Mercurial > repos > nick > dunovo

view err.log @ 11:0f8e0dc73d1d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
author nick
date Wed, 16 Feb 2022 22:59:00 +0000
parents
children
line wrap: on
line source

planemo couldn't find a target test-data directory, you should likely create a test-data directory or pass an explicit path using --test_data.
galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
Cloning into '/tmp/tmppmuqm8bo/galaxy-dev'...
done.
galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.0.0"
warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^3.4.2"
warning Resolution field "ua-parser-js@0.7.30" is incompatible with requested version "ua-parser-js@0.7.22"
warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.1.8"
warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.0.4"
warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.1.8"
warning "@galaxyproject/bootstrap-tour > bootstrap@5.0.2" has unmet peer dependency "@popperjs/core@^2.9.2".
warning " > @handsontable/vue@2.0.0" has incorrect peer dependency "handsontable@^4.0.0".
warning " > @hirez_io/observer-spy@2.0.0" has unmet peer dependency "typescript@>=2.8.1".
warning " > linkifyjs@2.1.9" has unmet peer dependency "react@>= 0.14.0".
warning " > linkifyjs@2.1.9" has unmet peer dependency "react-dom@>= 0.14.0".
warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the 'parcel' package. See https://v2.parceljs.org/getting-started/migration for details.
warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies
warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
warning parcel-bundler > htmlnano > uncss > jsdom > request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3142
warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported
warning parcel-bundler > htmlnano > uncss > request > uuid@3.4.0: Please upgrade  to version 7 or higher.  Older versions may use Math.random() in certain circumstances, which is known to be problematic.  See https://v8.dev/blog/math-random for details.
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
warning Workspaces can only be enabled in private projects.
warning plotly.js > color-rgba > color-space > mumath@3.3.4: Redundant dependency in your project.
warning copy-webpack-plugin > webpack-log > uuid@3.4.0: Please upgrade  to version 7 or higher.  Older versions may use Math.random() in certain circumstances, which is known to be problematic.  See https://v8.dev/blog/math-random for details.
warning webpack > watchpack > watchpack-chokidar2 > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies
warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
warning webpack > watchpack > watchpack-chokidar2 > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
warning webpack > watchpack > watchpack-chokidar2 > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies
warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
warning webpack > watchpack > watchpack-chokidar2 > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
warning extract-text-webpack-plugin@3.0.2: Deprecated. Please use https://github.com/webpack-contrib/mini-css-extract-plugin
warning " > extract-text-webpack-plugin@3.0.2" has incorrect peer dependency "webpack@^3.1.0".
warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the 'parcel' package. See https://v2.parceljs.org/getting-started/migration for details.
warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies
warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported
warning parcel-bundler > htmlnano > uncss > request > uuid@3.4.0: Please upgrade  to version 7 or higher.  Older versions may use Math.random() in certain circumstances, which is known to be problematic.  See https://v8.dev/blog/math-random for details.
warning parcel-bundler > htmlnano > uncss > jsdom > request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3142
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
warning fbjs > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
warning hyphy-vision > extract-text-webpack-plugin@2.1.2: Deprecated. Please use https://github.com/webpack-contrib/mini-css-extract-plugin
warning hyphy-vision > popper.js@1.16.1: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1
warning hyphy-vision > alignment.js > popper.js@1.16.1: You can find the new Popper v2 at @popperjs/core, this package is dedicated to the legacy v1
warning hyphy-vision > alignment.js > phylotree > rollup-plugin-node-resolve@3.4.0: This package has been deprecated and is no longer maintained. Please use @rollup/plugin-node-resolve.
warning webpack > watchpack > watchpack-chokidar2 > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies
warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
warning webpack > watchpack > watchpack-chokidar2 > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
warning "hyphy-vision > extract-text-webpack-plugin@2.1.2" has incorrect peer dependency "webpack@^2.2.0".
warning extract-text-webpack-plugin@3.0.2: Deprecated. Please use https://github.com/webpack-contrib/mini-css-extract-plugin
warning webpack > watchpack > watchpack-chokidar2 > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies
warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
warning webpack > watchpack > watchpack-chokidar2 > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
warning " > extract-text-webpack-plugin@3.0.2" has incorrect peer dependency "webpack@^3.1.0".
warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the 'parcel' package. See https://v2.parceljs.org/getting-started/migration for details.
warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies
warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
warning parcel-bundler > htmlnano > uncss > jsdom > request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3142
warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported
warning parcel-bundler > htmlnano > uncss > request > uuid@3.4.0: Please upgrade  to version 7 or higher.  Older versions may use Math.random() in certain circumstances, which is known to be problematic.  See https://v8.dev/blog/math-random for details.
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
warning axios@0.19.2: Critical security vulnerability fixed in v0.21.1. For more information, see https://github.com/axios/axios/pull/3410
warning babel-preset-env > babel-plugin-check-es2015-constants > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the 'parcel' package. See https://v2.parceljs.org/getting-started/migration for details.
warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies
warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported
warning parcel-bundler > htmlnano > uncss > request > uuid@3.4.0: Please upgrade  to version 7 or higher.  Older versions may use Math.random() in certain circumstances, which is known to be problematic.  See https://v8.dev/blog/math-random for details.
warning parcel-bundler > htmlnano > uncss > jsdom > request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3142
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
warning package.json: License should be a valid SPDX license expression
warning openseadragon@2.4.2: License should be a valid SPDX license expression
warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
warning package.json: License should be a valid SPDX license expression
warning bio-pv > sniper > ecstatic@0.5.8: This package is unmaintained and deprecated. See the GH Issue 259.
warning bio-pv > sniper > swig@1.4.2: This package is no longer maintained
warning bio-pv > sniper > biojs-util-snippets > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
warning bio-pv > browserify > glob > minimatch@2.0.10: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
warning bio-pv > browserify > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
warning bio-pv > sniper > biojs-util-snippets > request > har-validator@5.1.5: this library is no longer supported
warning bio-pv > sniper > biojs-util-snippets > request > uuid@3.4.0: Please upgrade  to version 7 or higher.  Older versions may use Math.random() in certain circumstances, which is known to be problematic.  See https://v8.dev/blog/math-random for details.
warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained. Please migrate to v2, which is published under the 'parcel' package. See https://v2.parceljs.org/getting-started/migration for details.
warning parcel-bundler > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
warning parcel-bundler > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
warning parcel-bundler > @parcel/watcher > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies
warning parcel-bundler > babylon-walk > babel-runtime > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
warning parcel-bundler > @parcel/watcher > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
warning parcel-bundler > cssnano > cssnano-preset-default > postcss-svgo > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
warning parcel-bundler > htmlnano > uncss > jsdom > request-promise-native@1.0.9: request-promise-native has been deprecated because it extends the now deprecated request package, see https://github.com/request/request/issues/3142
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
warning fbjs > core-js@2.6.12: core-js@<3.4 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
warning webpack > watchpack > watchpack-chokidar2 > chokidar@2.1.8: Chokidar 2 does not receive security updates since 2019. Upgrade to chokidar 3 with 15x fewer dependencies
warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
warning webpack > watchpack > watchpack-chokidar2 > chokidar > fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
Browserslist: caniuse-lite is outdated. Please run:
npx browserslist@latest --update-db
Browserslist: caniuse-lite is outdated. Please run:
npx browserslist@latest --update-db
[BABEL] Note: The code generator has deoptimised the styling of /tmp/tmppmuqm8bo/galaxy-dev/client/node_modules/bootstrap-vue/esm/icons/icons.js as it exceeds the max of 500KB.
duplicate attribute: :writable
[BABEL] Note: The code generator has deoptimised the styling of /tmp/tmppmuqm8bo/galaxy-dev/client/node_modules/handsontable/dist/handsontable.js as it exceeds the max of 500KB.
Browserslist: caniuse-lite is outdated. Please run next command `yarn upgrade caniuse-lite browserslist`
galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
[2022-02-16 16:20:15 -0500] [2610616] [INFO] Starting gunicorn 20.1.0
[2022-02-16 16:20:15 -0500] [2610616] [INFO] Listening at: http://127.0.0.1:9090 (2610616)
[2022-02-16 16:20:15 -0500] [2610616] [INFO] Using worker: sync
[2022-02-16 16:20:15 -0500] [2610618] [INFO] Booting worker with pid: 2610618
DEBUG:galaxy.app:python path is: /tmp/tmppmuqm8bo/galaxy-dev/lib, /tmp/tmppmuqm8bo/galaxy-dev, /home/me/.planemo/gx_venv_3/bin, /usr/lib/python38.zip, /usr/lib/python3.8, /usr/lib/python3.8/lib-dynload, /home/me/.planemo/gx_venv_3/lib/python3.8/site-packages
DEBUG:galaxy.config:Configuration directory is /tmp/tmppmuqm8bo
DEBUG:galaxy.config:Data directory is /tmp/tmppmuqm8bo/galaxy-dev/database
DEBUG:galaxy.config:Managed config directory is /tmp/tmppmuqm8bo
DEBUG:galaxy.containers:config file '/tmp/tmppmuqm8bo/containers_conf.yml' does not exist, running with default config
galaxy.model.migrate.check INFO 2022-02-16 16:20:19,706 [pN:MainProcess,p:2610618,tN:MainThread] Creating database for URI [sqlite:////tmp/tmppmuqm8bo/galaxy.sqlite?isolation_level=IMMEDIATE]
galaxy.model.migrate.check INFO 2022-02-16 16:20:19,707 [pN:MainProcess,p:2610618,tN:MainThread] Creating new database from scratch, skipping migrations
galaxy.config INFO 2022-02-16 16:20:21,165 [pN:MainProcess,p:2610618,tN:MainThread] Install database targetting Galaxy's database configuration.
galaxy.web_stack.handlers INFO 2022-02-16 16:20:21,198 [pN:main,p:2610618,tN:MainThread] JobConfiguration: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on <handlers> to override the default
galaxy.jobs INFO 2022-02-16 16:20:21,198 [pN:main,p:2610618,tN:MainThread] Job handler assignment methods set to: db-skip-locked
galaxy.jobs INFO 2022-02-16 16:20:21,198 [pN:main,p:2610618,tN:MainThread] Tag [_default_] handlers: main
/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py:587: SAWarning: relationship 'RepositoryRepositoryDependencyAssociation.repository' will copy column tool_shed_repository.id to column repository_repository_dependency_association.tool_shed_repository_id, which conflicts with relationship(s): 'ToolShedRepository.required_repositories' (copies tool_shed_repository.id to repository_repository_dependency_association.tool_shed_repository_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards.   To silence this warning, add the parameter 'overlaps="required_repositories"' to the 'RepositoryRepositoryDependencyAssociation.repository' relationship.
  for tool_shed_repository in self.context.query(self.install_model.ToolShedRepository) \
galaxy.queue_worker INFO 2022-02-16 16:20:21,557 [pN:main,p:2610618,tN:MainThread] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////tmp/tmppmuqm8bo/galaxy.sqlite?isolation_level=IMMEDIATE
galaxy.tools.data INFO 2022-02-16 16:20:21,574 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/all_fasta.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,574 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/bfast_indexes.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,575 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/blastdb.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,575 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/blastdb_p.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,575 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/blastdb_d.loc, reading sample
galaxy.tools.data WARNING 2022-02-16 16:20:21,576 [pN:main,p:2610618,tN:MainThread] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes'
galaxy.tools.data WARNING 2022-02-16 16:20:21,576 [pN:main,p:2610618,tN:MainThread] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color'
galaxy.tools.data INFO 2022-02-16 16:20:21,576 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/maf_index.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,577 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/ngs_sim_fasta.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,577 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/perm_base_index.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,578 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/perm_color_index.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,578 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/picard_index.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,578 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/picard_index.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,578 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/mosaik_index.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,579 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/twobit.loc, reading sample
galaxy.tools.data WARNING 2022-02-16 16:20:21,687 [pN:main,p:2610618,tN:MainThread] 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 INFO 2022-02-16 16:20:21,688 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/liftOver.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,689 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/bam_iobio.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,689 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/vcf_iobio.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,690 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/biom_simple_display.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,690 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/intermine_simple_display.loc, reading sample
galaxy.tools.data INFO 2022-02-16 16:20:21,691 [pN:main,p:2610618,tN:MainThread] Could not find tool data /tmp/tmppmuqm8bo/galaxy-dev/tool-data/icn3d_simple_display.loc, reading sample
galaxy.util WARNING 2022-02-16 16:20:21,838 [pN:main,p:2610618,tN:MainThread] directory not found: /tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/util/../../../config/plugins/activities
galaxy.tools WARNING 2022-02-16 16:20:21,838 [pN:main,p:2610618,tN:MainThread] The default shed tool config file (/tmp/tmppmuqm8bo/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2022-02-16 16:20:21,838 [pN:main,p:2610618,tN:MainThread] Parsing the tool configuration /tmp/tmppmuqm8bo/tool_conf.xml
galaxy.tools WARNING 2022-02-16 16:20:21,855 [pN:main,p:2610618,tN:MainThread] Tool with id 'dunovo': a when tag has not been defined for 'out_format (type) --> fasta', assuming empty inputs.
galaxy.util ERROR 2022-02-16 16:20:21,856 [pN:main,p:2610618,tN:MainThread] Error parsing file /home/me/annex/Work/PSU/Nekrutenko/code/duplex/galaxy/correct_barcodes.xml
Traceback (most recent call last):
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/util/__init__.py", line 255, in parse_xml
    tree = etree.parse(fname, parser=parser)
  File "src/lxml/etree.pyx", line 3521, in lxml.etree.parse
  File "src/lxml/parser.pxi", line 1859, in lxml.etree._parseDocument
  File "src/lxml/parser.pxi", line 1885, in lxml.etree._parseDocumentFromURL
  File "src/lxml/parser.pxi", line 1789, in lxml.etree._parseDocFromFile
  File "src/lxml/parser.pxi", line 1177, in lxml.etree._BaseParser._parseDocFromFile
  File "src/lxml/parser.pxi", line 615, in lxml.etree._ParserContext._handleParseResultDoc
  File "src/lxml/parser.pxi", line 725, in lxml.etree._handleParseResult
  File "src/lxml/parser.pxi", line 654, in lxml.etree._raiseParseError
  File "/home/me/annex/Work/PSU/Nekrutenko/code/duplex/galaxy/correct_barcodes.xml", line 27
lxml.etree.XMLSyntaxError: Attribute label redefined, line 27, column 336
galaxy.tool_util.toolbox.base ERROR 2022-02-16 16:20:21,857 [pN:main,p:2610618,tN:MainThread] Failed to load potential tool /home/me/annex/Work/PSU/Nekrutenko/code/duplex/galaxy/correct_barcodes.xml.
Traceback (most recent call last):
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 902, in quick_load
    tool = self.load_tool(tool_file, tool_cache_data_dir)
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/tool_util/toolbox/base.py", line 942, in load_tool
    tool = self.create_tool(config_file=config_file, tool_shed_repository=tool_shed_repository, guid=guid, tool_cache_data_dir=tool_cache_data_dir, **kwds)
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/tools/__init__.py", line 374, in create_tool
    tool_source = self.get_expanded_tool_source(config_file)
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/tools/__init__.py", line 391, in get_expanded_tool_source
    raise e
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/tools/__init__.py", line 382, in get_expanded_tool_source
    return get_tool_source(
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/tool_util/parser/factory.py", line 44, in get_tool_source
    tree, macro_paths = load_tool_with_refereces(config_file)
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/util/xml_macros.py", line 15, in load_with_references
    tree = raw_xml_tree(path)
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/util/xml_macros.py", line 56, in raw_xml_tree
    tree = parse_xml(path, strip_whitespace=False, remove_comments=True)
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/util/__init__.py", line 255, in parse_xml
    tree = etree.parse(fname, parser=parser)
  File "src/lxml/etree.pyx", line 3521, in lxml.etree.parse
  File "src/lxml/parser.pxi", line 1859, in lxml.etree._parseDocument
  File "src/lxml/parser.pxi", line 1885, in lxml.etree._parseDocumentFromURL
  File "src/lxml/parser.pxi", line 1789, in lxml.etree._parseDocFromFile
  File "src/lxml/parser.pxi", line 1177, in lxml.etree._BaseParser._parseDocFromFile
  File "src/lxml/parser.pxi", line 615, in lxml.etree._ParserContext._handleParseResultDoc
  File "src/lxml/parser.pxi", line 725, in lxml.etree._handleParseResult
  File "src/lxml/parser.pxi", line 654, in lxml.etree._raiseParseError
  File "/home/me/annex/Work/PSU/Nekrutenko/code/duplex/galaxy/correct_barcodes.xml", line 27
lxml.etree.XMLSyntaxError: Attribute label redefined, line 27, column 336
galaxy.tools WARNING 2022-02-16 16:20:21,862 [pN:main,p:2610618,tN:MainThread] The default shed tool config file (/tmp/tmppmuqm8bo/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2022-02-16 16:20:21,863 [pN:main,p:2610618,tN:MainThread] Parsing the tool configuration /tmp/tmppmuqm8bo/shed_tools_conf.xml
galaxy.tools WARNING 2022-02-16 16:20:21,863 [pN:main,p:2610618,tN:MainThread] The default shed tool config file (/tmp/tmppmuqm8bo/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file
galaxy.tool_util.toolbox.base INFO 2022-02-16 16:20:21,863 [pN:main,p:2610618,tN:MainThread] Parsing the tool configuration /tmp/tmppmuqm8bo/empty_tool_conf.xml
galaxy.datatypes.display_applications.application ERROR 2022-02-16 16:20:21,979 [pN:main,p:2610618,tN:MainThread] Error loading a set of Dynamic Display Application links: A format or a metadata can be defined for a DisplayApplicationParameter, but not both.
galaxy.datatypes.display_applications.application ERROR 2022-02-16 16:20:21,981 [pN:main,p:2610618,tN:MainThread] Error loading a set of Dynamic Display Application links: A format or a metadata can be defined for a DisplayApplicationParameter, but not both.
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,280 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,282 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image
galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,283 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,283 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz
galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,284 [pN:main,p:2610618,tN:MainThread] Visualizations plugin disabled: Circster. Skipping...
galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,285 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,285 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: csg
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,286 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,287 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,287 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: editor
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,288 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: example
galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,289 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,289 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,293 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,296 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_default
galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,296 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,296 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace
galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,297 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,297 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,301 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,304 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,306 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,308 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,310 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter
galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,311 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,311 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: audio_player
galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,312 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,312 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: video_player
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,312 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: msa
galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,312 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,313 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,315 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,316 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nora
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,320 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,322 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,323 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,325 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,329 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,333 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,337 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,341 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,344 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,348 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,353 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,357 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,362 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,363 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,367 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,369 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,370 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: phyloviz
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,371 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: pv
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,373 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot
galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,373 [pN:main,p:2610618,tN:MainThread] Visualizations plugin disabled: Sweepster. Skipping...
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,374 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster
galaxy.visualization.plugins.config_parser INFO 2022-02-16 16:20:22,374 [pN:main,p:2610618,tN:MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,374 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept
galaxy.visualization.plugins.registry INFO 2022-02-16 16:20:22,375 [pN:main,p:2610618,tN:MainThread] VisualizationsRegistry, loaded plugin: venn
galaxy.tours._impl INFO 2022-02-16 16:20:22,413 [pN:main,p:2610618,tN:MainThread] Loaded tour 'core.galaxy_ui'
galaxy.tours._impl INFO 2022-02-16 16:20:22,427 [pN:main,p:2610618,tN:MainThread] Loaded tour 'core.scratchbook'
galaxy.tours._impl INFO 2022-02-16 16:20:22,446 [pN:main,p:2610618,tN:MainThread] Loaded tour 'core.history'
galaxy.jobs INFO 2022-02-16 16:20:22,455 [pN:main,p:2610618,tN:MainThread] Handler 'main' will load all configured runner plugins
galaxy.jobs.handler INFO 2022-02-16 16:20:22,463 [pN:main,p:2610618,tN:MainThread] job handler stop queue started
galaxy.jobs.handler INFO 2022-02-16 16:20:22,479 [pN:main,p:2610618,tN:JobHandlerQueue.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method for handler 'main', tag(s): _default_
galaxy.jobs.handler INFO 2022-02-16 16:20:22,479 [pN:main,p:2610618,tN:MainThread] job handler queue started
galaxy.jobs.handler INFO 2022-02-16 16:20:22,481 [pN:main,p:2610618,tN:MainThread] job handler stop queue started
/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py:359: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly
  ~model.Job.table.c.id.in_(hda_not_ready),
/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py:360: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly
  ~model.Job.table.c.id.in_(ldda_not_ready))
galaxy.workflow.scheduling_manager INFO 2022-02-16 16:20:22,506 [pN:main,p:2610618,tN:MainThread] No workflow schedulers plugin config file defined, using default scheduler.
galaxy.web_stack.handlers INFO 2022-02-16 16:20:22,506 [pN:main,p:2610618,tN:MainThread] WorkflowSchedulingManager: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED', set the `assign_with` attribute on <handlers> to override the default
galaxy.jobs.handler INFO 2022-02-16 16:20:22,507 [pN:main,p:2610618,tN:WorkflowRequestMonitor.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method for handler 'main', tag(s): None, _default_
galaxy.queue_worker INFO 2022-02-16 16:20:22,510 [pN:main,p:2610618,tN:MainThread] Binding and starting galaxy control worker for main
galaxy.queue_worker INFO 2022-02-16 16:20:22,526 [pN:main,p:2610618,tN:MainThread] Queuing async task rebuild_toolbox_search_index for main.
galaxy.app INFO 2022-02-16 16:20:22,673 [pN:main,p:2610618,tN:MainThread] Galaxy app startup finished (3269.979 ms)
galaxy.queue_worker INFO 2022-02-16 16:20:22,718 [pN:main,p:2610618,tN:Thread-1] Instance 'main' received 'rebuild_toolbox_search_index' task, executing now.
/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py:359: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly
  ~model.Job.table.c.id.in_(hda_not_ready),
/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py:360: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly
  ~model.Job.table.c.id.in_(ldda_not_ready))
galaxy.web_stack INFO 2022-02-16 16:20:24,422 [pN:main,p:2610618,tN:MainThread] Galaxy server instance 'main' is running
/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/webapps/base/webapp.py:607: 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.
  user = self.sa_session.query(self.app.model.User).filter(self.app.model.User.table.c.email == remote_user_email).first()
/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/webapps/base/webapp.py:243: 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.
  if config.use_remote_user and self.galaxy_session.user.deleted:
127.0.0.1 - - [16/Feb/2022:16:20:24 -0400] "HEAD / HTTP/1.1" 200 - "-" "curl/7.68.0"
127.0.0.1 - - [16/Feb/2022:16:21:25 -0400] "GET / HTTP/1.1" 200 - "http://localhost:9090/admin/toolbox_dependencies" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0"
127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0"
127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0"
127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /api/webhooks HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0"
/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/model/__init__.py:2669: 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.
  rval = db_session.query(
127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0"
127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /welcome HTTP/1.1" 302 265 "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0"
127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0"
127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /api/tools?in_panel=true&view=default HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0"
127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0"
127.0.0.1 - - [16/Feb/2022:16:21:26 -0400] "GET /api/histories/2891970512fa2d5a/contents?limit=500&offset=0&details=54f2a3a23292eb07%2Ca90a30fafe298e1e%2Cb54fb481e575bccc%2C27ee89e2e3d631e0&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0"
127.0.0.1 - - [16/Feb/2022:16:21:27 -0400] "GET /history/set_as_current?id=2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0"
127.0.0.1 - - [16/Feb/2022:16:21:27 -0400] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0"
/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/managers/histories.py:570: 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.
