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annotate err2.log @ 11:0f8e0dc73d1d draft default tip

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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
parents
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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11
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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2 galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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3 Cloning into '/tmp/tmp1upz926i/galaxy-dev'...
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
4 done.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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5 galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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6 warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.0.0"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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7 warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^3.4.2"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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8 warning Resolution field "ua-parser-js@0.7.30" is incompatible with requested version "ua-parser-js@0.7.22"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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9 warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.1.8"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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10 warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.0.4"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
11 warning Resolution field "chokidar@3.4.0" is incompatible with requested version "chokidar@^2.1.8"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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12 warning "@galaxyproject/bootstrap-tour > bootstrap@5.0.2" has unmet peer dependency "@popperjs/core@^2.9.2".
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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13 warning " > @handsontable/vue@2.0.0" has incorrect peer dependency "handsontable@^4.0.0".
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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14 warning " > @hirez_io/observer-spy@2.0.0" has unmet peer dependency "typescript@>=2.8.1".
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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15 warning " > linkifyjs@2.1.9" has unmet peer dependency "react@>= 0.14.0".
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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16 warning " > linkifyjs@2.1.9" has unmet peer dependency "react-dom@>= 0.14.0".
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
21 warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
23 warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
26 warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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27 warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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28 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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29 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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30 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
31 warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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34 warning Workspaces can only be enabled in private projects.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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35 warning plotly.js > color-rgba > color-space > mumath@3.3.4: Redundant dependency in your project.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
38 warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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41 warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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42 warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
43 warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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45 warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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48 warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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49 warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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50 warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
51 warning extract-text-webpack-plugin@3.0.2: Deprecated. Please use https://github.com/webpack-contrib/mini-css-extract-plugin
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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52 warning " > extract-text-webpack-plugin@3.0.2" has incorrect peer dependency "webpack@^3.1.0".
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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57 warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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60 warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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61 warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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63 warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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65 warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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67 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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68 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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69 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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73 warning hyphy-vision > extract-text-webpack-plugin@2.1.2: Deprecated. Please use https://github.com/webpack-contrib/mini-css-extract-plugin
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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76 warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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79 warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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80 warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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81 warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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82 warning "hyphy-vision > extract-text-webpack-plugin@2.1.2" has incorrect peer dependency "webpack@^2.2.0".
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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83 warning extract-text-webpack-plugin@3.0.2: Deprecated. Please use https://github.com/webpack-contrib/mini-css-extract-plugin
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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85 warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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88 warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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89 warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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90 warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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91 warning " > extract-text-webpack-plugin@3.0.2" has incorrect peer dependency "webpack@^3.1.0".
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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96 warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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99 warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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100 warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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102 warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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103 warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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105 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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106 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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107 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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118 warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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121 warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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122 warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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123 warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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126 warning parcel-bundler > htmlnano > uncss > request > har-validator@5.1.5: this library is no longer supported
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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128 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
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129 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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130 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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131 warning package.json: License should be a valid SPDX license expression
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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132 warning openseadragon@2.4.2: License should be a valid SPDX license expression
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
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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
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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
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137 warning package.json: License should be a valid SPDX license expression
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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
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139 warning bio-pv > browserify > url > querystring@0.2.0: The querystring API is considered Legacy. new code should use the URLSearchParams API instead.
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140 warning bio-pv > sniper > ecstatic@0.5.8: This package is unmaintained and deprecated. See the GH Issue 259.
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141 warning bio-pv > sniper > swig@1.4.2: This package is no longer maintained
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142 warning bio-pv > sniper > biojs-util-snippets > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
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143 warning bio-pv > sniper > biojs-util-snippets > request > har-validator@5.1.5: this library is no longer supported
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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.
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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.
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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.
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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.
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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.
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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
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150 warning parcel-bundler > htmlnano > svgo@1.3.2: This SVGO version is no longer supported. Upgrade to v2.x.x.
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151 warning parcel-bundler > htmlnano > uncss > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
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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.
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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.
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154 warning parcel-bundler > htmlnano > uncss > jsdom > request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
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155 warning parcel-bundler > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
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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
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157 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
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158 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
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159 warning parcel-bundler > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
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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.
