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  1. UGENE
  2. UGENE-734

Crash adding sequence to alignment

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: 1.10
    • Fix Version/s: 1.10.1
    • Component/s: None
    • Labels:
      None
    • Environment:

      Ubuntu 11.10

      Description

      If I add a sequence from a file, there's no problem, but if I add the same sequence from current project, it crashes.

      Exception with code 11 - Segmentation fault

      Operation system: Linux

      UGENE version: 1.10.0

      ActiveWindow: test_alignment test_alignment

      Log:
      [10:40:34.382] [Input/Output] DbiPool: decreasing reference count. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, ref-count: 0
      [10:40:34.382] [Input/Output] SQLite: shutting down: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.382] [Input/Output] DBIPool: resource is released. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb
      [10:40:34.382] [Core Services] Allocated tmp dbi: /tmp/ugene_tmp/p8084/session_1.ugenedb
      [10:40:34.382] [Input/Output] DbiPool: Opening DBI. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, factory: SQLiteDbi
      [10:40:34.383] [Input/Output] SQLite: initialized: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.383] [Input/Output] DbiPool: decreasing reference count. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, ref-count: 0
      [10:40:34.383] [Input/Output] SQLite: shutting down: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.383] [Input/Output] DBIPool: resource is released. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb
      [10:40:34.383] [Input/Output] DbiPool: Opening DBI. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, factory: SQLiteDbi
      [10:40:34.384] [Input/Output] SQLite: initialized: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.384] [Input/Output] DbiPool: decreasing reference count. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, ref-count: 0
      [10:40:34.384] [Input/Output] SQLite: shutting down: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.384] [Input/Output] DBIPool: resource is released. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb
      [10:40:34.384] [Tasks] releasing resource: 'Threads':1, state: 0/1000
      [10:40:34.384] [Tasks] promoting task

      {Read document: 'test.TXT'}

      to 'Finished'
      [10:40:34.385] [Core Services] resource 'Project Document::/home/agu/Desktop/test.TXT' is released by 'Load 'test.TXT''
      [10:40:34.385] [Tasks] promoting task

      {Load 'test.TXT'}

      to 'Finished'
      [10:40:34.389] [Tasks] promoting task

      {Open view} to 'Prepared'
      [10:40:34.389] [Tasks] promoting task {Open new 'Sequence view'} to 'Prepared'
      [10:40:34.389] [Tasks] promoting task {Open view}

      to 'Running'
      [10:40:34.389] [Tasks] promoting task

      {Open new 'Sequence view'} to 'Running'
      [10:40:34.391] [Input/Output] DbiPool: Opening DBI. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, factory: SQLiteDbi
      [10:40:34.392] [Input/Output] SQLite: initialized: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.393] [Input/Output] DbiPool: decreasing reference count. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, ref-count: 0
      [10:40:34.393] [Input/Output] SQLite: shutting down: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.393] [Input/Output] DBIPool: resource is released. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb
      [10:40:34.398] [Input/Output] DbiPool: Opening DBI. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, factory: SQLiteDbi
      [10:40:34.399] [Input/Output] SQLite: initialized: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.399] [Input/Output] DbiPool: decreasing reference count. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, ref-count: 0
      [10:40:34.399] [Input/Output] SQLite: shutting down: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.399] [Input/Output] DBIPool: resource is released. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb
      [10:40:34.417] [Input/Output] DbiPool: Opening DBI. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, factory: SQLiteDbi
      [10:40:34.417] [Input/Output] SQLite: initialized: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.417] [Input/Output] DbiPool: decreasing reference count. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, ref-count: 0
      [10:40:34.417] [Input/Output] SQLite: shutting down: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.417] [Input/Output] DBIPool: resource is released. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb
      [10:40:34.457] [Tasks] promoting task {Open new 'Sequence view'}

      to 'Finished'
      [10:40:34.457] [Tasks] promoting task

      {Open view}

      to 'Finished'
      [10:40:34.457] [Tasks] promoting task

      {Load document: 'test.TXT'}

      to 'Finished'
      [10:40:34.457] [Tasks] promoting task

      {Opening view for document: test.TXT}

      to 'Finished'
      [10:40:34.556] [Input/Output] DbiPool: Opening DBI. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, factory: SQLiteDbi
      [10:40:34.558] [Input/Output] SQLite: initialized: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.558] [Input/Output] DbiPool: decreasing reference count. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, ref-count: 0
      [10:40:34.559] [Input/Output] SQLite: shutting down: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.559] [Input/Output] DBIPool: resource is released. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb
      [10:40:34.560] [Input/Output] DbiPool: Opening DBI. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, factory: SQLiteDbi
      [10:40:34.561] [Input/Output] SQLite: initialized: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.561] [Input/Output] DbiPool: decreasing reference count. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, ref-count: 0
      [10:40:34.562] [Input/Output] SQLite: shutting down: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.562] [Input/Output] DBIPool: resource is released. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb
      [10:40:34.562] [Input/Output] DbiPool: Opening DBI. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, factory: SQLiteDbi
      [10:40:34.564] [Input/Output] SQLite: initialized: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.564] [Input/Output] DbiPool: decreasing reference count. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, ref-count: 0
      [10:40:34.564] [Input/Output] SQLite: shutting down: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:34.564] [Input/Output] DBIPool: resource is released. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb
      [10:40:34.706] [Tasks] promoting task

      {Loading documents}

      to 'Finished'
      [10:40:34.706] [Tasks] Unregistering task: Loading documents
      [10:40:34.706] [Tasks] Deleting task: Adding document to project: /home/agu/Desktop/test.TXT
      [10:40:34.706] [Tasks] Deleting task: Read document: 'test.TXT'
      [10:40:34.706] [Tasks] Deleting task: Load 'test.TXT'
      [10:40:34.706] [Tasks] Deleting task: Open new 'Sequence view'
      [10:40:34.706] [Tasks] Deleting task: Open view
      [10:40:34.706] [Tasks] Deleting task: Load document: 'test.TXT'
      [10:40:34.706] [Tasks] Deleting task: Opening view for document: test.TXT
      [10:40:34.706] [Tasks] Deleting task: Loading documents
      [10:40:43.383] [Input/Output] DbiPool: Opening DBI. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, factory: SQLiteDbi
      [10:40:43.385] [Input/Output] SQLite: initialized: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:43.385] [Input/Output] DbiPool: decreasing reference count. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb, ref-count: 0
      [10:40:43.385] [Input/Output] SQLite: shutting down: /tmp/ugene_tmp/p8084/session_1.ugenedb

      [10:40:43.385] [Input/Output] DBIPool: resource is released. Url: /tmp/ugene_tmp/p8084/session_1.ugenedb

      Task tree:
      None
      Stack trace:

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            Assignee:
            kir Kirill Rasputin
            Reporter:
            agu Agustín Ure
            Watchers:
            1 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: