INFO 2018-02-07 10:10:56,453 template syntax is deprecated: use entry_point instead | |
| galaxy.web.base.pluginframework INFO 2018-02-07 10:10:56,453 VisualizationsRegistry, loaded plugin: csg | |
| galaxy.visualization.plugins.config_parser INFO 2018-02-07 10:10:56,454 template syntax is deprecated: use entry_point instead | |
| galaxy.web.base.pluginframework INFO 2018-02-07 10:10:56,454 VisualizationsRegistry, loaded plugin: graphviz | |
| galaxy.web.base.pluginframework INFO 2018-02-07 10:10:56,454 VisualizationsRegistry, loaded plugin: phyloviz | |
| galaxy.web.base.pluginframework INFO 2018-02-07 10:10:56,455 VisualizationsRegistry, loaded plugin: scatterplot | |
| galaxy.visualization.plugins.config_parser INFO 2018-02-07 10:10:56,455 Visualizations plugin disabled: Sweepster. Skipping... | |
| galaxy.web.base.pluginframework INFO 2018-02-07 10:10:56,456 VisualizationsRegistry, loaded plugin: trackster | |
| galaxy.visualization.plugins.config_parser INFO 2018-02-07 10:10:56,456 template syntax is deprecated: use entry_point instead | |
| galaxy.web.base.pluginframework INFO 2018-02-07 10:10:56,456 VisualizationsRegistry, loaded plugin: unipept | |
| galaxy.tours INFO 2018-02-07 10:10:56,464 Loaded tour 'core.scratchbook' | |
| galaxy.tours INFO 2018-02-07 10:10:56,480 Loaded tour 'core.history' | |
| galaxy.tours INFO 2018-02-07 10:10:56,502 Loaded tour 'core.galaxy_ui' | |
| galaxy.webhooks WARNING 2018-02-07 10:10:56,502 directory not found: /mnt/sda1/sdc1/Project/ML/trunk/galaxy/lib/galaxy/util/../../.././config/plugins/webhooks/demo/config | |
| galaxy.jobs.manager DEBUG 2018-02-07 10:10:56,538 Starting job handler | |
| galaxy.jobs INFO 2018-02-07 10:10:56,538 Handler 'main' will load all configured runner plugins | |
| galaxy.jobs.runners.state_handler_factory DEBUG 2018-02-07 10:10:56,541 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit | |
| galaxy.jobs.runners DEBUG 2018-02-07 10:10:56,541 Starting 5 LocalRunner workers | |
| galaxy.jobs DEBUG 2018-02-07 10:10:56,542 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local' | |
| galaxy.jobs DEBUG 2018-02-07 10:10:56,542 Legacy destination with id 'local:///', url 'local:///' converted, got params: | |
| galaxy.jobs.handler DEBUG 2018-02-07 10:10:56,542 Loaded job runners plugins: local | |
| galaxy.jobs.handler INFO 2018-02-07 10:10:56,550 job handler stop queue started | |
| galaxy.jobs.handler INFO 2018-02-07 10:10:56,562 job handler queue started | |
| galaxy.sample_tracking.external_service_types DEBUG 2018-02-07 10:10:56,565 Loaded external_service_type: Simple unknown sequencer 1.0.0 | |
| galaxy.sample_tracking.external_service_types DEBUG 2018-02-07 10:10:56,567 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 | |
| galaxy.workflow.scheduling_manager DEBUG 2018-02-07 10:10:56,573 Starting workflow schedulers | |
| galaxy.app INFO 2018-02-07 10:10:56,574 Galaxy app startup finished (213192.570 ms) | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,586 Enabling 'forms' controller, class: Forms | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,597 Enabling 'requests_common' controller, class: RequestsCommon | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,598 Enabling 'biostar' controller, class: BiostarController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,629 Enabling 'workflow' controller, class: WorkflowController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,785 Enabling 'admin_toolshed' controller, class: AdminGalaxy | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,785 Enabling 'admin_toolshed' controller, class: AdminToolshed | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,786 Enabling 'requests' controller, class: Requests | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,793 Enabling 'history' controller, class: HistoryController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,794 Enabling 'admin' controller, class: AdminGalaxy | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,795 Enabling 'async' controller, class: ASync | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,800 Enabling 'visualization' controller, class: VisualizationController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,800 Enabling 'interactive_environments' controller, class: InteractiveEnvironmentsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,803 Enabling 'requests_admin' controller, class: RequestsAdmin | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,805 Enabling 'external_service' controller, class: ExternalService | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,821 Enabling 'library_common' controller, class: LibraryCommon | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,821 Enabling 'error' controller, class: Error | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,822 Enabling 'tool_runner' controller, class: ToolRunner | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,823 Enabling 'data_manager' controller, class: DataManager | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,824 Enabling 'library_admin' controller, class: LibraryAdmin | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,825 Enabling 'library' controller, class: Library | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,829 Enabling 'root' controller, class: RootController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,830 Enabling 'tag' controller, class: TagsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,831 Enabling 'userskeys' controller, class: User | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,836 Enabling 'user' controller, class: User | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,837 Enabling 'external_services' controller, class: ExternalServiceController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,841 Enabling 'page' controller, class: PageController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,847 Enabling 'dataset' controller, class: DatasetInterface | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,850 Enabling 'request_type' controller, class: RequestType | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,856 Enabling 'users' API controller, class: UserAPIController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,857 Enabling 'toolshed' API controller, class: ToolShedController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,860 Enabling 'histories' API controller, class: HistoriesController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,860 Enabling 'forms' API controller, class: FormDefinitionAPIController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,866 Enabling 'library_datasets' API controller, class: LibraryDatasetsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,866 Enabling 'page_revisions' API controller, class: PageRevisionsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,867 Enabling 'requests' API controller, class: RequestsAPIController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,868 Enabling 'group_roles' API controller, class: GroupRolesAPIController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,868 Enabling 'webhooks' API controller, class: WebhooksController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,869 Enabling 'samples' API controller, class: SamplesAPIController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,870 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,870 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,871 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,871 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,872 Enabling 'group_users' API controller, class: GroupUsersAPIController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,873 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,873 Enabling 'history_tags' API controller, class: HistoryTagsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,873 Enabling 'workflow_tags' API controller, class: WorkflowTagsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,874 Enabling 'configuration' API controller, class: ConfigurationController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,874 Enabling 'roles' API controller, class: RoleAPIController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,878 Enabling 'workflows' API controller, class: WorkflowsAPIController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,878 Enabling 'tool_data' API controller, class: ToolData | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,879 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,880 Enabling 'pages' API controller, class: PagesController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,881 Enabling 'folders' API controller, class: FoldersController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,883 Enabling 'jobs' API controller, class: JobController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,886 Enabling 'tools' API controller, class: ToolsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,889 Enabling 'history_contents' API controller, class: HistoryContentsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,892 Enabling 'libraries' API controller, class: LibrariesController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,893 Enabling 'genomes' API controller, class: GenomesController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,893 Enabling 'groups' API controller, class: GroupAPIController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,895 Enabling 'datasets' API controller, class: DatasetsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,898 Enabling 'remote_files' API controller, class: RemoteFilesAPIController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,898 Enabling 'authenticate' API controller, class: AuthenticationController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,899 Enabling 'folder_contents' API controller, class: FolderContentsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,900 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,900 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,900 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,902 Enabling 'request_types' API controller, class: RequestTypeAPIController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,906 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,907 Enabling 'tours' API controller, class: ToursController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,907 Enabling 'metrics' API controller, class: MetricsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,908 Enabling 'quotas' API controller, class: QuotaAPIController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,909 Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,910 Enabling 'job_files' API controller, class: JobFilesAPIController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,918 Enabling 'search' API controller, class: SearchController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,920 Enabling 'library_contents' API controller, class: LibraryContentsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,921 Enabling 'visualizations' API controller, class: VisualizationsController | |
| galaxy.web.framework.base DEBUG 2018-02-07 10:10:56,922 Enabling 'datatypes' API controller, class: DatatypesController | |
| galaxy.webapps.util DEBUG 2018-02-07 10:10:57,144 Enabling 'paste.httpexceptions' middleware | |
| galaxy.webapps.util DEBUG 2018-02-07 10:10:57,145 Enabling 'RecursiveMiddleware' middleware | |
| galaxy.webapps.util DEBUG 2018-02-07 10:10:57,150 Enabling 'ErrorMiddleware' middleware | |
| galaxy.webapps.util DEBUG 2018-02-07 10:10:57,151 Enabling 'TransLogger' middleware | |
| galaxy.webapps.util DEBUG 2018-02-07 10:10:57,151 Enabling 'XForwardedHostMiddleware' middleware | |
| galaxy.webapps.util DEBUG 2018-02-07 10:10:57,152 Enabling 'RequestIDMiddleware' middleware | |
| galaxy.webapps.util DEBUG 2018-02-07 10:10:57,153 Enabling 'BatchMiddleware' middleware | |
| galaxy.webapps.util DEBUG 2018-02-07 10:10:57,153 Enabling 'wrap_in_static' middleware | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,156 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,156 added url, path to static middleware: /plugins/visualizations/csg/static, ./config/plugins/visualizations/csg/static | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,156 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,156 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,156 added url, path to static middleware: /plugins/visualizations/unipept/static, ./config/plugins/visualizations/unipept/static | |
| galaxy.queue_worker INFO 2018-02-07 10:10:57,156 Binding and starting galaxy control worker for main | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,160 Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 140387697166144)> is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,161 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 140386952861440)> is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,161 Prior to webapp return, Galaxy thread <Thread(ToolConfWatcher.thread, started daemon 140386944468736)> is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,161 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-4, started daemon 140386791806720)> is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,162 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-3, started daemon 140386800199424)> is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,162 Prior to webapp return, Galaxy thread <Thread(JobHandlerStopQueue.monitor_thread, started daemon 140386374776576)> is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,162 Prior to webapp return, Galaxy thread <Thread(WorkflowRequestMonitor.monitor_thread, started daemon 140386357991168)> is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,162 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-1, started daemon 140386816984832)> is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,163 Prior to webapp return, Galaxy thread <Thread(JobHandlerQueue.monitor_thread, started daemon 140386366383872)> is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,163 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-0, started daemon 140386825377536)> is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,163 Prior to webapp return, Galaxy thread <Thread(LocalRunner.work_thread-2, started daemon 140386808592128)> is alive. | |
| galaxy.webapps.galaxy.buildapp DEBUG 2018-02-07 10:10:57,163 Prior to webapp return, Galaxy thread <GalaxyQueueWorker(Thread-1, started daemon 140386330867456)> is alive. | |
| Starting server in PID 1931. | |
| serving on http://127.0.0.1:8080 | |
| 127.0.0.1 - - [07/ 2月/2018:10:21:57 +0800] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.108 Safari/537.36" | |
| 127.0.0.1 - - [07/ 2月/2018:10:21:57 +0800] "GET /api/webhooks/history-menu/all HTTP/1.1" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.108 Safari/537.36" | |
| 127.0.0.1 - - [07/ 2月/2018:10:21:57 +0800] "GET /api/webhooks/onload/all HTTP/1.1" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.108 Safari/537.36" | |
| 127.0.0.1 - - [07/ 2月/2018:10:21:57 +0800] "GET /api/webhooks/masthead/all HTTP/1.1" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.108 Safari/537.36" | |
| 127.0.0.1 - - [07/ 2月/2018:10:21:57 +0800] "GET /api/genomes HTTP/1.1" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.108 Safari/537.36" | |
| 127.0.0.1 - - [07/ 2月/2018:10:21:57 +0800] "GET /api/datatypes?extension_only=False HTTP/1.1" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.108 Safari/537.36" | |
| 127.0.0.1 - - [07/ 2月/2018:10:21:57 +0800] "GET /welcome HTTP/1.1" 302 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.108 Safari/537.36" | |
| 127.0.0.1 - - [07/ 2月/2018:10:21:57 +0800] "GET /history/current_history_json HTTP/1.1" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.108 Safari/537.36" | |
| 127.0.0.1 - - [07/ 2月/2018:10:21:57 +0800] "GET /api/users/current HTTP/1.1" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.108 Safari/537.36" | |
| 127.0.0.1 - - [07/ 2月/2018:10:21:57 +0800] "GET /api/histories/f2db41e1fa331b3e/contents?limit=500&offset=0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.108 Safari/537.36" | |
| 127.0.0.1 - - [07/ 2月/2018:10:21:58 +0800] "GET /api/histories/f2db41e1fa331b3e?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.108 Safari/537.36" | |
| 127.0.0.1 - - [07/ 2月/2018:10:22:00 +0800] "GET /api/histories/f2db41e1fa331b3e/contents?keys=type_id%2Celement_count&order=hid&v=dev&q=history_content_type&q=deleted&q=purged&q=visible&qv=dataset_collection&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://127.0.0.1:8080/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/63.0.3239.108 Safari/537.36" |
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