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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
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162 warning webpack > micromatch > snapdragon > source-map-resolve@0.5.3: See https://github.com/lydell/source-map-resolve#deprecated
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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.
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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.
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165 warning webpack > micromatch > snapdragon > source-map-resolve > resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
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166 warning webpack > micromatch > snapdragon > source-map-resolve > source-map-url@0.4.1: See https://github.com/lydell/source-map-url#deprecated
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167 warning webpack > micromatch > snapdragon > source-map-resolve > urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
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168 Browserslist: caniuse-lite is outdated. Please run:
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169 npx browserslist@latest --update-db
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170 Browserslist: caniuse-lite is outdated. Please run:
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171 npx browserslist@latest --update-db
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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.
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173 duplicate attribute: :writable
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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.
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175 Browserslist: caniuse-lite is outdated. Please run next command `yarn upgrade caniuse-lite browserslist`
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176 galaxy.util.commands WARNING: Passing program arguments as a string may be a security hazard if combined with untrusted input
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177 [2022-02-16 17:19:24 -0500] [2654000] [INFO] Starting gunicorn 20.1.0
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178 [2022-02-16 17:19:24 -0500] [2654000] [INFO] Listening at: http://127.0.0.1:9090 (2654000)
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179 [2022-02-16 17:19:24 -0500] [2654000] [INFO] Using worker: sync
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180 [2022-02-16 17:19:24 -0500] [2654005] [INFO] Booting worker with pid: 2654005
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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
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182 DEBUG:galaxy.config:Configuration directory is /tmp/tmp1upz926i
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183 DEBUG:galaxy.config:Data directory is /tmp/tmp1upz926i/galaxy-dev/database
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184 DEBUG:galaxy.config:Managed config directory is /tmp/tmp1upz926i
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185 DEBUG:galaxy.containers:config file '/tmp/tmp1upz926i/containers_conf.yml' does not exist, running with default config
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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]
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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
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188 galaxy.config INFO 2022-02-16 17:19:29,872 [pN:MainProcess,p:2654005,tN:MainThread] Install database targetting Galaxy's database configuration.
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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
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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
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191 galaxy.jobs INFO 2022-02-16 17:19:29,895 [pN:main,p:2654005,tN:MainThread] Tag [_default_] handlers: main
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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.
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193 for tool_shed_repository in self.context.query(self.install_model.ToolShedRepository) \
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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
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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
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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
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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
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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
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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
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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'
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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'
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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
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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
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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
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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
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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
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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
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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
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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
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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):
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211 <Server-Side Genome List>
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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.
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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
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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
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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
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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
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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.
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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.
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228 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,996 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: aequatus
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229 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,996 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: annotate_image
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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
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231 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,997 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: chiraviz
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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...
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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
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234 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,998 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: csg
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235 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,999 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: cytoscape
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236 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,999 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: drawrna
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237 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:30,999 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: editor
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238 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,000 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: example
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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
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240 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,000 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: graphviz
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241 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,002 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster
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242 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,003 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: heatmap_default
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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
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244 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,004 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: hivtrace
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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
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246 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,004 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: hyphyvision
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247 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,006 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar
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248 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,007 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_box
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249 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,009 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram
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250 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,010 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_line
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251 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,012 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter
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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
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253 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,012 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: audio_player
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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
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255 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,013 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: video_player
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256 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,013 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: msa
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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
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258 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,013 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: mvpapp
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259 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,014 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: ngl
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260 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,015 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nora
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261 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,017 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar
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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
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263 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,020 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram
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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
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265 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,023 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal
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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
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267 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,026 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_line
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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
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269 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,029 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie
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270 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,030 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter
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271 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,032 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea
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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
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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
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274 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,039 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: openlayers
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275 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,040 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: openseadragon
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276 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,042 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: phylocanvas
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277 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,042 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: phyloviz
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278 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,043 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: pv
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279 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,044 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: scatterplot
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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...