  for hda in history.datasets:
127.0.0.1 - - [16/Feb/2022:16:21:27 -0400] "GET /api/histories/2891970512fa2d5a?view=betawebclient HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0"
[2022-02-16 16:21:34 -0500] [2610616] [INFO] Handling signal: int
[2022-02-16 16:21:34 -0500] [2610618] [INFO] Worker exiting (pid: 2610618)
galaxy.jobs.handler ERROR 2022-02-16 16:21:34,396 [pN:main,p:2610618,tN:JobHandlerQueue.monitor_thread] Exception in monitor_step
Traceback (most recent call last):
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
    self.dialect.do_execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
    cursor.execute(statement, parameters)
sqlite3.OperationalError: no such table: job

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py", line 307, in __monitor
    self.__monitor_step()
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py", line 325, in __monitor_step
    self.__handle_waiting_jobs()
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py", line 373, in __handle_waiting_jobs
    jobs_to_check = ready_query.all()
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2709, in all
    return self._iter().all()
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
    result = self.session.execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
    result = conn._execute_20(statement, params or {}, execution_options)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
    return meth(self, args_10style, kwargs_10style, execution_options)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
    return connection._execute_clauseelement(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
    ret = self._execute_context(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
    self._handle_dbapi_exception(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
    util.raise_(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
    raise exception
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
    self.dialect.do_execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: job
[SQL: SELECT job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.galaxy_version AS job_galaxy_version, job.dynamic_tool_id AS job_dynamic_tool_id, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.job_messages AS job_job_messages, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.job_stdout AS job_job_stdout, job.job_stderr AS job_job_stderr, job.tool_stdout AS job_tool_stdout, job.tool_stderr AS job_tool_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler, EXISTS (SELECT history_dataset_collection_association.id 
FROM history_dataset_collection_association, job_to_output_dataset_collection 
WHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = 1) AS anon_1, EXISTS (SELECT history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.validated_state, history_dataset_association.validated_state_message, history_dataset_association.hidden_beneath_collection_instance_id 
FROM history_dataset_association, job_to_output_dataset 
WHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = 1) AS anon_2 
FROM job LEFT OUTER JOIN galaxy_user ON galaxy_user.id = job.user_id 
WHERE job.state = ? AND job.handler = ? AND (job.id NOT IN (SELECT anon_3.id 
FROM (SELECT job.id AS id 
FROM job JOIN job_to_input_dataset ON job.id = job_to_input_dataset.job_id JOIN history_dataset_association ON history_dataset_association.id = job_to_input_dataset.dataset_id JOIN dataset ON dataset.id = history_dataset_association.dataset_id 
WHERE job.state = ? AND dataset.state IN (?, ?, ?, ?, ?)) AS anon_3)) AND (job.id NOT IN (SELECT anon_4.id 
FROM (SELECT job.id AS id 
FROM job JOIN job_to_input_library_dataset ON job.id = job_to_input_library_dataset.job_id JOIN library_dataset_dataset_association ON library_dataset_dataset_association.id = job_to_input_library_dataset.ldda_id JOIN dataset ON dataset.id = library_dataset_dataset_association.dataset_id 
WHERE job.state = ? AND dataset.state IN (?, ?, ?, ?, ?)) AS anon_4)) ORDER BY job.id]
[parameters: (<states.NEW: 'new'>, 'main', <states.NEW: 'new'>, 'new', 'upload', 'queued', 'running', 'setting_metadata', <states.NEW: 'new'>, 'new', 'upload', 'queued', 'running', 'setting_metadata')]
(Background on this error at: http://sqlalche.me/e/14/e3q8)
kombu.mixins WARNING 2022-02-16 16:21:34,671 [pN:main,p:2610618,tN:Thread-1] Connection to broker lost, trying to re-establish connection...
Traceback (most recent call last):
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
    self.dialect.do_execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
    cursor.execute(statement, parameters)
sqlite3.OperationalError: no such table: kombu_queue

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/mixins.py", line 172, in run
    for _ in self.consume(limit=None, **kwargs):
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/mixins.py", line 194, in consume
    conn.drain_events(timeout=safety_interval)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/connection.py", line 318, in drain_events
    return self.transport.drain_events(self.connection, **kwargs)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 960, in drain_events
    get(self._deliver, timeout=timeout)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/utils/scheduling.py", line 52, in get
    return self.fun(resource, callback, **kwargs)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 998, in _drain_channel
    return channel.drain_events(callback=callback, timeout=timeout)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 742, in drain_events
    return self._poll(self.cycle, callback, timeout=timeout)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 399, in _poll
    return cycle.get(callback)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/utils/scheduling.py", line 52, in get
    return self.fun(resource, callback, **kwargs)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 402, in _get_and_deliver
    message = self._get(queue)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/sqlalchemy/__init__.py", line 112, in _get
    obj = self._get_or_create(queue)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/sqlalchemy/__init__.py", line 79, in _get_or_create
    obj = self.session.query(self.queue_cls) \
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first
    return self.limit(1)._iter().first()
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
    result = self.session.execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
    result = conn._execute_20(statement, params or {}, execution_options)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
    return meth(self, args_10style, kwargs_10style, execution_options)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
    return connection._execute_clauseelement(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
    ret = self._execute_context(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
    self._handle_dbapi_exception(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
    util.raise_(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
    raise exception
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
    self.dialect.do_execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: kombu_queue
[SQL: SELECT kombu_queue.id AS kombu_queue_id, kombu_queue.name AS kombu_queue_name 
FROM kombu_queue 
WHERE kombu_queue.name = ?
 LIMIT ? OFFSET ?]
[parameters: ('control.main@aziz', 1, 0)]
(Background on this error at: http://sqlalche.me/e/14/e3q8)
galaxy.app ERROR 2022-02-16 16:21:34,675 [pN:main,p:2610618,tN:MainThread] Failed to shutdown database heartbeat cleanly
Traceback (most recent call last):
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
    self.dialect.do_execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
    cursor.execute(statement, parameters)
sqlite3.OperationalError: no such table: worker_process

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/app.py", line 92, in shutdown
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/app.py", line 397, in _shutdown_database_heartbeat
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 48, in shutdown
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 77, in worker_process
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first
    return self.limit(1)._iter().first()
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
    result = self.session.execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
    result = conn._execute_20(statement, params or {}, execution_options)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
    return meth(self, args_10style, kwargs_10style, execution_options)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
    return connection._execute_clauseelement(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
    ret = self._execute_context(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
    self._handle_dbapi_exception(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
    util.raise_(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
    raise exception
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
    self.dialect.do_execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: worker_process
[SQL: SELECT worker_process.id AS worker_process_id, worker_process.server_name AS worker_process_server_name, worker_process.hostname AS worker_process_hostname, worker_process.pid AS worker_process_pid, worker_process.update_time AS worker_process_update_time 
FROM worker_process 
WHERE worker_process.server_name = ? AND worker_process.hostname = ?
