Mercurial > repos > nick > dunovo
diff err2.log @ 11:0f8e0dc73d1d draft default tip
"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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/err2.log Wed Feb 16 22:59:00 2022 +0000 @@ -0,0 +1,1139 @@ +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/tmp1upz926i/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3.4 is no longer maintained and not recommended for usage due to the number of issues.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 +warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained.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 > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated +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 > 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@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 > 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 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 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 > 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 > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#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 > 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 > 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 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 > 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 > extract-text-webpack-plugin@2.1.2: Deprecated. Please use https://github.com/webpack-contrib/mini-css-extract-plugin +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 > 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 +warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#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 > 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 " > 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 > 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@2.88.2: request has been deprecated, 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 > 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 parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#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 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 > resolve-url@0.2.1: https://github.com/lydell/resolve-url#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 > 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 > 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 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 > resolve-url@0.2.1: https://github.com/lydell/resolve-url#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 > 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 > 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 > 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 > 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 > 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 > @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 > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142 +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 > 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 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 +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/tmp1upz926i/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/tmp1upz926i/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 17:19:24 -0500] [2654000] [INFO] Starting gunicorn 20.1.0 +[2022-02-16 17:19:24 -0500] [2654000] [INFO] Listening at: http://127.0.0.1:9090 (2654000) +[2022-02-16 17:19:24 -0500] [2654000] [INFO] Using worker: sync +[2022-02-16 17:19:24 -0500] [2654005] [INFO] Booting worker with pid: 2654005 +DEBUG:galaxy.app:python path is: /tmp/tmp1upz926i/galaxy-dev/lib, /tmp/tmp1upz926i/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/tmp1upz926i +DEBUG:galaxy.config:Data directory is /tmp/tmp1upz926i/galaxy-dev/database +DEBUG:galaxy.config:Managed config directory is /tmp/tmp1upz926i +DEBUG:galaxy.containers:config file '/tmp/tmp1upz926i/containers_conf.yml' does not exist, running with default config +galaxy.model.migrate.check INFO 2022-02-16 17:19:28,513 [pN:MainProcess,p:2654005,tN:MainThread] Creating database for URI [sqlite:////tmp/tmp1upz926i/galaxy.sqlite?isolation_level=IMMEDIATE] +galaxy.model.migrate.check INFO 2022-02-16 17:19:28,514 [pN:MainProcess,p:2654005,tN:MainThread] Creating new database from scratch, skipping migrations +galaxy.config INFO 2022-02-16 17:19:29,872 [pN:MainProcess,p:2654005,tN:MainThread] Install database targetting Galaxy's database configuration. +galaxy.web_stack.handlers INFO 2022-02-16 17:19:29,895 [pN:main,p:2654005,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 17:19:29,895 [pN:main,p:2654005,tN:MainThread] Job handler assignment methods set to: db-skip-locked +galaxy.jobs INFO 2022-02-16 17:19:29,895 [pN:main,p:2654005,tN:MainThread] Tag [_default_] handlers: main +/tmp/tmp1upz926i/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 17:19:30,292 [pN:main,p:2654005,tN:MainThread] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////tmp/tmp1upz926i/galaxy.sqlite?isolation_level=IMMEDIATE +galaxy.tools.data INFO 2022-02-16 17:19:30,309 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/all_fasta.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,309 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/bfast_indexes.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,310 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/blastdb.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,310 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/blastdb_p.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,311 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/blastdb_d.loc, reading sample +galaxy.tools.data WARNING 2022-02-16 17:19:30,311 [pN:main,p:2654005,tN:MainThread] Cannot find index file 'bwa_index.loc' for tool data table 'bwa_indexes' +galaxy.tools.data WARNING 2022-02-16 17:19:30,311 [pN:main,p:2654005,tN:MainThread] Cannot find index file 'bwa_index_color.loc' for tool data table 'bwa_indexes_color' +galaxy.tools.data INFO 2022-02-16 17:19:30,311 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/maf_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,312 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/ngs_sim_fasta.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,312 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/perm_base_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,313 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/perm_color_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,313 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/picard_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,313 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/picard_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,313 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/mosaik_index.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,314 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/twobit.loc, reading sample +galaxy.tools.data WARNING 2022-02-16 17:19:30,403 [pN:main,p:2654005,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 17:19:30,404 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/liftOver.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,405 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/bam_iobio.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,406 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/vcf_iobio.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,406 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/biom_simple_display.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,407 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/intermine_simple_display.loc, reading sample +galaxy.tools.data INFO 2022-02-16 17:19:30,407 [pN:main,p:2654005,tN:MainThread] Could not find tool data /tmp/tmp1upz926i/galaxy-dev/tool-data/icn3d_simple_display.loc, reading sample +galaxy.util WARNING 2022-02-16 17:19:30,585 [pN:main,p:2654005,tN:MainThread] directory not found: /tmp/tmp1upz926i/galaxy-dev/lib/galaxy/util/../../../config/plugins/activities +galaxy.tools WARNING 2022-02-16 17:19:30,586 [pN:main,p:2654005,tN:MainThread] The default shed tool config file (/tmp/tmp1upz926i/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 17:19:30,586 [pN:main,p:2654005,tN:MainThread] Parsing the tool configuration /tmp/tmp1upz926i/tool_conf.xml +galaxy.tools WARNING 2022-02-16 17:19:30,608 [pN:main,p:2654005,tN:MainThread] Tool with id 'dunovo': a when tag has not been defined for 'out_format (type) --> fasta', assuming empty inputs. +galaxy.tools WARNING 2022-02-16 17:19:30,619 [pN:main,p:2654005,tN:MainThread] The default shed tool config file (/tmp/tmp1upz926i/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 17:19:30,619 [pN:main,p:2654005,tN:MainThread] Parsing the tool configuration /tmp/tmp1upz926i/shed_tools_conf.xml +galaxy.tools WARNING 2022-02-16 17:19:30,619 [pN:main,p:2654005,tN:MainThread] The default shed tool config file (/tmp/tmp1upz926i/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 17:19:30,619 [pN:main,p:2654005,tN:MainThread] Parsing the tool configuration /tmp/tmp1upz926i/empty_tool_conf.xml +galaxy.datatypes.display_applications.application ERROR 2022-02-16 17:19:30,724 [pN:main,p:2654005,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 17:19:30,726 [pN:main,p:2654005,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 17:19:30,996 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,996 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:30,997 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,997 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:30,998 [pN:main,p:2654005,tN:MainThread] Visualizations plugin disabled: Circster. Skipping... +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:30,998 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,998 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: csg +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,999 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,999 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,999 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: editor +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,000 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: example +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,000 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,000 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,002 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,003 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_default +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,004 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,004 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,004 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,004 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,006 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,007 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,009 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,010 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,012 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,012 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,012 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: audio_player +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,012 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,013 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: video_player +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,013 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: msa +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,013 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,013 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,014 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,015 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nora +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,017 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,018 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,020 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,021 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,023 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,025 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,026 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,028 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,029 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,030 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,032 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,035 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,038 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,039 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,040 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,042 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,042 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: phyloviz +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,043 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: pv +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,044 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,045 [pN:main,p:2654005,tN:MainThread] Visualizations plugin disabled: Sweepster. Skipping... +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,045 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster +galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,046 [pN:main,p:2654005,tN:MainThread] template syntax is deprecated: use entry_point instead +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,046 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept +galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,047 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: venn +galaxy.tours._impl INFO 2022-02-16 17:19:31,068 [pN:main,p:2654005,tN:MainThread] Loaded tour 'core.galaxy_ui' +galaxy.tours._impl INFO 2022-02-16 17:19:31,074 [pN:main,p:2654005,tN:MainThread] Loaded tour 'core.scratchbook' +galaxy.tours._impl INFO 2022-02-16 17:19:31,093 [pN:main,p:2654005,tN:MainThread] Loaded tour 'core.history' +galaxy.jobs INFO 2022-02-16 17:19:31,108 [pN:main,p:2654005,tN:MainThread] Handler 'main' will load all configured runner plugins +galaxy.jobs.handler INFO 2022-02-16 17:19:31,120 [pN:main,p:2654005,tN:MainThread] job handler stop queue started +galaxy.jobs.handler INFO 2022-02-16 17:19:31,137 [pN:main,p:2654005,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 17:19:31,137 [pN:main,p:2654005,tN:MainThread] job handler queue started +galaxy.jobs.handler INFO 2022-02-16 17:19:31,139 [pN:main,p:2654005,tN:MainThread] job handler stop queue started +/tmp/tmp1upz926i/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/tmp1upz926i/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 17:19:31,192 [pN:main,p:2654005,tN:MainThread] No workflow schedulers plugin config file defined, using default scheduler. +galaxy.web_stack.handlers INFO 2022-02-16 17:19:31,197 [pN:main,p:2654005,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 17:19:31,199 [pN:main,p:2654005,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 17:19:31,202 [pN:main,p:2654005,tN:MainThread] Binding and starting galaxy control worker for main +galaxy.queue_worker INFO 2022-02-16 17:19:31,216 [pN:main,p:2654005,tN:MainThread] Queuing async task rebuild_toolbox_search_index for main. +galaxy.app INFO 2022-02-16 17:19:31,373 [pN:main,p:2654005,tN:MainThread] Galaxy app startup finished (3111.728 ms) +galaxy.queue_worker INFO 2022-02-16 17:19:31,411 [pN:main,p:2654005,tN:Thread-1] Instance 'main' received 'rebuild_toolbox_search_index' task, executing now. +/tmp/tmp1upz926i/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/tmp1upz926i/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 17:19:33,106 [pN:main,p:2654005,tN:MainThread] Galaxy server instance 'main' is running +/tmp/tmp1upz926i/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/tmp1upz926i/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/2022:17:19:33 -0400] "HEAD / HTTP/1.1" 200 - "-" "curl/7.68.0" +127.0.0.1 - - [16/Feb/2022:17:24:00 -0400] "GET / HTTP/1.1" 200 - "http://localhost:9090/datasets/b842d972534ccb3e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:24:01 -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/2022:17:24:01 -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/2022:17:24:01 -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/tmp1upz926i/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/2022:17:24:01 -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/2022:17:24:01 -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/2022:17:24:01 -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/2022:17:24:01 -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/2022:17:24:01 -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/2022:17:24:01 -0400] "GET /api/histories/2891970512fa2d5a/contents?limit=500&offset=0&details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&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/2022:17:24:01 -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/2022:17:24:01 -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/tmp1upz926i/galaxy-dev/lib/galaxy/managers/histories.py:525: 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. + 'empty': lambda i, k, **c: (len(i.datasets) + len(i.dataset_collections)) <= 0, +127.0.0.1 - - [16/Feb/2022:17:24:01 -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" +127.0.0.1 - - [16/Feb/2022:17:24:11 -0400] "GET /api/users/current 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/2022:17:24:11 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:24:11 -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/2022:17:24:11 -0400] "GET /api/datatypes?extension_only=False 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/2022:17:24:11 -0400] "GET /api/genomes 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/2022:17:24:22 -0400] "POST /api/uploads HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.tools INFO 2022-02-16 17:24:22,679 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (34.599 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:24:22,820 [pN:main,p:2654005,tN:MainThread] (Job[id=1,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:24:22 -0400] "POST /api/tools 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/2022:17:24:22 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A01.681Z&qv=False&qv=False 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/2022:17:24:22 -0400] "POST /api/uploads HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.tools INFO 2022-02-16 17:24:22,987 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (21.183 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:24:23,084 [pN:main,p:2654005,tN:MainThread] (Job[id=2,tool_id=upload1]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:24:22 -0400] "POST /api/tools 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/2022:17:24:23 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A22.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/__init__.py:1440: SAWarning: Coercing Subquery object into a select() for use in IN(); please pass a select() construct explicitly + .where(HistoryDatasetCollectionAssociation.table.c.id.in_(subq)) \ +galaxy.jobs.handler INFO 2022-02-16 17:24:23,572 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (1) Job dispatched +galaxy.jobs.handler INFO 2022-02-16 17:24:23,740 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched +galaxy.jobs.command_factory INFO 2022-02-16 17:24:23,827 [pN:main,p:2654005,tN:LocalRunner.work_thread-0] Built script [/tmp/tmp1upz926i/job_working_directory/000/1/tool_script.sh] for tool command [python '/tmp/tmp1upz926i/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp1upz926i/galaxy-dev' '/tmp/tmp1upz926i/job_working_directory/000/1/registry.xml' '/tmp/tmp1upz926i/job_working_directory/000/1/upload_params.json' '1:/tmp/tmp1upz926i/job_working_directory/000/1/working/dataset_1_files:/tmp/tmp1upz926i/files/000/dataset_1.dat'] +galaxy.jobs.command_factory INFO 2022-02-16 17:24:23,958 [pN:main,p:2654005,tN:LocalRunner.work_thread-1] Built script [/tmp/tmp1upz926i/job_working_directory/000/2/tool_script.sh] for tool command [python '/tmp/tmp1upz926i/galaxy-dev/tools/data_source/upload.py' '/tmp/tmp1upz926i/galaxy-dev' '/tmp/tmp1upz926i/job_working_directory/000/2/registry.xml' '/tmp/tmp1upz926i/job_working_directory/000/2/upload_params.json' '2:/tmp/tmp1upz926i/job_working_directory/000/2/working/dataset_2_files:/tmp/tmp1upz926i/files/000/dataset_2.dat'] +127.0.0.1 - - [16/Feb/2022:17:24:27 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A23.000Z&qv=False&qv=False 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/2022:17:24:30 -0400] "GET /api/tools/precheck/build?version=3.0.2&__identifer=40d6p2ywjn5&tool_version=3.0.2 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/2022:17:24:30 -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/2022:17:24:30 -0400] "GET /api/users/current 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/2022:17:24:30 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:24:30 -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/2022:17:24:30 -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/2022:17:24:30 -0400] "GET /api/tools/precheck/citations 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/2022:17:24:31 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A27.000Z&qv=False&qv=False 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/2022:17:24:31 -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" +127.0.0.1 - - [16/Feb/2022:17:24:31 -0400] "POST /api/tools/precheck/build 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/2022:17:24:31 -0400] "POST /api/tools/precheck/build 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/2022:17:24:31 -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/2022:17:24:31 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:24:31 -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/2022:17:24:33 -0400] "POST /api/tools/precheck/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.tools INFO 2022-02-16 17:24:35,395 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (24.284 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:35,416 [pN:main,p:2654005,tN:MainThread] Handled output named output1 for tool CONVERTER_gz_to_uncompressed (0.957 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:35,416 [pN:main,p:2654005,tN:MainThread] Added output datasets to history (0.175 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:35,418 [pN:main,p:2654005,tN:MainThread] Setup for job Job[unflushed,tool_id=CONVERTER_gz_to_uncompressed] complete, ready to be enqueued (0.967 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:35,437 [pN:main,p:2654005,tN:MainThread] Flushed transaction for job Job[id=3,tool_id=CONVERTER_gz_to_uncompressed] (19.325 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:24:35,449 [pN:main,p:2654005,tN:MainThread] Flushed transaction for Job[id=3,tool_id=CONVERTER_gz_to_uncompressed] (11.057 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:24:35,449 [pN:main,p:2654005,tN:MainThread] (Job[id=3,tool_id=CONVERTER_gz_to_uncompressed]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +galaxy.tools.actions INFO 2022-02-16 17:24:35,529 [pN:main,p:2654005,tN:MainThread] Handled output named output for tool precheck (0.824 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:35,538 [pN:main,p:2654005,tN:MainThread] Added output datasets to history (8.923 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:35,540 [pN:main,p:2654005,tN:MainThread] Setup for job Job[unflushed,tool_id=precheck] complete, ready to be enqueued (1.379 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:24:35,558 [pN:main,p:2654005,tN:MainThread] (Job[id=4,tool_id=precheck]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:24:35 -0400] "POST /api/tools 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/2022:17:24:35 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A31.000Z&qv=False&qv=False 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/2022:17:24:35 -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/2022:17:24:35 -0400] "POST /api/tools/precheck/build 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/2022:17:24:35 -0400] "POST /api/tools/precheck/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.jobs.handler INFO 2022-02-16 17:24:36,218 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (3) Job dispatched +galaxy.jobs.command_factory INFO 2022-02-16 17:24:36,321 [pN:main,p:2654005,tN:LocalRunner.work_thread-2] Built script [/tmp/tmp1upz926i/job_working_directory/000/3/tool_script.sh] for tool command [cp '/tmp/tmp1upz926i/job_working_directory/000/3/configs/tmp4ea73yop' 'galaxy.json' && gzip -dcf '/tmp/tmp1upz926i/files/000/dataset_1.dat' > '/tmp/tmp1upz926i/files/000/dataset_3.dat'] +127.0.0.1 - - [16/Feb/2022:17:24:39 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A35.000Z&qv=False&qv=False 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/2022:17:24:39 -0400] "POST /api/tools/precheck/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.jobs.handler INFO 2022-02-16 17:24:40,402 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (4) Job dispatched +galaxy.jobs.command_factory INFO 2022-02-16 17:24:40,536 [pN:main,p:2654005,tN:LocalRunner.work_thread-3] Built script [/tmp/tmp1upz926i/job_working_directory/000/4/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/me/miniconda3/envs/__dunovo@3.0.2')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; precheck.py --no-check-ids --tag-length 12 --constant-length 5 --min-reads 3 '/tmp/tmp1upz926i/files/000/dataset_3.dat' '/tmp/tmp1upz926i/files/000/dataset_2.dat' > '/tmp/tmp1upz926i/files/000/dataset_4.dat'] +127.0.0.1 - - [16/Feb/2022:17:24:43 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A39.000Z&qv=False&qv=False 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/2022:17:24:43 -0400] "POST /api/tools/precheck/build 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/2022:17:24:43 -0400] "POST /api/tools/precheck/build 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/2022:17:24:44 -0400] "GET /api/tools/make_families/build?version=3.0.2&__identifer=zn5n7gxymri&tool_version=3.0.2 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/2022:17:24:44 -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/2022:17:24:44 -0400] "GET /api/users/current 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/2022:17:24:44 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:24:44 -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/2022:17:24:44 -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/2022:17:24:44 -0400] "GET /api/tools/make_families/citations 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/2022:17:24:47 -0400] "POST /api/tools/make_families/build 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/2022:17:24:47 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A43.000Z&qv=False&qv=False 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/2022:17:24:47 -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" +127.0.0.1 - - [16/Feb/2022:17:24:47 -0400] "POST /api/tools/make_families/build 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/2022:17:24:47 -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/2022:17:24:48 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:24:48 -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/2022:17:24:48 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/8155e4b4bf1581ff HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.tools INFO 2022-02-16 17:24:50,841 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (25.627 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:50,864 [pN:main,p:2654005,tN:MainThread] Handled output named output for tool make_families (0.943 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:50,885 [pN:main,p:2654005,tN:MainThread] Added output datasets to history (21.017 ms) +galaxy.tools.actions INFO 2022-02-16 17:24:50,886 [pN:main,p:2654005,tN:MainThread] Setup for job Job[unflushed,tool_id=make_families] complete, ready to be enqueued (1.339 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:24:50,908 [pN:main,p:2654005,tN:MainThread] (Job[id=5,tool_id=make_families]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:24:50 -0400] "POST /api/tools 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/2022:17:24:50 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A47.000Z&qv=False&qv=False 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/2022:17:24:50 -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/2022:17:24:51 -0400] "POST /api/tools/make_families/build 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/2022:17:24:51 -0400] "POST /api/tools/make_families/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.jobs.handler INFO 2022-02-16 17:24:51,907 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (5) Job dispatched +galaxy.jobs.command_factory INFO 2022-02-16 17:24:52,048 [pN:main,p:2654005,tN:LocalRunner.work_thread-0] Built script [/tmp/tmp1upz926i/job_working_directory/000/5/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/me/miniconda3/envs/__dunovo@3.0.2')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; make-consensi.py --version > /tmp/tmp1upz926i/job_working_directory/000/5/outputs/COMMAND_VERSION 2>&1; make-families.sh -t 12 -i 5 '/tmp/tmp1upz926i/files/000/dataset_3.dat' '/tmp/tmp1upz926i/files/000/dataset_2.dat' > '/tmp/tmp1upz926i/files/000/dataset_5.dat'] +127.0.0.1 - - [16/Feb/2022:17:24:53 -0400] "GET /api/tools/correct_barcodes/build?version=3.0.2&__identifer=zqs52bkurng&tool_version=3.0.2 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/2022:17:24:53 -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/2022:17:24:53 -0400] "GET /api/users/current 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/2022:17:24:53 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:24:53 -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/2022:17:24:53 -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/2022:17:24:53 -0400] "GET /api/tools/correct_barcodes/citations 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/2022:17:24:55 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A50.000Z&qv=False&qv=False 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/2022:17:24:55 -0400] "POST /api/tools/correct_barcodes/build 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/2022:17:24:59 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A55.000Z&qv=False&qv=False 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/2022:17:24:59 -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" +127.0.0.1 - - [16/Feb/2022:17:24:59 -0400] "POST /api/tools/correct_barcodes/build 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/2022:17:24:59 -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/2022:17:24:59 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:24:59 -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" +galaxy.tools INFO 2022-02-16 17:25:01,164 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (11.425 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:01,197 [pN:main,p:2654005,tN:MainThread] Handled output named output for tool correct_barcodes (1.188 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:01,213 [pN:main,p:2654005,tN:MainThread] Added output datasets to history (16.650 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:01,215 [pN:main,p:2654005,tN:MainThread] Setup for job Job[unflushed,tool_id=correct_barcodes] complete, ready to be enqueued (1.661 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:25:01,250 [pN:main,p:2654005,tN:MainThread] (Job[id=6,tool_id=correct_barcodes]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:25:01 -0400] "POST /api/tools 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/2022:17:25:01 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A24%3A59.000Z&qv=False&qv=False 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/2022:17:25:01 -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/2022:17:25:01 -0400] "POST /api/tools/correct_barcodes/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.jobs.handler INFO 2022-02-16 17:25:02,399 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (6) Job dispatched +galaxy.jobs.command_factory INFO 2022-02-16 17:25:02,522 [pN:main,p:2654005,tN:LocalRunner.work_thread-1] Built script [/tmp/tmp1upz926i/job_working_directory/000/6/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/me/miniconda3/envs/__dunovo@3.0.2')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; correct.py --version > /tmp/tmp1upz926i/job_working_directory/000/6/outputs/COMMAND_VERSION 2>&1; baralign.sh -c 512 -t ${GALAXY_SLOTS:-1} -g '/tmp/tmp1upz926i/files/000/dataset_5.dat' refdir correct.sam && correct.py --galaxy --no-check-ids --dist 3 --mapq 20 --pos 2 '/tmp/tmp1upz926i/files/000/dataset_5.dat' refdir/barcodes.fa correct.sam > families.corrected.tsv && sort families.corrected.tsv > '/tmp/tmp1upz926i/files/000/dataset_6.dat'] +127.0.0.1 - - [16/Feb/2022:17:25:03 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/7b55dbb89df8f4e5 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/2022:17:25:05 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A01.000Z&qv=False&qv=False 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/2022:17:25:05 -0400] "POST /api/tools/correct_barcodes/build 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/2022:17:25:08 -0400] "GET /api/tools/align_families/build?version=3.0.2&__identifer=vace8ey3usq&tool_version=3.0.2 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/2022:17:25:08 -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/2022:17:25:08 -0400] "GET /api/users/current 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/2022:17:25:08 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:25:08 -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/2022:17:25:08 -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/2022:17:25:08 -0400] "GET /api/tools/align_families/citations 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/2022:17:25:09 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A05.000Z&qv=False&qv=False 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/2022:17:25:09 -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" +127.0.0.1 - - [16/Feb/2022:17:25:09 -0400] "POST /api/tools/align_families/build 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/2022:17:25:09 -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/2022:17:25:09 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:25:09 -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" +galaxy.tools INFO 2022-02-16 17:25:22,658 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (10.704 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:22,676 [pN:main,p:2654005,tN:MainThread] Handled output named output for tool align_families (0.967 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:22,685 [pN:main,p:2654005,tN:MainThread] Added output datasets to history (8.847 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:22,687 [pN:main,p:2654005,tN:MainThread] Setup for job Job[unflushed,tool_id=align_families] complete, ready to be enqueued (1.427 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:25:22,707 [pN:main,p:2654005,tN:MainThread] (Job[id=7,tool_id=align_families]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:25:22 -0400] "POST /api/tools 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/2022:17:25:22 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A09.000Z&qv=False&qv=False 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/2022:17:25:22 -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/2022:17:25:22 -0400] "POST /api/tools/align_families/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.jobs.handler INFO 2022-02-16 17:25:23,244 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (7) Job dispatched +galaxy.jobs.command_factory INFO 2022-02-16 17:25:23,341 [pN:main,p:2654005,tN:LocalRunner.work_thread-2] Built script [/tmp/tmp1upz926i/job_working_directory/000/7/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/me/miniconda3/envs/__dunovo@3.0.2')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; align-families.py --version > /tmp/tmp1upz926i/job_working_directory/000/7/outputs/COMMAND_VERSION 2>&1; align-families.py --no-check-ids --aligner kalign --galaxy --processes ${GALAXY_SLOTS:-1} '/tmp/tmp1upz926i/files/000/dataset_6.dat' > '/tmp/tmp1upz926i/files/000/dataset_7.dat'] +127.0.0.1 - - [16/Feb/2022:17:25:26 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A22.000Z&qv=False&qv=False 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/2022:17:25:26 -0400] "POST /api/tools/align_families/build 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/2022:17:25:28 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/fa6d20d0fb68383f 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/2022:17:25:29 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/683bc220e21425bb?keys=rerunnable%2Ccreating_job 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/2022:17:25:30 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e%2C683bc220e21425bb&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A26.000Z&qv=False&qv=False 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/2022:17:25:31 -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" +127.0.0.1 - - [16/Feb/2022:17:25:31 -0400] "POST /api/tools/align_families/build 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/2022:17:25:31 -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/2022:17:25:31 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:25:31 -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/2022:17:25:32 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/683bc220e21425bb 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/2022:17:25:35 -0400] "GET /api/tools/make_families/build?version=3.0.2&__identifer=xwrkqkk592&tool_version=3.0.2 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/2022:17:25:35 -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/2022:17:25:35 -0400] "GET /api/users/current 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/2022:17:25:35 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:25:35 -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/2022:17:25:35 -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/2022:17:25:35 -0400] "GET /api/tools/make_families/citations 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/2022:17:25:36 -0400] "GET /api/tools/dunovo/build?version=3.0.2&__identifer=7uf3g9o8xek&tool_version=3.0.2 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/2022:17:25:36 -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/2022:17:25:37 -0400] "GET /api/users/current 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/2022:17:25:37 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:25:37 -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/2022:17:25:37 -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/2022:17:25:37 -0400] "GET /api/tools/dunovo/citations HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.tools INFO 2022-02-16 17:25:50,497 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (16.036 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:50,523 [pN:main,p:2654005,tN:MainThread] Handled output named dcs1 for tool dunovo (3.862 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:50,525 [pN:main,p:2654005,tN:MainThread] Handled output named dcs2 for tool dunovo (2.181 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:50,535 [pN:main,p:2654005,tN:MainThread] Added output datasets to history (9.707 ms) +galaxy.tools.actions INFO 2022-02-16 17:25:50,537 [pN:main,p:2654005,tN:MainThread] Setup for job Job[unflushed,tool_id=dunovo] complete, ready to be enqueued (1.539 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:25:50,560 [pN:main,p:2654005,tN:MainThread] (Job[id=8,tool_id=dunovo]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:25:50 -0400] "POST /api/tools 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/2022:17:25:50 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A30.000Z&qv=False&qv=False 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/2022:17:25:50 -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/2022:17:25:50 -0400] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.jobs.handler INFO 2022-02-16 17:25:51,414 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (8) Job dispatched +galaxy.security.object_wrapper WARNING 2022-02-16 17:25:51,498 [pN:main,p:2654005,tN:LocalRunner.work_thread-3] Unable to create dynamic subclass SafeStringWrapper(galaxy.model.none_like.None:<class 'NoneType'>,<class 'NotImplementedType'>,<class 'bool'>,<class 'bytearray'>,<class 'ellipsis'>,<class 'galaxy.security.object_wrapper.SafeStringWrapper'>,<class 'galaxy.tools.wrappers.ToolParameterValueWrapper'>,<class 'numbers.Number'>) for <class 'galaxy.model.none_like.NoneDataset'>, None: type() doesn't support MRO entry resolution; use types.new_class() +galaxy.jobs.command_factory INFO 2022-02-16 17:25:51,526 [pN:main,p:2654005,tN:LocalRunner.work_thread-3] Built script [/tmp/tmp1upz926i/job_working_directory/000/8/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/me/miniconda3/envs/__dunovo@3.0.2')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; make-consensi.py --version > /tmp/tmp1upz926i/job_working_directory/000/8/outputs/COMMAND_VERSION 2>&1; make-consensi.py --galaxy --processes ${GALAXY_SLOTS:-1} --aligner biopython --qual 25 --qual-format sanger --min-reads 3 --cons-thres 0.5 --min-cons-reads 0 '/tmp/tmp1upz926i/files/000/dataset_7.dat' --dcs1 '/tmp/tmp1upz926i/files/000/dataset_8.dat' --dcs2 '/tmp/tmp1upz926i/files/000/dataset_9.dat'] +127.0.0.1 - - [16/Feb/2022:17:25:54 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A50.000Z&qv=False&qv=False 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/2022:17:25:54 -0400] "POST /api/tools/dunovo/build 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/2022:17:25:55 -0400] "POST /api/tools/dunovo/build 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/2022:17:25:58 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0%2Ca90a30fafe298e1e%2Cb842d972534ccb3e&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A54.000Z&qv=False&qv=False 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/2022:17:25:59 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/b842d972534ccb3e 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/2022:17:25:59 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/a90a30fafe298e1e 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/2022:17:25:59 -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" +127.0.0.1 - - [16/Feb/2022:17:25:59 -0400] "POST /api/tools/dunovo/build 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/2022:17:25:59 -0400] "POST /api/tools/dunovo/build 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/2022:17:25:59 -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/2022:17:25:59 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:25:59 -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/2022:17:26:00 