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281 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,045 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: trackster
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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
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283 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,046 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: unipept
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284 galaxy.visualization.plugins.registry INFO 2022-02-16 17:19:31,047 [pN:main,p:2654005,tN:MainThread] VisualizationsRegistry, loaded plugin: venn
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285 galaxy.tours._impl INFO 2022-02-16 17:19:31,068 [pN:main,p:2654005,tN:MainThread] Loaded tour 'core.galaxy_ui'
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286 galaxy.tours._impl INFO 2022-02-16 17:19:31,074 [pN:main,p:2654005,tN:MainThread] Loaded tour 'core.scratchbook'
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287 galaxy.tours._impl INFO 2022-02-16 17:19:31,093 [pN:main,p:2654005,tN:MainThread] Loaded tour 'core.history'
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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
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289 galaxy.jobs.handler INFO 2022-02-16 17:19:31,120 [pN:main,p:2654005,tN:MainThread] job handler stop queue started
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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_
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291 galaxy.jobs.handler INFO 2022-02-16 17:19:31,137 [pN:main,p:2654005,tN:MainThread] job handler queue started
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292 galaxy.jobs.handler INFO 2022-02-16 17:19:31,139 [pN:main,p:2654005,tN:MainThread] job handler stop queue started
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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
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294 ~model.Job.table.c.id.in_(hda_not_ready),
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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
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296 ~model.Job.table.c.id.in_(ldda_not_ready))
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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.
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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
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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_
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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
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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.
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302 galaxy.app INFO 2022-02-16 17:19:31,373 [pN:main,p:2654005,tN:MainThread] Galaxy app startup finished (3111.728 ms)
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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.
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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
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305 ~model.Job.table.c.id.in_(hda_not_ready),
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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
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307 ~model.Job.table.c.id.in_(ldda_not_ready))
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308 galaxy.web_stack INFO 2022-02-16 17:19:33,106 [pN:main,p:2654005,tN:MainThread] Galaxy server instance 'main' is running
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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.
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310 user = self.sa_session.query(self.app.model.User).filter(self.app.model.User.table.c.email == remote_user_email).first()
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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.
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312 if config.use_remote_user and self.galaxy_session.user.deleted:
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313 127.0.0.1 - - [16/Feb/2022:17:19:33 -0400] "HEAD / HTTP/1.1" 200 - "-" "curl/7.68.0"
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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"
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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"
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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"
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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"
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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.
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319 rval = db_session.query(
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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"
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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"
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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"
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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"
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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"
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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"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
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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.
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329 'empty': lambda i, k, **c: (len(i.datasets) + len(i.dataset_collections)) <= 0,
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
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347 .where(HistoryDatasetCollectionAssociation.table.c.id.in_(subq)) \
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348 galaxy.jobs.handler INFO 2022-02-16 17:24:23,572 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (1) Job dispatched
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349 galaxy.jobs.handler INFO 2022-02-16 17:24:23,740 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (2) Job dispatched
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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']
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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']
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
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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)
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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)
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
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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)
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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384 galaxy.jobs.handler INFO 2022-02-16 17:24:36,218 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (3) Job dispatched
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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']
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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388 galaxy.jobs.handler INFO 2022-02-16 17:24:40,402 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (4) Job dispatched
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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')" ] || {
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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390 MAX_TRIES=3
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391 COUNT=0
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392 while [ $COUNT -lt $MAX_TRIES ]; do
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393 . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1
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394 if [ $? -eq 0 ];then
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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395 break
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396 else
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397 let COUNT=COUNT+1
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398 if [ $COUNT -eq $MAX_TRIES ];then
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399 echo "Failed to activate conda environment! Error was:"
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400 cat conda_activate.log
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401 exit 1
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402 fi
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403 sleep 10s
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404 fi
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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405 done
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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']
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
435 galaxy.jobs.handler INFO 2022-02-16 17:24:51,907 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (5) Job dispatched
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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')" ] || {
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
437 MAX_TRIES=3
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
438 COUNT=0
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
439 while [ $COUNT -lt $MAX_TRIES ]; do
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
440 . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
441 if [ $? -eq 0 ];then
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
442 break
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
443 else
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
444 let COUNT=COUNT+1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
445 if [ $COUNT -eq $MAX_TRIES ];then
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
446 echo "Failed to activate conda environment! Error was:"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
447 cat conda_activate.log
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
448 exit 1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
449 fi
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
450 sleep 10s
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
451 fi
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
452 done
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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']
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
478 galaxy.jobs.handler INFO 2022-02-16 17:25:02,399 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (6) Job dispatched
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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')" ] || {
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
480 MAX_TRIES=3
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
481 COUNT=0
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
482 while [ $COUNT -lt $MAX_TRIES ]; do
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
483 . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
484 if [ $? -eq 0 ];then
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
485 break
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
486 else
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
487 let COUNT=COUNT+1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
488 if [ $COUNT -eq $MAX_TRIES ];then
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
489 echo "Failed to activate conda environment! Error was:"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
490 cat conda_activate.log
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
491 exit 1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
492 fi
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
493 sleep 10s
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
494 fi
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
495 done
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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']
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
522 galaxy.jobs.handler INFO 2022-02-16 17:25:23,244 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (7) Job dispatched
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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')" ] || {
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
524 MAX_TRIES=3
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
525 COUNT=0
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
526 while [ $COUNT -lt $MAX_TRIES ]; do
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
527 . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
528 if [ $? -eq 0 ];then
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
529 break
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
530 else
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
531 let COUNT=COUNT+1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
532 if [ $COUNT -eq $MAX_TRIES ];then
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
533 echo "Failed to activate conda environment! Error was:"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
534 cat conda_activate.log
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
535 exit 1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
536 fi
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
537 sleep 10s
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
538 fi
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
539 done
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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']
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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576 galaxy.jobs.handler INFO 2022-02-16 17:25:51,414 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (8) Job dispatched
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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()
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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')" ] || {
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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579 MAX_TRIES=3
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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580 COUNT=0
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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581 while [ $COUNT -lt $MAX_TRIES ]; do
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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582 . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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583 if [ $? -eq 0 ];then
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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584 break
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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585 else
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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586 let COUNT=COUNT+1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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587 if [ $COUNT -eq $MAX_TRIES ];then
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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588 echo "Failed to activate conda environment! Error was:"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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589 cat conda_activate.log
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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590 exit 1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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591 fi
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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592 sleep 10s
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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593 fi
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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594 done
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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']
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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629 galaxy.jobs.handler INFO 2022-02-16 17:26:16,479 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] (9) Job dispatched
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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')" ] || {
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
631 MAX_TRIES=3
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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632 COUNT=0
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
633 while [ $COUNT -lt $MAX_TRIES ]; do
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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634 . '/home/me/miniconda3/bin/activate' '/home/me/miniconda3/envs/__dunovo@3.0.2' > conda_activate.log 2>&1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
635 if [ $? -eq 0 ];then
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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636 break
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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637 else
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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638 let COUNT=COUNT+1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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639 if [ $COUNT -eq $MAX_TRIES ];then
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
640 echo "Failed to activate conda environment! Error was:"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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641 cat conda_activate.log
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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642 exit 1
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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643 fi
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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644 sleep 10s
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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645 fi
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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646 done
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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']
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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664 return self.text_metrics + self.numeric_metrics
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
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"
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
742 [2022-02-16 17:28:33 -0500] [2654000] [INFO] Handling signal: int
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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743 [2022-02-16 17:28:33 -0500] [2654005] [INFO] Worker exiting (pid: 2654005)
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744 galaxy.jobs.handler ERROR 2022-02-16 17:28:34,121 [pN:main,p:2654005,tN:JobHandlerStopQueue.monitor_thread] Exception in monitor_step
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745 Traceback (most recent call last):
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746 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
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747 self.dialect.do_execute(
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748 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
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749 cursor.execute(statement, parameters)
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750 sqlite3.OperationalError: no such table: job
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751
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752 The above exception was the direct cause of the following exception:
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753
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754 Traceback (most recent call last):
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755 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 927, in monitor
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756 self.monitor_step()
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757 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 958, in monitor_step
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758 newly_deleted_jobs = self.sa_session.query(model.Job).enable_eagerloads(False) \
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759 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2709, in all
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760 return self._iter().all()
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761 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
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762 result = self.session.execute(
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763 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
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764 result = conn._execute_20(statement, params or {}, execution_options)
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765 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
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766 return meth(self, args_10style, kwargs_10style, execution_options)
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767 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
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768 return connection._execute_clauseelement(
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769 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
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770 ret = self._execute_context(
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771 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
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772 self._handle_dbapi_exception(
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773 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
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774 util.raise_(
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775 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
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776 raise exception
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777 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
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778 self.dialect.do_execute(
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779 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
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780 cursor.execute(statement, parameters)
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781 sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: job
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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
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783 FROM history_dataset_collection_association, job_to_output_dataset_collection
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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
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785 FROM history_dataset_association, job_to_output_dataset
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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
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787 FROM job
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788 WHERE job.state IN (?, ?, ?) AND job.handler = ?]
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789 [parameters: (<states.DELETED_NEW: 'deleted_new'>, <states.DELETING: 'deleting'>, <states.STOPPING: 'stop'>, 'main')]
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790 (Background on this error at: http://sqlalche.me/e/14/e3q8)
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791 galaxy.jobs.handler ERROR 2022-02-16 17:28:34,777 [pN:main,p:2654005,tN:JobHandlerQueue.monitor_thread] Exception in monitor_step
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792 Traceback (most recent call last):
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793 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
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794 self.dialect.do_execute(
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795 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
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796 cursor.execute(statement, parameters)
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797 sqlite3.OperationalError: no such table: job
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798
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799 The above exception was the direct cause of the following exception:
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800
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801 Traceback (most recent call last):
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802 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 307, in __monitor
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803 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 325, in __monitor_step
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804 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 373, in __handle_waiting_jobs
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805 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2709, in all
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806 return self._iter().all()
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807 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
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808 result = self.session.execute(
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809 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
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810 result = conn._execute_20(statement, params or {}, execution_options)
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811 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
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812 return meth(self, args_10style, kwargs_10style, execution_options)
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813 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
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814 return connection._execute_clauseelement(
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815 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
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816 ret = self._execute_context(
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817 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
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818 self._handle_dbapi_exception(
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819 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
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820 util.raise_(
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821 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
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822 raise exception
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823 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
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824 self.dialect.do_execute(
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825 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
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826 cursor.execute(statement, parameters)
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827 sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: job
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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
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829 FROM history_dataset_collection_association, job_to_output_dataset_collection
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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
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831 FROM history_dataset_association, job_to_output_dataset
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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
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833 FROM job LEFT OUTER JOIN galaxy_user ON galaxy_user.id = job.user_id
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834 WHERE job.state = ? AND job.handler = ? AND (job.id NOT IN (SELECT anon_3.id
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835 FROM (SELECT job.id AS id
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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
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837 WHERE job.state = ? AND dataset.state IN (?, ?, ?, ?, ?)) AS anon_3)) AND (job.id NOT IN (SELECT anon_4.id
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838 FROM (SELECT job.id AS id
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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
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840 WHERE job.state = ? AND dataset.state IN (?, ?, ?, ?, ?)) AS anon_4)) ORDER BY job.id]
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841 [parameters: (<states.NEW: 'new'>, 'main', <states.NEW: 'new'>, 'new', 'upload', 'queued', 'running', 'setting_metadata', <states.NEW: 'new'>, 'new', 'upload', 'queued', 'running', 'setting_metadata')]
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842 (Background on this error at: http://sqlalche.me/e/14/e3q8)
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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...
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844 Traceback (most recent call last):
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845 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
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846 self.dialect.do_execute(
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847 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
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848 cursor.execute(statement, parameters)
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849 sqlite3.OperationalError: no such table: kombu_queue
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850
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851 The above exception was the direct cause of the following exception:
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852
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853 Traceback (most recent call last):
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854 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/mixins.py", line 172, in run
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855 for _ in self.consume(limit=None, **kwargs):
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856 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/mixins.py", line 194, in consume
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857 conn.drain_events(timeout=safety_interval)
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858 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/connection.py", line 318, in drain_events
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859 return self.transport.drain_events(self.connection, **kwargs)
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860 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 960, in drain_events
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861 get(self._deliver, timeout=timeout)
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862 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/utils/scheduling.py", line 52, in get
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863 return self.fun(resource, callback, **kwargs)
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864 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 998, in _drain_channel
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865 return channel.drain_events(callback=callback, timeout=timeout)
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866 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 742, in drain_events
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867 return self._poll(self.cycle, callback, timeout=timeout)
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868 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 399, in _poll
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869 return cycle.get(callback)
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870 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/utils/scheduling.py", line 52, in get
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871 return self.fun(resource, callback, **kwargs)
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872 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/virtual/base.py", line 402, in _get_and_deliver
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873 message = self._get(queue)
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874 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/sqlalchemy/__init__.py", line 112, in _get
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875 obj = self._get_or_create(queue)
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876 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/kombu/transport/sqlalchemy/__init__.py", line 79, in _get_or_create
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877 obj = self.session.query(self.queue_cls) \
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878 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first
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879 return self.limit(1)._iter().first()
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880 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
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881 result = self.session.execute(
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882 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
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883 result = conn._execute_20(statement, params or {}, execution_options)
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884 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
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885 return meth(self, args_10style, kwargs_10style, execution_options)
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886 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
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887 return connection._execute_clauseelement(
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888 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
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889 ret = self._execute_context(
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890 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
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891 self._handle_dbapi_exception(
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892 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
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diff changeset
893 util.raise_(
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894 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
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895 raise exception
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diff changeset
896 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
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diff changeset
897 self.dialect.do_execute(
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898 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
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diff changeset
899 cursor.execute(statement, parameters)
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diff changeset
900 sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: kombu_queue
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diff changeset
901 [SQL: SELECT kombu_queue.id AS kombu_queue_id, kombu_queue.name AS kombu_queue_name
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diff changeset
902 FROM kombu_queue
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diff changeset
903 WHERE kombu_queue.name = ?
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diff changeset
904 LIMIT ? OFFSET ?]
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diff changeset
905 [parameters: ('control.main@aziz', 1, 0)]
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906 (Background on this error at: http://sqlalche.me/e/14/e3q8)
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diff changeset
907 galaxy.app ERROR 2022-02-16 17:28:34,855 [pN:main,p:2654005,tN:MainThread] Failed to shutdown database heartbeat cleanly
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908 Traceback (most recent call last):
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909 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
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diff changeset
910 self.dialect.do_execute(
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911 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
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912 cursor.execute(statement, parameters)
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diff changeset
913 sqlite3.OperationalError: no such table: worker_process
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914
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915 The above exception was the direct cause of the following exception:
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916
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917 Traceback (most recent call last):
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918 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 92, in shutdown
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919 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 397, in _shutdown_database_heartbeat
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920 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 48, in shutdown
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921 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 77, in worker_process
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922 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first
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diff changeset
923 return self.limit(1)._iter().first()
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924 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
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925 result = self.session.execute(
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926 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
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927 result = conn._execute_20(statement, params or {}, execution_options)
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diff changeset
928 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
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diff changeset
929 return meth(self, args_10style, kwargs_10style, execution_options)
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930 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
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diff changeset
931 return connection._execute_clauseelement(
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diff changeset
932 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
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933 ret = self._execute_context(
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diff changeset
934 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
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diff changeset
935 self._handle_dbapi_exception(
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diff changeset
936 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
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937 util.raise_(
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938 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
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939 raise exception
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940 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
941 self.dialect.do_execute(
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942 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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943 cursor.execute(statement, parameters)
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944 sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: worker_process
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diff changeset
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
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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946 FROM worker_process
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diff changeset
947 WHERE worker_process.server_name = ? AND worker_process.hostname = ?
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
948 LIMIT ? OFFSET ?]
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diff changeset
949 [parameters: ('main', 'aziz', 1, 0)]
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950 (Background on this error at: http://sqlalche.me/e/14/e3q8)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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diff changeset
951 galaxy.jobs.handler INFO 2022-02-16 17:28:34,855 [pN:main,p:2654005,tN:MainThread] sending stop signal to worker thread
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952 galaxy.jobs.handler ERROR 2022-02-16 17:28:35,130 [pN:main,p:2654005,tN:JobHandlerStopQueue.monitor_thread] Exception in monitor_step
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953 Traceback (most recent call last):
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954 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
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955 self.dialect.do_execute(
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956 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
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957 cursor.execute(statement, parameters)
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958 sqlite3.OperationalError: no such table: job
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959
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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960 The above exception was the direct cause of the following exception:
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961
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962 Traceback (most recent call last):
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963 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 927, in monitor
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964 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/jobs/handler.py", line 958, in monitor_step
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965 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2709, in all
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diff changeset
966 return self._iter().all()
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967 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
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968 result = self.session.execute(
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969 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
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970 result = conn._execute_20(statement, params or {}, execution_options)
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diff changeset
971 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
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972 return meth(self, args_10style, kwargs_10style, execution_options)
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973 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
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974 return connection._execute_clauseelement(
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975 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
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976 ret = self._execute_context(
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977 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
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978 self._handle_dbapi_exception(
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979 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
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980 util.raise_(
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981 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
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982 raise exception
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983 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
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984 self.dialect.do_execute(
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985 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
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986 cursor.execute(statement, parameters)
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987 sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: job
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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
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989 FROM history_dataset_collection_association, job_to_output_dataset_collection
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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
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991 FROM history_dataset_association, job_to_output_dataset
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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
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993 FROM job
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994 WHERE job.state IN (?, ?, ?) AND job.handler = ?]