 LIMIT ? OFFSET ?]
[parameters: ('main', 'aziz', 1, 0)]
(Background on this error at: http://sqlalche.me/e/14/e3q8)
galaxy.jobs.handler INFO 2022-02-16 16:21:34,676 [pN:main,p:2610618,tN:MainThread] sending stop signal to worker thread
galaxy.jobs.handler ERROR 2022-02-16 16:21:35,057 [pN:main,p:2610618,tN:JobHandlerStopQueue.monitor_thread] Exception in monitor_step
Traceback (most recent call last):
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
    self.dialect.do_execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
    cursor.execute(statement, parameters)
sqlite3.OperationalError: no such table: job

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py", line 927, in monitor
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/jobs/handler.py", line 958, in monitor_step
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2709, in all
    return self._iter().all()
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
    result = self.session.execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
    result = conn._execute_20(statement, params or {}, execution_options)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
    return meth(self, args_10style, kwargs_10style, execution_options)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
    return connection._execute_clauseelement(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
    ret = self._execute_context(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
    self._handle_dbapi_exception(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
    util.raise_(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
    raise exception
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
    self.dialect.do_execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: job
[SQL: SELECT job.id AS job_id, job.create_time AS job_create_time, job.update_time AS job_update_time, job.history_id AS job_history_id, job.library_folder_id AS job_library_folder_id, job.tool_id AS job_tool_id, job.tool_version AS job_tool_version, job.galaxy_version AS job_galaxy_version, job.dynamic_tool_id AS job_dynamic_tool_id, job.state AS job_state, job.info AS job_info, job.copied_from_job_id AS job_copied_from_job_id, job.command_line AS job_command_line, job.dependencies AS job_dependencies, job.job_messages AS job_job_messages, job.param_filename AS job_param_filename, job.runner_name AS job_runner_name_1, job.job_stdout AS job_job_stdout, job.job_stderr AS job_job_stderr, job.tool_stdout AS job_tool_stdout, job.tool_stderr AS job_tool_stderr, job.exit_code AS job_exit_code, job.traceback AS job_traceback, job.session_id AS job_session_id, job.user_id AS job_user_id, job.job_runner_name AS job_job_runner_name, job.job_runner_external_id AS job_job_runner_external_id, job.destination_id AS job_destination_id, job.destination_params AS job_destination_params, job.object_store_id AS job_object_store_id, job.imported AS job_imported, job.params AS job_params, job.handler AS job_handler, EXISTS (SELECT history_dataset_collection_association.id 
FROM history_dataset_collection_association, job_to_output_dataset_collection 
WHERE job.id = job_to_output_dataset_collection.job_id AND history_dataset_collection_association.id = job_to_output_dataset_collection.dataset_collection_id AND history_dataset_collection_association.deleted = 1) AS anon_1, EXISTS (SELECT history_dataset_association.id, history_dataset_association.history_id, history_dataset_association.dataset_id, history_dataset_association.create_time, history_dataset_association.update_time, history_dataset_association.state, history_dataset_association.copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id, history_dataset_association.name, history_dataset_association.info, history_dataset_association.blurb, history_dataset_association.peek, history_dataset_association.tool_version, history_dataset_association.extension, history_dataset_association.metadata, history_dataset_association.parent_id, history_dataset_association.designation, history_dataset_association.deleted, history_dataset_association.visible, history_dataset_association.extended_metadata_id, history_dataset_association.version, history_dataset_association.hid, history_dataset_association.purged, history_dataset_association.validated_state, history_dataset_association.validated_state_message, history_dataset_association.hidden_beneath_collection_instance_id 
FROM history_dataset_association, job_to_output_dataset 
WHERE job.id = job_to_output_dataset.job_id AND history_dataset_association.id = job_to_output_dataset.dataset_id AND history_dataset_association.deleted = 1) AS anon_2 
FROM job 
WHERE job.state IN (?, ?, ?) AND job.handler = ?]
[parameters: (<states.DELETED_NEW: 'deleted_new'>, <states.DELETING: 'deleting'>, <states.STOPPING: 'stop'>, 'main')]
(Background on this error at: http://sqlalche.me/e/14/e3q8)
galaxy.jobs.handler INFO 2022-02-16 16:21:35,676 [pN:main,p:2610618,tN:MainThread] job handler queue stopped
galaxy.jobs.runners INFO 2022-02-16 16:21:35,676 [pN:main,p:2610618,tN:MainThread] LocalRunner: Sending stop signal to 4 job worker threads
galaxy.jobs.runners INFO 2022-02-16 16:21:35,677 [pN:main,p:2610618,tN:MainThread] Waiting up to 30 seconds for job worker threads to shutdown...
galaxy.jobs.runners INFO 2022-02-16 16:21:35,677 [pN:main,p:2610618,tN:MainThread] All job worker threads shutdown cleanly
galaxy.jobs.handler INFO 2022-02-16 16:21:35,677 [pN:main,p:2610618,tN:MainThread] sending stop signal to worker thread
galaxy.jobs.handler INFO 2022-02-16 16:21:35,677 [pN:main,p:2610618,tN:MainThread] job handler stop queue stopped
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
    self.dialect.do_execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
    cursor.execute(statement, parameters)
sqlite3.OperationalError: no such table: worker_process

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/app.py", line 92, in shutdown
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/app.py", line 397, in _shutdown_database_heartbeat
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 48, in shutdown
  File "/tmp/tmppmuqm8bo/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 77, in worker_process
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first
    return self.limit(1)._iter().first()
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
    result = self.session.execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
    result = conn._execute_20(statement, params or {}, execution_options)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
    return meth(self, args_10style, kwargs_10style, execution_options)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
    return connection._execute_clauseelement(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
    ret = self._execute_context(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
    self._handle_dbapi_exception(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
    util.raise_(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
    raise exception
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
    self.dialect.do_execute(
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: worker_process
[SQL: SELECT worker_process.id AS worker_process_id, worker_process.server_name AS worker_process_server_name, worker_process.hostname AS worker_process_hostname, worker_process.pid AS worker_process_pid, worker_process.update_time AS worker_process_update_time 
FROM worker_process 
WHERE worker_process.server_name = ? AND worker_process.hostname = ?
 LIMIT ? OFFSET ?]
[parameters: ('main', 'aziz', 1, 0)]
(Background on this error at: http://sqlalche.me/e/14/e3q8)
sqlalchemy.pool.impl.NullPool ERROR 2022-02-16 16:21:35,859 [pN:main,p:2610618,tN:MainThread] Exception during reset or similar
Traceback (most recent call last):
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 682, in _finalize_fairy
    fairy._reset(pool)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 887, in _reset
    pool._dialect.do_rollback(self)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 667, in do_rollback
    dbapi_connection.rollback()
sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 140222822082304 and this is thread id 140224748214080.
sqlalchemy.pool.impl.NullPool ERROR 2022-02-16 16:21:35,860 [pN:main,p:2610618,tN:MainThread] Exception closing connection <sqlite3.Connection object at 0x7f88065f34e0>
Traceback (most recent call last):
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 682, in _finalize_fairy
    fairy._reset(pool)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 887, in _reset
    pool._dialect.do_rollback(self)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 667, in do_rollback
    dbapi_connection.rollback()
sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 140222822082304 and this is thread id 140224748214080.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 244, in _close_connection
    self._dialect.do_close(connection)
  File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 673, in do_close
    dbapi_connection.close()
sqlite3.ProgrammingError: SQLite objects created in a thread can only be used in that same thread. The object was created in thread id 140222822082304 and this is thread id 140224748214080.
[2022-02-16 16:21:36 -0500] [2610616] [INFO] Shutting down: Master
Traceback (most recent call last):
  File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 665, in _config_directory
    yield config_directory
  File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 540, in local_galaxy_config
    yield LocalGalaxyConfig(
  File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 237, in galaxy_config
    yield config
  File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 48, in _serve
    exit_code = run_galaxy_command(
  File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/run.py", line 118, in run_galaxy_command
    exit_code = shell(command, env=env)
  File "/home/me/.local/lib/python3.8/site-packages/galaxy/util/commands.py", line 60, in shell
    return p.wait()
  File "/usr/lib/python3.8/subprocess.py", line 1083, in wait
    return self._wait(timeout=timeout)
  File "/usr/lib/python3.8/subprocess.py", line 1806, in _wait
    (pid, sts) = self._try_wait(0)
  File "/usr/lib/python3.8/subprocess.py", line 1764, in _try_wait
    (pid, sts) = os.waitpid(self.pid, wait_flags)
KeyboardInterrupt

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/me/.local/bin/planemo", line 8, in <module>
    sys.exit(planemo())
  File "/usr/lib/python3/dist-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/usr/lib/python3/dist-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/lib/python3/dist-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/usr/lib/python3/dist-packages/click/decorators.py", line 64, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/home/me/.local/lib/python3.8/site-packages/planemo/cli.py", line 98, in handle_blended_options
    return f(*args, **kwds)
  File "/home/me/.local/lib/python3.8/site-packages/planemo/commands/cmd_serve.py", line 43, in cli
    galaxy_serve(ctx, runnables, **kwds)
  File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 25, in serve
    return _serve(ctx, runnables, **kwds)
  File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 72, in _serve
    return config
  File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
    self.gen.throw(type, value, traceback)
  File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 237, in galaxy_config
    yield config
  File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
    self.gen.throw(type, value, traceback)
  File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 540, in local_galaxy_config
    yield LocalGalaxyConfig(
  File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
    self.gen.throw(type, value, traceback)
  File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 669, in _config_directory
    shutil.rmtree(config_directory)
  File "/usr/lib/python3.8/shutil.py", line 722, in rmtree
    onerror(os.rmdir, path, sys.exc_info())
  File "/usr/lib/python3.8/shutil.py", line 720, in rmtree
    os.rmdir(path)
OSError: [Errno 39] Directory not empty: '/tmp/tmppmuqm8bo'