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/a90a30fafe298e1e 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/2022:17:26:02 -0400] "GET /api/jobs/a90a30fafe298e1e/build_for_rerun 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/2022:17:26:02 -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/2022:17:26:02 -0400] "GET /api/users/current 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/2022:17:26:02 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:26:02 -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/2022:17:26:02 -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/2022:17:26:02 -0400] "GET /api/tools/dunovo/citations 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/2022:17:26:06 -0400] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.tools INFO 2022-02-16 17:26:15,534 [pN:main,p:2654005,tN:MainThread] Validated and populated state for tool request (18.785 ms) +galaxy.tools.actions INFO 2022-02-16 17:26:15,555 [pN:main,p:2654005,tN:MainThread] Handled output named dcs1 for tool dunovo (1.139 ms) +galaxy.tools.actions INFO 2022-02-16 17:26:15,556 [pN:main,p:2654005,tN:MainThread] Handled output named dcs2 for tool dunovo (0.677 ms) +galaxy.tools.actions INFO 2022-02-16 17:26:15,558 [pN:main,p:2654005,tN:MainThread] Handled output named sscs1 for tool dunovo (2.141 ms) +galaxy.tools.actions INFO 2022-02-16 17:26:15,560 [pN:main,p:2654005,tN:MainThread] Handled output named sscs2 for tool dunovo (1.773 ms) +galaxy.tools.actions INFO 2022-02-16 17:26:15,570 [pN:main,p:2654005,tN:MainThread] Added output datasets to history (10.279 ms) +galaxy.tools.actions INFO 2022-02-16 17:26:15,572 [pN:main,p:2654005,tN:MainThread] Setup for job Job[unflushed,tool_id=dunovo] complete, ready to be enqueued (1.936 ms) +galaxy.web_stack.handlers INFO 2022-02-16 17:26:15,593 [pN:main,p:2654005,tN:MainThread] (Job[id=9,tool_id=dunovo]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED' assignment method +127.0.0.1 - - [16/Feb/2022:17:26:15 -0400] "POST /api/tools 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/2022:17:26:15 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A25%3A59.000Z&qv=False&qv=False 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/2022:17:26:15 -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/2022:17:26:15 -0400] "POST /api/tools/dunovo/build HTTP/1.1" 200 - "http://localhost:9090/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +galaxy.jobs.handler INFO 2022-02-16 17:26:16,479 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (9) Job dispatched +galaxy.jobs.command_factory INFO 2022-02-16 17:26:16,612 [pN:main,p:2654005,tN:LocalRunner.work_thread-0] Built script [/tmp/tmp1upz926i/job_working_directory/000/9/tool_script.sh] for tool command [[ "$(basename "$CONDA_DEFAULT_ENV")" = "$(basename '/home/me/miniconda3/envs/__dunovo@3.0.2')" ] || { +MAX_TRIES=3 +COUNT=0 +while [ $COUNT -lt $MAX_TRIES ]; do + . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1 + if [ $? -eq 0 ];then + break + else + let COUNT=COUNT+1 + if [ $COUNT -eq $MAX_TRIES ];then + echo "Failed to activate conda environment! Error was:" + cat conda_activate.log + exit 1 + fi + sleep 10s + fi +done +} ; make-consensi.py --version > /tmp/tmp1upz926i/job_working_directory/000/9/outputs/COMMAND_VERSION 2>&1; make-consensi.py --galaxy --processes ${GALAXY_SLOTS:-1} --fastq-out 40 --aligner swalign --qual 25 --qual-format sanger --min-reads 3 --cons-thres 0.5 --min-cons-reads 0 '/tmp/tmp1upz926i/files/000/dataset_7.dat' --dcs1 '/tmp/tmp1upz926i/files/000/dataset_10.dat' --dcs2 '/tmp/tmp1upz926i/files/000/dataset_11.dat' --sscs1 '/tmp/tmp1upz926i/files/000/dataset_12.dat' --sscs2 '/tmp/tmp1upz926i/files/000/dataset_13.dat'] +127.0.0.1 - - [16/Feb/2022:17:26:18 -0400] "GET /api/jobs/b842d972534ccb3e/build_for_rerun 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/2022:17:26:18 -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/2022:17:26:18 -0400] "GET /api/users/current 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/2022:17:26:19 -0400] "GET /api/histories?view=summary&keys=size 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/2022:17:26:19 -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/2022:17:26:19 -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/2022:17:26:19 -0400] "GET /api/tools/dunovo/citations 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/2022:17:26:19 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A26%3A15.000Z&qv=False&qv=False 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/2022:17:26:20 -0400] "POST /api/tools/dunovo/build 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/2022:17:26:20 -0400] "POST /api/tools/dunovo/build 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/2022:17:26:20 -0400] "POST /api/tools/dunovo/build 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/2022:17:26:20 -0400] "POST /api/tools/dunovo/build 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/2022:17:26:21 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/datasets/b54fb481e575bccc HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/__init__.py:383: 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. + return self.text_metrics + self.numeric_metrics +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/jobs/b842d972534ccb3e?full=True HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/datasets/b54fb481e575bccc/parameters_display?hda_ldda=hda HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/jobs/b842d972534ccb3e?full=true HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/datasets/b54fb481e575bccc/storage HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/datasets/b54fb481e575bccc/inheritance_chain HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/datasets/b54fb481e575bccc/metrics?hda_ldda=hda HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/jobs/b842d972534ccb3e/destination_params HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/configuration/decode/b54fb481e575bccc HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/configuration/decode/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/configuration/decode/b842d972534ccb3e HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/datasets/683bc220e21425bb HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:22 -0400] "GET /api/datasets/9ce08b2254e4d5ed HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:23 -0400] "GET /api/datasets/80b8022ff3f677b7 HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:23 -0400] "GET /api/histories/2891970512fa2d5a/contents?details=b54fb481e575bccc%2C27ee89e2e3d631e0&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2022-02-16T22%3A26%3A19.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:24 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/b54fb481e575bccc HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:24 -0400] "GET /api/histories/2891970512fa2d5a?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:24 -0400] "GET /api/users/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:24 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:24 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:28 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/b842d972534ccb3e HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/jobs/b842d972534ccb3e?full=True HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/datasets/b54fb481e575bccc/parameters_display?hda_ldda=hda HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/configuration/decode/b842d972534ccb3e HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/datasets/b54fb481e575bccc/storage HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/datasets/b54fb481e575bccc/inheritance_chain HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/configuration/decode/b54fb481e575bccc HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/configuration/decode/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:26:36 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:00 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/5449172d6ff5669b HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:22 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/80b8022ff3f677b7 HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:24 -0400] "GET /datasets/80b8022ff3f677b7/display/?preview=True HTTP/1.1" 200 - "http://localhost:9090/datasets/b54fb481e575bccc/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/jobs/b842d972534ccb3e?full=True HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/datasets/80b8022ff3f677b7/parameters_display?hda_ldda=hda HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/configuration/decode/b842d972534ccb3e HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/datasets/80b8022ff3f677b7/storage HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/datasets/80b8022ff3f677b7/inheritance_chain HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/datasets/80b8022ff3f677b7/metrics?hda_ldda=hda HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/configuration/decode/80b8022ff3f677b7 HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/configuration/decode/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:29 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:35 -0400] "GET /api/histories/2891970512fa2d5a/contents/datasets/a90a30fafe298e1e HTTP/1.1" 200 - "http://localhost:9090/datasets/80b8022ff3f677b7/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:37 -0400] "GET /api/configuration HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/datasets/a90a30fafe298e1e HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/jobs/a90a30fafe298e1e?full=True HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/datasets/a90a30fafe298e1e/parameters_display?hda_ldda=hda HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/jobs/a90a30fafe298e1e?full=true HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/datasets/a90a30fafe298e1e/storage HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/datasets/a90a30fafe298e1e/inheritance_chain HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/datasets/a90a30fafe298e1e/metrics?hda_ldda=hda HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/jobs/a90a30fafe298e1e/destination_params HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/configuration/decode/a90a30fafe298e1e HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/configuration/decode/2891970512fa2d5a HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/configuration/decode/a90a30fafe298e1e HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/histories?view=summary&keys=size HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /history/current_history_json HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +127.0.0.1 - - [16/Feb/2022:17:27:38 -0400] "GET /api/datasets/b842d972534ccb3e HTTP/1.1" 200 - "http://localhost:9090/datasets/a90a30fafe298e1e/details" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:97.0) Gecko/20100101 Firefox/97.0" +[2022-02-16 17:28:33 -0500] [2654000] [INFO] Handling signal: int +[2022-02-16 17:28:33 -0500] [2654005] [INFO] Worker exiting (pid: 2654005) +galaxy.jobs.handler ERROR 2022-02-16 17:28:34,121 [pN:main,p:2654005,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/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 927, in monitor + self.monitor_step() + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 958, in monitor_step + newly_deleted_jobs = self.sa_session.query(model.Job).enable_eagerloads(False) \ + 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 ERROR 2022-02-16 17:28:34,777 [pN:main,p:2654005,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/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 307, in __monitor + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 325, in __monitor_step + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 373, in __handle_waiting_jobs + 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 17:28:34,851 [pN:main,p:2654005,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 17:28:34,855 [pN:main,p:2654005,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/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 92, in shutdown + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 397, in _shutdown_database_heartbeat + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 48, in shutdown + File "/tmp/tmp1upz926i/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 17:28:34,855 [pN:main,p:2654005,tN:MainThread] sending stop signal to worker thread +galaxy.jobs.handler ERROR 2022-02-16 17:28:35,130 [pN:main,p:2654005,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/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 927, in monitor + File "/tmp/tmp1upz926i/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 17:28:35,856 [pN:main,p:2654005,tN:MainThread] job handler queue stopped +galaxy.jobs.runners INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] LocalRunner: Sending stop signal to 4 job worker threads +galaxy.jobs.runners INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] Waiting up to 30 seconds for job worker threads to shutdown... +galaxy.jobs.runners INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] All job worker threads shutdown cleanly +galaxy.jobs.handler INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] sending stop signal to worker thread +galaxy.jobs.handler INFO 2022-02-16 17:28:35,857 [pN:main,p:2654005,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/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 92, in shutdown + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 397, in _shutdown_database_heartbeat + File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 48, in shutdown + File "/tmp/tmp1upz926i/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 17:28:36,070 [pN:main,p:2654005,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 140196716734208 and this is thread id 140198646921024. +sqlalchemy.pool.impl.NullPool ERROR 2022-02-16 17:28:36,071 [pN:main,p:2654005,tN:MainThread] Exception closing connection <sqlite3.Connection object at 0x7f82368a03f0> +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 140196716734208 and this is thread id 140198646921024. + +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 140196716734208 and this is thread id 140198646921024. +[2022-02-16 17:28:36 -0500] [2654000] [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/tmp1upz926i'