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995 [parameters: (<states.DELETED_NEW: 'deleted_new'>, <states.DELETING: 'deleting'>, <states.STOPPING: 'stop'>, 'main')]
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996 (Background on this error at: http://sqlalche.me/e/14/e3q8)
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997 galaxy.jobs.handler INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] job handler queue stopped
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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
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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...
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1000 galaxy.jobs.runners INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] All job worker threads shutdown cleanly
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1001 galaxy.jobs.handler INFO 2022-02-16 17:28:35,856 [pN:main,p:2654005,tN:MainThread] sending stop signal to worker thread
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1002 galaxy.jobs.handler INFO 2022-02-16 17:28:35,857 [pN:main,p:2654005,tN:MainThread] job handler stop queue stopped
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1003 Error in atexit._run_exitfuncs:
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1004 Traceback (most recent call last):
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1005 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
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1006 self.dialect.do_execute(
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1007 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
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1008 cursor.execute(statement, parameters)
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1009 sqlite3.OperationalError: no such table: worker_process
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1010
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1011 The above exception was the direct cause of the following exception:
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1012
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1013 Traceback (most recent call last):
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1014 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 92, in shutdown
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1015 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/app.py", line 397, in _shutdown_database_heartbeat
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1016 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 48, in shutdown
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1017 File "/tmp/tmp1upz926i/galaxy-dev/lib/galaxy/model/database_heartbeat.py", line 77, in worker_process
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1018 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2760, in first
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1019 return self.limit(1)._iter().first()
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1020 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/query.py", line 2844, in _iter
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1021 result = self.session.execute(
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1022 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1689, in execute
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1023 result = conn._execute_20(statement, params or {}, execution_options)
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1024 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1582, in _execute_20
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1025 return meth(self, args_10style, kwargs_10style, execution_options)
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1026 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection
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1027 return connection._execute_clauseelement(
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1028 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1451, in _execute_clauseelement
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1029 ret = self._execute_context(
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1030 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1813, in _execute_context
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1031 self._handle_dbapi_exception(
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1032 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1994, in _handle_dbapi_exception
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1033 util.raise_(
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1034 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
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1035 raise exception
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1036 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1770, in _execute_context
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1037 self.dialect.do_execute(
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1038 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 717, in do_execute
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1039 cursor.execute(statement, parameters)
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1040 sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) no such table: worker_process
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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
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1042 FROM worker_process
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1043 WHERE worker_process.server_name = ? AND worker_process.hostname = ?
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1044 LIMIT ? OFFSET ?]
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1045 [parameters: ('main', 'aziz', 1, 0)]
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1046 (Background on this error at: http://sqlalche.me/e/14/e3q8)
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1047 sqlalchemy.pool.impl.NullPool ERROR 2022-02-16 17:28:36,070 [pN:main,p:2654005,tN:MainThread] Exception during reset or similar
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1048 Traceback (most recent call last):
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1049 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 682, in _finalize_fairy
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1050 fairy._reset(pool)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1051 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 887, in _reset
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1052 pool._dialect.do_rollback(self)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1053 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 667, in do_rollback
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1054 dbapi_connection.rollback()
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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>
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1057 Traceback (most recent call last):
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1058 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 682, in _finalize_fairy
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1059 fairy._reset(pool)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1060 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 887, in _reset
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1061 pool._dialect.do_rollback(self)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1062 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 667, in do_rollback
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1063 dbapi_connection.rollback()
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1065
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1066 During handling of the above exception, another exception occurred:
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1067
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1068 Traceback (most recent call last):
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1069 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 244, in _close_connection
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1070 self._dialect.do_close(connection)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1071 File "/home/me/.planemo/gx_venv_3/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 673, in do_close
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1072 dbapi_connection.close()
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
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.
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1074 [2022-02-16 17:28:36 -0500] [2654000] [INFO] Shutting down: Master
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1075 Traceback (most recent call last):
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1076 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 665, in _config_directory
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1077 yield config_directory
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1078 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 540, in local_galaxy_config
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1079 yield LocalGalaxyConfig(
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1080 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 237, in galaxy_config
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1081 yield config
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1082 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 48, in _serve
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1083 exit_code = run_galaxy_command(
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1084 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/run.py", line 118, in run_galaxy_command
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1085 exit_code = shell(command, env=env)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1086 File "/home/me/.local/lib/python3.8/site-packages/galaxy/util/commands.py", line 60, in shell
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1087 return p.wait()
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1088 File "/usr/lib/python3.8/subprocess.py", line 1083, in wait
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1089 return self._wait(timeout=timeout)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1090 File "/usr/lib/python3.8/subprocess.py", line 1806, in _wait
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1091 (pid, sts) = self._try_wait(0)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1092 File "/usr/lib/python3.8/subprocess.py", line 1764, in _try_wait
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1093 (pid, sts) = os.waitpid(self.pid, wait_flags)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1094 KeyboardInterrupt
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1095
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1096 During handling of the above exception, another exception occurred:
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1097
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1098 Traceback (most recent call last):
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1099 File "/home/me/.local/bin/planemo", line 8, in <module>
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1100 sys.exit(planemo())
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1101 File "/usr/lib/python3/dist-packages/click/core.py", line 764, in __call__
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1102 return self.main(*args, **kwargs)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1103 File "/usr/lib/python3/dist-packages/click/core.py", line 717, in main
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1104 rv = self.invoke(ctx)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1105 File "/usr/lib/python3/dist-packages/click/core.py", line 1137, in invoke
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1106 return _process_result(sub_ctx.command.invoke(sub_ctx))
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1107 File "/usr/lib/python3/dist-packages/click/core.py", line 956, in invoke
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1108 return ctx.invoke(self.callback, **ctx.params)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1109 File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1110 return callback(*args, **kwargs)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1111 File "/usr/lib/python3/dist-packages/click/decorators.py", line 64, in new_func
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1112 return ctx.invoke(f, obj, *args, **kwargs)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1113 File "/usr/lib/python3/dist-packages/click/core.py", line 555, in invoke
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1114 return callback(*args, **kwargs)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1115 File "/home/me/.local/lib/python3.8/site-packages/planemo/cli.py", line 98, in handle_blended_options
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1116 return f(*args, **kwds)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1117 File "/home/me/.local/lib/python3.8/site-packages/planemo/commands/cmd_serve.py", line 43, in cli
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1118 galaxy_serve(ctx, runnables, **kwds)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1119 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 25, in serve
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1120 return _serve(ctx, runnables, **kwds)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1121 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/serve.py", line 72, in _serve
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1122 return config
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1123 File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1124 self.gen.throw(type, value, traceback)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1125 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 237, in galaxy_config
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1126 yield config
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1127 File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1128 self.gen.throw(type, value, traceback)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1129 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 540, in local_galaxy_config
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1130 yield LocalGalaxyConfig(
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1131 File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1132 self.gen.throw(type, value, traceback)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
parents:
diff changeset
1133 File "/home/me/.local/lib/python3.8/site-packages/planemo/galaxy/config.py", line 669, in _config_directory
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
nick
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diff changeset
1134 shutil.rmtree(config_directory)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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1135 File "/usr/lib/python3.8/shutil.py", line 722, in rmtree
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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1136 onerror(os.rmdir, path, sys.exc_info())
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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1137 File "/usr/lib/python3.8/shutil.py", line 720, in rmtree
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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1138 os.rmdir(path)
0f8e0dc73d1d "planemo upload for repository https://github.com/galaxyproject/dunovo commit dbd33f95b486dc556c435f1b42736b818a2b9802-dirty"
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1139 OSError: [Errno 39] Directory not empty: '/tmp/tmp1upz926i'