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  1. UGENE
  2. UGENE-8119

[Crash, msa] Bad_alloc copy custom format

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    Details

    • Type: Bug
    • Status: Tested
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 1.17, 1.18, 1.19, 1.20, 1.21, 1.22, 1.23, 1.24, 1.25, 1.26, 1.26.1, 1.26.2, 1.26.3, 1.27, 1.28, 1.28.1, 1.29, 1.30, 1.31, 1.31.1, 1.32, 33, 34, 35, 36, 37, 38, 39, 38.1, 40, 41, 40.1, 42, 43, 44, 45, 46, 47, 48, 49, 50
    • Fix Version/s: 51
    • Component/s: Basic-MSA
    • Tests Type:
      Manual scenario
    • Sprint:
      DEV-51-3, DEV-51-4
    • User Requests Number:
      1
    • Affect Type:
      Userdefined

      Description

      1. Reset the settings:
        1. Start UGENE.
        2. Click "Preferences" in the main menu.
          The "Application Settings" dialog appears.
        3. Check "Reset settings to default on the next run".
        4. Click "OK".
        5. Restart UGENE.
      2. Generate a 1k bases x 1m sequence alignment (~1.3 Gb of storage):
        1. "Tools"->"Random sequence generator".
          The "Generate Sequence" dialog appears.
        2. Fill the dialog:
          1. Length=1000,
          2. Number of sequences=1,000,000,
          3. Content=Base content (%),
          4. Set any correct "Output File",
          5. Format=CLUSTALW,
          6. "Add to project" must be checked.
        3. Click "Generate".
      3. The "Generate sequence task" task has started. Wait until the AE appears (~11 min).
      4. In the AE, select all sequences except one:
        1. Click "Sequence 2" to select the entire sequence.
        2. Scroll down to the last sequence (drag the thumb instead of scrolling the wheel). The application may freeze for a short time.
        3. Hold shift and click the last sequence to select almost the entire alignment.
      5. Press Ctrl+Shift+C (Shift-Command-C) (Copy (custom format)).
        The "Copy formatted alignment to the clipboard" task has started.
      6. Wait for the crash (~20 min).
        Expected:
        1. option isn't available (disabled), if the selection is too large and copying will fail,
        2. or the user receives a task error that copying is impossible (immediately or after attempting to copy),
        3. or the data is copied successfully.

      If the size of data copied to the buffer is strictly limited from above, write the limitation as a comment.

      The "Copy formatted alignment to the clipboard" task (step 4) can be invoked in several ways:

      1. shortcut (as in the scenario),
      2. right-click on the selected alignment->"Copy/Paste"->"Copy (custom format)",
      3. the corresponding main menu item "Actions">"Copy/Paste"->"Copy (custom format)",
      4. the "General" tab of the Options Panel, the "Copy (custom format)" parameter. There are several copy formats. Setting the format in the tab affects the behavior of other copy methods. Not all formats cause the crash: the FASTA format is successfully copied (~995 Mb of storage), possibly with a temporary freeze of UGENE. Other formats haven't been tested but should be analyzed as part of the task.

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              Assignee:
              biserova Evelina
              Reporter:
              biserova Evelina
              Assigned Tester:
              Svetlana Samoilenko
              Watchers:
              2 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: