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"planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
author nick
date Wed, 16 Feb 2022 22:59:00 +0000
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10:9dc43bf7d1db 11:0f8e0dc73d1d
1 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.
2 galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
3 Cloning into '/tmp/tmp1upz926i/galaxy-dev'...
4 done.
5 galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
6 warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.0.0"
7 warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^3.4.2"
8 warning Resolution field "ua-parser-js@0.7.30" is incompatible with requested version "ua-parser-js@0.7.22"
9 warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.1.8"
10 warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.0.4"
11 warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.1.8"
12 warning "@galaxyproject/bootstrap-tour > bootstrap@5.0.2" has unmet peer dependency "@popperjs/core@^2.9.2".
13 warning " > @handsontable/vue@2.0.0" has incorrect peer dependency "handsontable@^4.0.0".
14 warning " > @hirez_io/observer-spy@2.0.0" has unmet peer dependency "typescript@>=2.8.1".
15 warning " > linkifyjs@2.1.9" has unmet peer dependency "react@>= 0.14.0".
16 warning " > linkifyjs@2.1.9" has unmet peer dependency "react-dom@>= 0.14.0".
17 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3.4 is no longer maintained and not recommended for usage due to the number of issues.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.
18 warning parcel-bundler@1.12.5: Parcel v1 is no longer maintained.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.
19 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.
20 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
21 warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
22 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.
23 warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
24 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.
25 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.
26 warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
27 warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
28 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
29 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
30 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
31 warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported
32 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.
33 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
34 warning Workspaces can only be enabled in private projects.
35 warning plotly.js > color-rgba > color-space > mumath@3.3.4: Redundant dependency in your project.
36 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.
37 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
38 warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
39 warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
40 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.
41 warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
42 warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
43 warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
44 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
45 warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
46 warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
47 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.
48 warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
49 warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
50 warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
51 warning extract-text-webpack-plugin@3.0.2: Deprecated. Please use https://github.com/webpack-contrib/mini-css-extract-plugin
52 warning " > extract-text-webpack-plugin@3.0.2" has incorrect peer dependency "webpack@^3.1.0".
53 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.
54 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.
55 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.
56 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
57 warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
58 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.
59 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.
60 warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
61 warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
62 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.
63 warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
64 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
65 warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported
66 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.
67 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
68 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
69 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
70 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.
71 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
72 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
73 warning hyphy-vision > extract-text-webpack-plugin@2.1.2: Deprecated. Please use https://github.com/webpack-contrib/mini-css-extract-plugin
74 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.
75 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
76 warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
77 warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
78 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.
79 warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
80 warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
81 warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
82 warning "hyphy-vision > extract-text-webpack-plugin@2.1.2" has incorrect peer dependency "webpack@^2.2.0".
83 warning extract-text-webpack-plugin@3.0.2: Deprecated. Please use https://github.com/webpack-contrib/mini-css-extract-plugin
84 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
85 warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
86 warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
87 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.
88 warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
89 warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
90 warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
91 warning " > extract-text-webpack-plugin@3.0.2" has incorrect peer dependency "webpack@^3.1.0".
92 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.
93 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.
94 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.
95 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
96 warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
97 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.
98 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.
99 warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
100 warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
101 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.
102 warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
103 warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported
104 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.
105 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
106 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
107 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
108 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
109 warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
110 warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
111 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
112 warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
113 warning axios@0.19.2: Critical security vulnerability fixed in v0.21.1. For more information, see https://github.com/axios/axios/pull/3410
114 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.
115 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.
116 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.
117 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
118 warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
119 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.
120 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.
121 warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
122 warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
123 warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
124 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.
125 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
126 warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported
127 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.
128 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
129 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
130 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
131 warning package.json: License should be a valid SPDX license expression
132 warning openseadragon@2.4.2: License should be a valid SPDX license expression
133 warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
134 warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
135 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
136 warning cpy-cli > cpy > globby > fast-glob > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
137 warning package.json: License should be a valid SPDX license expression
138 warning bio-pv > browserify > glob > minimatch@2.0.10: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
139 warning bio-pv > browserify > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
140 warning bio-pv > sniper > ecstatic@0.5.8: This package is unmaintained and deprecated. See the GH Issue 259.
141 warning bio-pv > sniper > swig@1.4.2: This package is no longer maintained
142 warning bio-pv > sniper > biojs-util-snippets > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
143 warning bio-pv > sniper > biojs-util-snippets > request > har-validator@5.1.5: this library is no longer supported
144 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.
145 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.
146 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.
147 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.
148 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.
149 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
150 warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
151 warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
152 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.
153 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.
154 warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
155 warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
156 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
157 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
158 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
159 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
160 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.
161 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
162 warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
163 warning webpack > node-libs-browser > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
164 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.
165 warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
166 warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
167 warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
168 Browserslist: caniuse-lite is outdated. Please run:
169 npx browserslist@latest --update-db
170 Browserslist: caniuse-lite is outdated. Please run:
171 npx browserslist@latest --update-db
172 [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.
173 duplicate attribute: :writable
174 [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.
175 Browserslist: caniuse-lite is outdated. Please run next command `yarn upgrade caniuse-lite browserslist`
176 galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
177 [2022-02-16 17:19:24 -0500] [2654000] [INFO] Starting gunicorn 20.1.0
178 [2022-02-16 17:19:24 -0500] [2654000] [INFO] Listening at: http://127.0.0.1:9090 (2654000)
179 [2022-02-16 17:19:24 -0500] [2654000] [INFO] Using worker: sync
180 [2022-02-16 17:19:24 -0500] [2654005] [INFO] Booting worker with pid: 2654005
181 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
182 DEBUG:galaxy.config:Configuration directory is /tmp/tmp1upz926i
183 DEBUG:galaxy.config:Data directory is /tmp/tmp1upz926i/galaxy-dev/database
184 DEBUG:galaxy.config:Managed config directory is /tmp/tmp1upz926i
185 DEBUG:galaxy.containers:config file '/tmp/tmp1upz926i/containers_conf.yml' does not exist, running with default config
186 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]
187 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
188 galaxy.config INFO 2022-02-16 17:19:29,872 [pN:MainProcess,p:2654005,tN:MainThread] Install database targetting Galaxy's database configuration.
189 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
190 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
191 galaxy.jobs INFO 2022-02-16 17:19:29,895 [pN:main,p:2654005,tN:MainThread] Tag [_default_] handlers: main
192 /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.
193 for tool_shed_repository in self.context.query(self.install_model.ToolShedRepository) \
194 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
195 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
196 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
197 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
198 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
199 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
200 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'
201 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'
202 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
203 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
204 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
205 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
206 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
207 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
208 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
209 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
210 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):
211 <Server-Side Genome List>
212 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
213 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
214 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
215 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
216 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
217 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
218 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
219 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
220 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
221 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.
222 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
223 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
224 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
225 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
226 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.
227 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.
228 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,996 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus
229 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,996 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image
230 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
231 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,997 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz
232 galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:30,998 [pN:main,p:2654005,tN:MainThread] Visualizations plugin disabled: Circster. Skipping...
233 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
234 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,998 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: csg
235 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,999 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape
236 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,999 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna
237 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,999 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: editor
238 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,000 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: example
239 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
240 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,000 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz
241 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,002 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster
242 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,003 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_default
243 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
244 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,004 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace
245 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
246 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,004 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision
247 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,006 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar
248 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,007 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box
249 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,009 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram
250 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,010 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line
251 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,012 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter
252 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
253 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,012 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: audio_player
254 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
255 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,013 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: video_player
256 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,013 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: msa
257 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
258 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,013 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp
259 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,014 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl
260 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,015 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nora
261 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,017 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar
262 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,018 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked
263 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,020 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram
264 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,021 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete
265 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,023 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal
266 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,025 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked
267 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,026 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line
268 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,028 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus
269 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,029 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie
270 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,030 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter
271 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,032 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea
272 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,035 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full
273 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,038 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream
274 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,039 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers
275 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,040 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon
276 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,042 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas
277 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,042 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: phyloviz
278 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,043 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: pv
279 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,044 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot
280 galaxy.visualization.plugins.config_parser INFO 2022-02-16 17:19:31,045 [pN:main,p:2654005,tN:MainThread] Visualizations plugin disabled: Sweepster. Skipping...
281 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,045 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster
282 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
283 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,046 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept
284 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,047 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: venn
285 galaxy.tours._impl INFO 2022-02-16 17:19:31,068 [pN:main,p:2654005,tN:MainThread] Loaded tour 'core.galaxy_ui'
286 galaxy.tours._impl INFO 2022-02-16 17:19:31,074 [pN:main,p:2654005,tN:MainThread] Loaded tour 'core.scratchbook'
287 galaxy.tours._impl INFO 2022-02-16 17:19:31,093 [pN:main,p:2654005,tN:MainThread] Loaded tour 'core.history'
288 galaxy.jobs INFO 2022-02-16 17:19:31,108 [pN:main,p:2654005,tN:MainThread] Handler 'main' will load all configured runner plugins
289 galaxy.jobs.handler INFO 2022-02-16 17:19:31,120 [pN:main,p:2654005,tN:MainThread] job handler stop queue started
290 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_
291 galaxy.jobs.handler INFO 2022-02-16 17:19:31,137 [pN:main,p:2654005,tN:MainThread] job handler queue started
292 galaxy.jobs.handler INFO 2022-02-16 17:19:31,139 [pN:main,p:2654005,tN:MainThread] job handler stop queue started
293 /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
294 ~model.Job.table.c.id.in_(hda_not_ready),
295 /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
296 ~model.Job.table.c.id.in_(ldda_not_ready))
297 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.
298 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
299 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_
300 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
301 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.
302 galaxy.app INFO 2022-02-16 17:19:31,373 [pN:main,p:2654005,tN:MainThread] Galaxy app startup finished (3111.728 ms)
303 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.
304 /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
305 ~model.Job.table.c.id.in_(hda_not_ready),
306 /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
307 ~model.Job.table.c.id.in_(ldda_not_ready))
308 galaxy.web_stack INFO 2022-02-16 17:19:33,106 [pN:main,p:2654005,tN:MainThread] Galaxy server instance 'main' is running
309 /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.
310 user = self.sa_session.query(self.app.model.User).filter(self.app.model.User.table.c.email == remote_user_email).first()
311 /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.
312 if config.use_remote_user and self.galaxy_session.user.deleted:
313 127.0.0.1 - - [16/Feb/2022:17:19:33 -0400] "HEAD / HTTP/1.1" 200 - "-" "curl/7.68.0"
314 127.0.0.1 - - [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"
315 127.0.0.1 - - [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"
316 127.0.0.1 - - [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"
317 127.0.0.1 - - [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"
318 /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.
319 rval = db_session.query(
320 127.0.0.1 - - [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"
321 127.0.0.1 - - [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"
322 127.0.0.1 - - [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"
323 127.0.0.1 - - [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"
324 127.0.0.1 - - [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"
325 127.0.0.1 - - [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"
326 127.0.0.1 - - [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"
327 127.0.0.1 - - [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"
328 /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.
329 'empty': lambda i, k, **c: (len(i.datasets) + len(i.dataset_collections)) <= 0,
330 127.0.0.1 - - [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"
331 127.0.0.1 - - [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"
332 127.0.0.1 - - [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"
333 127.0.0.1 - - [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"
334 127.0.0.1 - - [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"
335 127.0.0.1 - - [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"
336 127.0.0.1 - - [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"
337 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)
338 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
339 127.0.0.1 - - [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"
340 127.0.0.1 - - [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"
341 127.0.0.1 - - [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"
342 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)
343 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
344 127.0.0.1 - - [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"
345 127.0.0.1 - - [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"
346 /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
347 .where(HistoryDatasetCollectionAssociation.table.c.id.in_(subq)) \
348 galaxy.jobs.handler INFO 2022-02-16 17:24:23,572 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (1) Job dispatched
349 galaxy.jobs.handler INFO 2022-02-16 17:24:23,740 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched
350 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']
351 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']
352 127.0.0.1 - - [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"
353 127.0.0.1 - - [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"
354 127.0.0.1 - - [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"
355 127.0.0.1 - - [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"
356 127.0.0.1 - - [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"
357 127.0.0.1 - - [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"
358 127.0.0.1 - - [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"
359 127.0.0.1 - - [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"
360 127.0.0.1 - - [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"
361 127.0.0.1 - - [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"
362 127.0.0.1 - - [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"
363 127.0.0.1 - - [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"
364 127.0.0.1 - - [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"
365 127.0.0.1 - - [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"
366 127.0.0.1 - - [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"
367 127.0.0.1 - - [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"
368 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)
369 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)
370 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)
371 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)
372 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)
373 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)
374 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
375 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)
376 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)
377 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)
378 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
379 127.0.0.1 - - [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"
380 127.0.0.1 - - [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"
381 127.0.0.1 - - [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"
382 127.0.0.1 - - [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"
383 127.0.0.1 - - [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"
384 galaxy.jobs.handler INFO 2022-02-16 17:24:36,218 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (3) Job dispatched
385 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']
386 127.0.0.1 - - [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"
387 127.0.0.1 - - [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"
388 galaxy.jobs.handler INFO 2022-02-16 17:24:40,402 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (4) Job dispatched
389 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')" ] || {
390 MAX_TRIES=3
391 COUNT=0
392 while [ $COUNT -lt $MAX_TRIES ]; do
393 . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1
394 if [ $? -eq 0 ];then
395 break
396 else
397 let COUNT=COUNT+1
398 if [ $COUNT -eq $MAX_TRIES ];then
399 echo "Failed to activate conda environment! Error was:"
400 cat conda_activate.log
401 exit 1
402 fi
403 sleep 10s
404 fi
405 done
406 } ; 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']
407 127.0.0.1 - - [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"
408 127.0.0.1 - - [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"
409 127.0.0.1 - - [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"
410 127.0.0.1 - - [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"
411 127.0.0.1 - - [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"
412 127.0.0.1 - - [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"
413 127.0.0.1 - - [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"
414 127.0.0.1 - - [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"
415 127.0.0.1 - - [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"
416 127.0.0.1 - - [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"
417 127.0.0.1 - - [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"
418 127.0.0.1 - - [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"
419 127.0.0.1 - - [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"
420 127.0.0.1 - - [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"
421 127.0.0.1 - - [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"
422 127.0.0.1 - - [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"
423 127.0.0.1 - - [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"
424 127.0.0.1 - - [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"
425 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)
426 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)
427 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)
428 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)
429 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
430 127.0.0.1 - - [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"
431 127.0.0.1 - - [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"
432 127.0.0.1 - - [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"
433 127.0.0.1 - - [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"
434 127.0.0.1 - - [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"
435 galaxy.jobs.handler INFO 2022-02-16 17:24:51,907 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (5) Job dispatched
436 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')" ] || {
437 MAX_TRIES=3
438 COUNT=0
439 while [ $COUNT -lt $MAX_TRIES ]; do
440 . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1
441 if [ $? -eq 0 ];then
442 break
443 else
444 let COUNT=COUNT+1
445 if [ $COUNT -eq $MAX_TRIES ];then
446 echo "Failed to activate conda environment! Error was:"
447 cat conda_activate.log
448 exit 1
449 fi
450 sleep 10s
451 fi
452 done
453 } ; 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']
454 127.0.0.1 - - [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"
455 127.0.0.1 - - [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"
456 127.0.0.1 - - [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"
457 127.0.0.1 - - [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"
458 127.0.0.1 - - [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"
459 127.0.0.1 - - [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"
460 127.0.0.1 - - [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"
461 127.0.0.1 - - [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"
462 127.0.0.1 - - [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"
463 127.0.0.1 - - [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"
464 127.0.0.1 - - [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"
465 127.0.0.1 - - [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"
466 127.0.0.1 - - [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"
467 127.0.0.1 - - [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"
468 127.0.0.1 - - [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"
469 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)
470 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)
471 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)
472 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)
473 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
474 127.0.0.1 - - [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"
475 127.0.0.1 - - [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"
476 127.0.0.1 - - [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"
477 127.0.0.1 - - [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"
478 galaxy.jobs.handler INFO 2022-02-16 17:25:02,399 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (6) Job dispatched
479 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')" ] || {
480 MAX_TRIES=3
481 COUNT=0
482 while [ $COUNT -lt $MAX_TRIES ]; do
483 . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1
484 if [ $? -eq 0 ];then
485 break
486 else
487 let COUNT=COUNT+1
488 if [ $COUNT -eq $MAX_TRIES ];then
489 echo "Failed to activate conda environment! Error was:"
490 cat conda_activate.log
491 exit 1
492 fi
493 sleep 10s
494 fi
495 done
496 } ; 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']
497 127.0.0.1 - - [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"
498 127.0.0.1 - - [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"
499 127.0.0.1 - - [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"
500 127.0.0.1 - - [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"
501 127.0.0.1 - - [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"
502 127.0.0.1 - - [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"
503 127.0.0.1 - - [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"
504 127.0.0.1 - - [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"
505 127.0.0.1 - - [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"
506 127.0.0.1 - - [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"
507 127.0.0.1 - - [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"
508 127.0.0.1 - - [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"
509 127.0.0.1 - - [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"
510 127.0.0.1 - - [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"
511 127.0.0.1 - - [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"
512 127.0.0.1 - - [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"
513 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)
514 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)
515 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)
516 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)
517 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
518 127.0.0.1 - - [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"
519 127.0.0.1 - - [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"
520 127.0.0.1 - - [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"
521 127.0.0.1 - - [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"
522 galaxy.jobs.handler INFO 2022-02-16 17:25:23,244 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (7) Job dispatched
523 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')" ] || {
524 MAX_TRIES=3
525 COUNT=0
526 while [ $COUNT -lt $MAX_TRIES ]; do
527 . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1
528 if [ $? -eq 0 ];then
529 break
530 else
531 let COUNT=COUNT+1
532 if [ $COUNT -eq $MAX_TRIES ];then
533 echo "Failed to activate conda environment! Error was:"
534 cat conda_activate.log
535 exit 1
536 fi
537 sleep 10s
538 fi
539 done
540 } ; 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']
541 127.0.0.1 - - [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"
542 127.0.0.1 - - [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"
543 127.0.0.1 - - [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"
544 127.0.0.1 - - [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"
545 127.0.0.1 - - [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"
546 127.0.0.1 - - [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"
547 127.0.0.1 - - [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"
548 127.0.0.1 - - [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"
549 127.0.0.1 - - [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"
550 127.0.0.1 - - [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"
551 127.0.0.1 - - [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"
552 127.0.0.1 - - [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"
553 127.0.0.1 - - [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"
554 127.0.0.1 - - [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"
555 127.0.0.1 - - [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"
556 127.0.0.1 - - [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"
557 127.0.0.1 - - [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"
558 127.0.0.1 - - [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"
559 127.0.0.1 - - [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"
560 127.0.0.1 - - [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"
561 127.0.0.1 - - [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"
562 127.0.0.1 - - [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"
563 127.0.0.1 - - [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"
564 127.0.0.1 - - [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"
565 127.0.0.1 - - [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"
566 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)
567 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)
568 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)
569 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)
570 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)
571 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
572 127.0.0.1 - - [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"
573 127.0.0.1 - - [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"
574 127.0.0.1 - - [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"
575 127.0.0.1 - - [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"
576 galaxy.jobs.handler INFO 2022-02-16 17:25:51,414 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (8) Job dispatched
577 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()
578 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')" ] || {
579 MAX_TRIES=3
580 COUNT=0
581 while [ $COUNT -lt $MAX_TRIES ]; do
582 . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1
583 if [ $? -eq 0 ];then
584 break
585 else
586 let COUNT=COUNT+1
587 if [ $COUNT -eq $MAX_TRIES ];then
588 echo "Failed to activate conda environment! Error was:"
589 cat conda_activate.log
590 exit 1
591 fi
592 sleep 10s
593 fi
594 done
595 } ; 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']
596 127.0.0.1 - - [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"
597 127.0.0.1 - - [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"
598 127.0.0.1 - - [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"
599 127.0.0.1 - - [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"
600 127.0.0.1 - - [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"
601 127.0.0.1 - - [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"
602 127.0.0.1 - - [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"
603 127.0.0.1 - - [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"
604 127.0.0.1 - - [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"
605 127.0.0.1 - - [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"
606 127.0.0.1 - - [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"
607 127.0.0.1 - - [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"
608 127.0.0.1 - - [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"
609 127.0.0.1 - - [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"
610 127.0.0.1 - - [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"
611 127.0.0.1 - - [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"
612 127.0.0.1 - - [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"
613 127.0.0.1 - - [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"
614 127.0.0.1 - - [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"
615 127.0.0.1 - - [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"
616 127.0.0.1 - - [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"
617 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)
618 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)
619 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)
620 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)
621 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)
622 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)
623 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)
624 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
625 127.0.0.1 - - [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"
626 127.0.0.1 - - [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"
627 127.0.0.1 - - [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"
628 127.0.0.1 - - [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"
629 galaxy.jobs.handler INFO 2022-02-16 17:26:16,479 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (9) Job dispatched
630 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')" ] || {
631 MAX_TRIES=3
632 COUNT=0
633 while [ $COUNT -lt $MAX_TRIES ]; do
634 . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1
635 if [ $? -eq 0 ];then
636 break
637 else
638 let COUNT=COUNT+1
639 if [ $COUNT -eq $MAX_TRIES ];then
640 echo "Failed to activate conda environment! Error was:"
641 cat conda_activate.log
642 exit 1
643 fi
644 sleep 10s
645 fi
646 done
647 } ; 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']
648 127.0.0.1 - - [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"
649 127.0.0.1 - - [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"
650 127.0.0.1 - - [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"
651 127.0.0.1 - - [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"
652 127.0.0.1 - - [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"
653 127.0.0.1 - - [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"
654 127.0.0.1 - - [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"
655 127.0.0.1 - - [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"
656 127.0.0.1 - - [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"
657 127.0.0.1 - - [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"
658 127.0.0.1 - - [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"
659 127.0.0.1 - - [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"
660 127.0.0.1 - - [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"
661 127.0.0.1 - - [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"
662 127.0.0.1 - - [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"
663 /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.
664 return self.text_metrics + self.numeric_metrics
665 127.0.0.1 - - [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"
666 127.0.0.1 - - [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"
667 127.0.0.1 - - [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"
668 127.0.0.1 - - [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"
669 127.0.0.1 - - [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"
670 127.0.0.1 - - [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"
671 127.0.0.1 - - [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"
672 127.0.0.1 - - [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"
673 127.0.0.1 - - [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"
674 127.0.0.1 - - [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"
675 127.0.0.1 - - [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"
676 127.0.0.1 - - [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"
677 127.0.0.1 - - [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"
678 127.0.0.1 - - [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"
679 127.0.0.1 - - [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"
680 127.0.0.1 - - [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"
681 127.0.0.1 - - [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"
682 127.0.0.1 - - [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"
683 127.0.0.1 - - [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"
684 127.0.0.1 - - [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"
685 127.0.0.1 - - [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"
686 127.0.0.1 - - [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"
687 127.0.0.1 - - [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"
688 127.0.0.1 - - [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"
689 127.0.0.1 - - [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"
690 127.0.0.1 - - [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"
691 127.0.0.1 - - [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"
692 127.0.0.1 - - [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"
693 127.0.0.1 - - [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"
694 127.0.0.1 - - [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"
695 127.0.0.1 - - [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"
696 127.0.0.1 - - [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"
697 127.0.0.1 - - [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"
698 127.0.0.1 - - [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"
699 127.0.0.1 - - [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"
700 127.0.0.1 - - [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"
701 127.0.0.1 - - [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"
702 127.0.0.1 - - [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"
703 127.0.0.1 - - [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"
704 127.0.0.1 - - [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"
705 127.0.0.1 - - [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"
706 127.0.0.1 - - [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"
707 127.0.0.1 - - [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"
708 127.0.0.1 - - [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"
709 127.0.0.1 - - [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"
710 127.0.0.1 - - [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"
711 127.0.0.1 - - [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"
712 127.0.0.1 - - [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"
713 127.0.0.1 - - [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"
714 127.0.0.1 - - [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"
715 127.0.0.1 - - [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"
716 127.0.0.1 - - [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"
717 127.0.0.1 - - [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"
718 127.0.0.1 - - [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"
719 127.0.0.1 - - [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"
720 127.0.0.1 - - [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"
721 127.0.0.1 - - [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"
722 127.0.0.1 - - [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"
723 127.0.0.1 - - [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"
724 127.0.0.1 - - [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"
725 127.0.0.1 - - [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"
726 127.0.0.1 - - [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"
727 127.0.0.1 - - [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"
728 127.0.0.1 - - [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"
729 127.0.0.1 - - [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"
730 127.0.0.1 - - [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"
731 127.0.0.1 - - [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"
732 127.0.0.1 - - [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"
733 127.0.0.1 - - [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"
734 127.0.0.1 - - [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"
735 127.0.0.1 - - [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"
736 127.0.0.1 - - [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"
737 127.0.0.1 - - [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"
738 127.0.0.1 - - [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"
739 127.0.0.1 - - [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"
740 127.0.0.1 - - [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"
741 127.0.0.1 - - [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"
742 [2022-02-16 17:28:33 -0500] [2654000] [INFO] Handling signal: int
743 [2022-02-16 17:28:33 -0500] [2654005] [INFO] Worker exiting (pid: 2654005)
744 galaxy.jobs.handler ERROR 2022-02-16 17:28:34,121 [pN:main,p:2654005,tN:JobHandlerStopQueue.monitor_thread] Exception in monitor_step
745 Traceback (most recent call last):
746 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
747 self.dialect.do_execute(
748 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
749 cursor.execute(statement, parameters)
750 sqlite3.OperationalError: no such table: job
751
752 The above exception was the direct cause of the following exception:
753
754 Traceback (most recent call last):
755 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 927, in monitor
756 self.monitor_step()
757 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 958, in monitor_step
758 newly_deleted_jobs = self.sa_session.query(model.Job).enable_eagerloads(False) \
759 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2709, in all
760 return self._iter().all()
761 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
762 result = self.session.execute(
763 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
764 result = conn._execute_20(statement, params or {}, execution_options)
765 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
766 return meth(self, args_10style, kwargs_10style, execution_options)
767 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
768 return connection._execute_clauseelement(
769 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
770 ret = self._execute_context(
771 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
772 self._handle_dbapi_exception(
773 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
774 util.raise_(
775 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
776 raise exception
777 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
778 self.dialect.do_execute(
779 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
780 cursor.execute(statement, parameters)
781 sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: job
782 [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
783 FROM history_dataset_collection_association, job_to_output_dataset_collection
784 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
785 FROM history_dataset_association, job_to_output_dataset
786 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
787 FROM job
788 WHERE job.state IN (?, ?, ?) AND job.handler = ?]
789 [parameters: (<states.DELETED_NEW: 'deleted_new'>, <states.DELETING: 'deleting'>, <states.STOPPING: 'stop'>, 'main')]
790 (Background on this error at: http://sqlalche.me/e/14/e3q8)
791 galaxy.jobs.handler ERROR 2022-02-16 17:28:34,777 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] Exception in monitor_step
792 Traceback (most recent call last):
793 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
794 self.dialect.do_execute(
795 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
796 cursor.execute(statement, parameters)
797 sqlite3.OperationalError: no such table: job
798
799 The above exception was the direct cause of the following exception:
800
801 Traceback (most recent call last):
802 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 307, in __monitor
803 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 325, in __monitor_step
804 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 373, in __handle_waiting_jobs
805 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2709, in all
806 return self._iter().all()
807 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
808 result = self.session.execute(
809 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
810 result = conn._execute_20(statement, params or {}, execution_options)
811 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
812 return meth(self, args_10style, kwargs_10style, execution_options)
813 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
814 return connection._execute_clauseelement(
815 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
816 ret = self._execute_context(
817 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
818 self._handle_dbapi_exception(
819 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
820 util.raise_(
821 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
822 raise exception
823 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
824 self.dialect.do_execute(
825 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
826 cursor.execute(statement, parameters)
827 sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: job
828 [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
829 FROM history_dataset_collection_association, job_to_output_dataset_collection
830 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
831 FROM history_dataset_association, job_to_output_dataset
832 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
833 FROM job LEFT OUTER JOIN galaxy_user ON galaxy_user.id = job.user_id
834 WHERE job.state = ? AND job.handler = ? AND (job.id NOT IN (SELECT anon_3.id
835 FROM (SELECT job.id AS id
836 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
837 WHERE job.state = ? AND dataset.state IN (?, ?, ?, ?, ?)) AS anon_3)) AND (job.id NOT IN (SELECT anon_4.id
838 FROM (SELECT job.id AS id
839 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
840 WHERE job.state = ? AND dataset.state IN (?, ?, ?, ?, ?)) AS anon_4)) ORDER BY job.id]
841 [parameters: (<states.NEW: 'new'>, 'main', <states.NEW: 'new'>, 'new', 'upload', 'queued', 'running', 'setting_metadata', <states.NEW: 'new'>, 'new', 'upload', 'queued', 'running', 'setting_metadata')]
842 (Background on this error at: http://sqlalche.me/e/14/e3q8)
843 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...
844 Traceback (most recent call last):
845 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
846 self.dialect.do_execute(
847 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
848 cursor.execute(statement, parameters)
849 sqlite3.OperationalError: no such table: kombu_queue
850
851 The above exception was the direct cause of the following exception:
852
853 Traceback (most recent call last):
854 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/mixins.py", line 172, in run
855 for _ in self.consume(limit=None, **kwargs):
856 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/mixins.py", line 194, in consume
857 conn.drain_events(timeout=safety_interval)
858 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/connection.py", line 318, in drain_events
859 return self.transport.drain_events(self.connection, **kwargs)
860 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 960, in drain_events
861 get(self._deliver, timeout=timeout)
862 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/utils/scheduling.py", line 52, in get
863 return self.fun(resource, callback, **kwargs)
864 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 998, in _drain_channel
865 return channel.drain_events(callback=callback, timeout=timeout)
866 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 742, in drain_events
867 return self._poll(self.cycle, callback, timeout=timeout)
868 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 399, in _poll
869 return cycle.get(callback)
870 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/utils/scheduling.py", line 52, in get
871 return self.fun(resource, callback, **kwargs)
872 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 402, in _get_and_deliver
873 message = self._get(queue)
874 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/sqlalchemy/__init__.py", line 112, in _get
875 obj = self._get_or_create(queue)
876 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/sqlalchemy/__init__.py", line 79, in _get_or_create
877 obj = self.session.query(self.queue_cls) \
878 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first
879 return self.limit(1)._iter().first()
880 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
881 result = self.session.execute(
882 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
883 result = conn._execute_20(statement, params or {}, execution_options)
884 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
885 return meth(self, args_10style, kwargs_10style, execution_options)
886 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
887 return connection._execute_clauseelement(
888 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
889 ret = self._execute_context(
890 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
891 self._handle_dbapi_exception(
892 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
893 util.raise_(
894 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
895 raise exception
896 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
897 self.dialect.do_execute(
898 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
899 cursor.execute(statement, parameters)
900 sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: kombu_queue
901 [SQL: SELECT kombu_queue.id AS kombu_queue_id, kombu_queue.name AS kombu_queue_name
902 FROM kombu_queue
903 WHERE kombu_queue.name = ?
904 LIMIT ? OFFSET ?]
905 [parameters: ('control.main@aziz', 1, 0)]
906 (Background on this error at: http://sqlalche.me/e/14/e3q8)
907 galaxy.app ERROR 2022-02-16 17:28:34,855 [pN:main,p:2654005,tN:MainThread] Failed to shutdown database heartbeat cleanly
908 Traceback (most recent call last):
909 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
910 self.dialect.do_execute(
911 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
912 cursor.execute(statement, parameters)
913 sqlite3.OperationalError: no such table: worker_process
914
915 The above exception was the direct cause of the following exception:
916
917 Traceback (most recent call last):
918 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 92, in shutdown
919 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 397, in _shutdown_database_heartbeat
920 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 48, in shutdown
921 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 77, in worker_process
922 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first
923 return self.limit(1)._iter().first()
924 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
925 result = self.session.execute(
926 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
927 result = conn._execute_20(statement, params or {}, execution_options)
928 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
929 return meth(self, args_10style, kwargs_10style, execution_options)
930 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
931 return connection._execute_clauseelement(
932 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
933 ret = self._execute_context(
934 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
935 self._handle_dbapi_exception(
936 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
937 util.raise_(
938 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
939 raise exception
940 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
941 self.dialect.do_execute(
942 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
943 cursor.execute(statement, parameters)
944 sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: worker_process
945 [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
946 FROM worker_process
947 WHERE worker_process.server_name = ? AND worker_process.hostname = ?
948 LIMIT ? OFFSET ?]
949 [parameters: ('main', 'aziz', 1, 0)]
950 (Background on this error at: http://sqlalche.me/e/14/e3q8)
951 galaxy.jobs.handler INFO 2022-02-16 17:28:34,855 [pN:main,p:2654005,tN:MainThread] sending stop signal to worker thread
952 galaxy.jobs.handler ERROR 2022-02-16 17:28:35,130 [pN:main,p:2654005,tN:JobHandlerStopQueue.monitor_thread] Exception in monitor_step
953 Traceback (most recent call last):
954 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
955 self.dialect.do_execute(
956 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
957 cursor.execute(statement, parameters)
958 sqlite3.OperationalError: no such table: job
959
960 The above exception was the direct cause of the following exception:
961
962 Traceback (most recent call last):
963 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 927, in monitor
964 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 958, in monitor_step
965 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2709, in all
966 return self._iter().all()
967 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
968 result = self.session.execute(
969 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
970 result = conn._execute_20(statement, params or {}, execution_options)
971 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
972 return meth(self, args_10style, kwargs_10style, execution_options)
973 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
974 return connection._execute_clauseelement(
975 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
976 ret = self._execute_context(
977 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
978 self._handle_dbapi_exception(
979 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
980 util.raise_(
981 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
982 raise exception
983 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
984 self.dialect.do_execute(
985 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
986 cursor.execute(statement, parameters)
987 sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: job
988 [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
989 FROM history_dataset_collection_association, job_to_output_dataset_collection
990 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
991 FROM history_dataset_association, job_to_output_dataset
992 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
993 FROM job
994 WHERE job.state IN (?, ?, ?) AND job.handler = ?]
995 [parameters: (<states.DELETED_NEW: 'deleted_new'>, <states.DELETING: 'deleting'>, <states.STOPPING: 'stop'>, 'main')]
996 (Background on this error at: http://sqlalche.me/e/14/e3q8)
997 galaxy.jobs.handler INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] job handler queue stopped
998 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
999 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...
1000 galaxy.jobs.runners INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] All job worker threads shutdown cleanly
1001 galaxy.jobs.handler INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] sending stop signal to worker thread
1002 galaxy.jobs.handler INFO 2022-02-16 17:28:35,857 [pN:main,p:2654005,tN:MainThread] job handler stop queue stopped
1003 Error in atexit._run_exitfuncs:
1004 Traceback (most recent call last):
1005 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
1006 self.dialect.do_execute(
1007 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
1008 cursor.execute(statement, parameters)
1009 sqlite3.OperationalError: no such table: worker_process
1010
1011 The above exception was the direct cause of the following exception:
1012
1013 Traceback (most recent call last):
1014 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 92, in shutdown
1015 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 397, in _shutdown_database_heartbeat
1016 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 48, in shutdown
1017 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 77, in worker_process
1018 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first
1019 return self.limit(1)._iter().first()
1020 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
1021 result = self.session.execute(
1022 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
1023 result = conn._execute_20(statement, params or {}, execution_options)
1024 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
1025 return meth(self, args_10style, kwargs_10style, execution_options)
1026 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
1027 return connection._execute_clauseelement(
1028 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
1029 ret = self._execute_context(
1030 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
1031 self._handle_dbapi_exception(
1032 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
1033 util.raise_(
1034 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
1035 raise exception
1036 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
1037 self.dialect.do_execute(
1038 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
1039 cursor.execute(statement, parameters)
1040 sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: worker_process
1041 [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
1042 FROM worker_process
1043 WHERE worker_process.server_name = ? AND worker_process.hostname = ?
1044 LIMIT ? OFFSET ?]
1045 [parameters: ('main', 'aziz', 1, 0)]
1046 (Background on this error at: http://sqlalche.me/e/14/e3q8)
1047 sqlalchemy.pool.impl.NullPool ERROR 2022-02-16 17:28:36,070 [pN:main,p:2654005,tN:MainThread] Exception during reset or similar
1048 Traceback (most recent call last):
1049 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 682, in _finalize_fairy
1050 fairy._reset(pool)
1051 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 887, in _reset
1052 pool._dialect.do_rollback(self)
1053 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 667, in do_rollback
1054 dbapi_connection.rollback()
1055 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.
1056 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>
1057 Traceback (most recent call last):
1058 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 682, in _finalize_fairy
1059 fairy._reset(pool)
1060 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 887, in _reset
1061 pool._dialect.do_rollback(self)
1062 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 667, in do_rollback
1063 dbapi_connection.rollback()
1064 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.
1065
1066 During handling of the above exception, another exception occurred:
1067
1068 Traceback (most recent call last):
1069 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 244, in _close_connection
1070 self._dialect.do_close(connection)
1071 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 673, in do_close
1072 dbapi_connection.close()
1073 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.
1074 [2022-02-16 17:28:36 -0500] [2654000] [INFO] Shutting down: Master
1075 Traceback (most recent call last):
1076 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 665, in _config_directory
1077 yield config_directory
1078 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 540, in local_galaxy_config
1079 yield LocalGalaxyConfig(
1080 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 237, in galaxy_config
1081 yield config
1082 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 48, in _serve
1083 exit_code = run_galaxy_command(
1084 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/run.py", line 118, in run_galaxy_command
1085 exit_code = shell(command, env=env)
1086 File "/home/me/.local/lib/python3.8/site-packages/galaxy/util/commands.py", line 60, in shell
1087 return p.wait()
1088 File "/usr/lib/python3.8/subprocess.py", line 1083, in wait
1089 return self._wait(timeout=timeout)
1090 File "/usr/lib/python3.8/subprocess.py", line 1806, in _wait
1091 (pid, sts) = self._try_wait(0)
1092 File "/usr/lib/python3.8/subprocess.py", line 1764, in _try_wait
1093 (pid, sts) = os.waitpid(self.pid, wait_flags)
1094 KeyboardInterrupt
1095
1096 During handling of the above exception, another exception occurred:
1097
1098 Traceback (most recent call last):
1099 File "/home/me/.local/bin/planemo", line 8, in <module>
1100 sys.exit(planemo())
1101 File "/usr/lib/python3/dist-packages/click/core.py", line 764, in __call__
1102 return self.main(*args, **kwargs)
1103 File "/usr/lib/python3/dist-packages/click/core.py", line 717, in main
1104 rv = self.invoke(ctx)
1105 File "/usr/lib/python3/dist-packages/click/core.py", line 1137, in invoke
1106 return _process_result(sub_ctx.command.invoke(sub_ctx))
1107 File "/usr/lib/python3/dist-packages/click/core.py", line 956, in invoke
1108 return ctx.invoke(self.callback, **ctx.params)
1109 File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke
1110 return callback(*args, **kwargs)
1111 File "/usr/lib/python3/dist-packages/click/decorators.py", line 64, in new_func
1112 return ctx.invoke(f, obj, *args, **kwargs)
1113 File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke
1114 return callback(*args, **kwargs)
1115 File "/home/me/.local/lib/python3.8/site-packages/planemo/cli.py", line 98, in handle_blended_options
1116 return f(*args, **kwds)
1117 File "/home/me/.local/lib/python3.8/site-packages/planemo/commands/cmd_serve.py", line 43, in cli
1118 galaxy_serve(ctx, runnables, **kwds)
1119 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 25, in serve
1120 return _serve(ctx, runnables, **kwds)
1121 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 72, in _serve
1122 return config
1123 File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
1124 self.gen.throw(type, value, traceback)
1125 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 237, in galaxy_config
1126 yield config
1127 File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
1128 self.gen.throw(type, value, traceback)
1129 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 540, in local_galaxy_config
1130 yield LocalGalaxyConfig(
1131 File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
1132 self.gen.throw(type, value, traceback)
1133 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 669, in _config_directory
1134 shutil.rmtree(config_directory)
1135 File "/usr/lib/python3.8/shutil.py", line 722, in rmtree
1136 onerror(os.rmdir, path, sys.exc_info())
1137 File "/usr/lib/python3.8/shutil.py", line 720, in rmtree
1138 os.rmdir(path)
1139 OSError: [Errno 39] Directory not empty: '/tmp/tmp1upz926i'