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  1. UGENE
  2. UGENE-5860

Sanger mapping does not work with a gapped reference

    Details

    • Story Points:
      3
    • Tests Type:
      GUI automatic
    • Epic Link:
    • Sprint:
      DEV-29-1
    • Affect Type:
      Userdefined

      Description

      The issue appeared in release 1.28.

      Affected test:
      GUITest_regression_scenarios_test_5622

      Scenario:

      1. Open the "Map Sanger Reads to Reference" dialog.
      2. Set reference to "gaps _common_data/sanger/reference_gapped.gb".
      3. Add reads from the "_common_data/sanger" folder.
      4. Click the "Map" button.
        Expected state: the mapping has been finished without errors.
        Actual state: 
        Task {Map Sanger reads to reference} finished with error: Subtask {Format DB task wrapper} is failed: Subtask {Run NCBI FormatDB task} is failed: Subtask {MakeBLASTDB tool} is failed: MakeBLASTDB tool exited with code 1

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          s.samoilenko Svetlana Samoilenko added a comment - - edited

          There are many Sangers tests failed on Windows platform where reference without gaps are used.
          GUITest_common_scenarios_mca_editor_test_0010
          GUITest_common_scenarios_mca_editor_test_0011
          GUITest_common_scenarios_mca_editor_test_0012_1
          GUITest_common_scenarios_mca_editor_test_0012_2
          GUITest_common_scenarios_mca_editor_test_0013_1
          GUITest_common_scenarios_mca_editor_test_0013_2
          GUITest_common_scenarios_mca_editor_test_0013_3
          GUITest_common_scenarios_mca_editor_test_0014
          GUITest_common_scenarios_mca_editor_test_0015_1
          GUITest_common_scenarios_mca_editor_test_0015_2
          GUITest_common_scenarios_mca_editor_test_0016_2
          GUITest_common_scenarios_mca_editor_test_0017_1
          GUITest_common_scenarios_mca_editor_test_0017_2
          GUITest_common_scenarios_mca_editor_test_0018_1
          GUITest_common_scenarios_mca_editor_test_0021
          GUITest_common_scenarios_mca_editor_test_0022_1
          GUITest_common_scenarios_mca_editor_test_0022_3
          GUITest_common_scenarios_mca_editor_test_0023_2
          GUITest_common_scenarios_mca_editor_test_0023_3
          GUITest_common_scenarios_mca_editor_test_0024_1
          GUITest_common_scenarios_mca_editor_test_0024_2
          GUITest_common_scenarios_mca_editor_test_0024_3
          GUITest_common_scenarios_mca_editor_test_0025_1
          GUITest_common_scenarios_mca_editor_test_0025_2
          GUITest_common_scenarios_mca_editor_test_0025_3
          GUITest_common_scenarios_mca_editor_test_0026_1
          GUITest_common_scenarios_mca_editor_test_0026_2
          GUITest_common_scenarios_mca_editor_test_0026_3
          GUITest_common_scenarios_mca_editor_test_0027_1
          GUITest_common_scenarios_mca_editor_test_0027_2
          GUITest_common_scenarios_mca_editor_test_0027_3
          GUITest_common_scenarios_mca_editor_test_0028
          GUITest_common_scenarios_mca_editor_test_0029
          GUITest_common_scenarios_mca_editor_test_0030
          GUITest_common_scenarios_mca_editor_test_0034
          GUITest_common_scenarios_mca_editor_test_0038

          process:7500>Subtask {Align reads with BLAST & SW task} is failed: Subtask {Align one read with BLAST & SW task} is failed: Subtask {Run NCBI Blast+ task} is failed: Error: NCBI C++ Exception:
          Show
          s.samoilenko Svetlana Samoilenko added a comment - - edited There are many Sangers tests failed on Windows platform where reference without gaps are used. GUITest_common_scenarios_mca_editor_test_0010 GUITest_common_scenarios_mca_editor_test_0011 GUITest_common_scenarios_mca_editor_test_0012_1 GUITest_common_scenarios_mca_editor_test_0012_2 GUITest_common_scenarios_mca_editor_test_0013_1 GUITest_common_scenarios_mca_editor_test_0013_2 GUITest_common_scenarios_mca_editor_test_0013_3 GUITest_common_scenarios_mca_editor_test_0014 GUITest_common_scenarios_mca_editor_test_0015_1 GUITest_common_scenarios_mca_editor_test_0015_2 GUITest_common_scenarios_mca_editor_test_0016_2 GUITest_common_scenarios_mca_editor_test_0017_1 GUITest_common_scenarios_mca_editor_test_0017_2 GUITest_common_scenarios_mca_editor_test_0018_1 GUITest_common_scenarios_mca_editor_test_0021 GUITest_common_scenarios_mca_editor_test_0022_1 GUITest_common_scenarios_mca_editor_test_0022_3 GUITest_common_scenarios_mca_editor_test_0023_2 GUITest_common_scenarios_mca_editor_test_0023_3 GUITest_common_scenarios_mca_editor_test_0024_1 GUITest_common_scenarios_mca_editor_test_0024_2 GUITest_common_scenarios_mca_editor_test_0024_3 GUITest_common_scenarios_mca_editor_test_0025_1 GUITest_common_scenarios_mca_editor_test_0025_2 GUITest_common_scenarios_mca_editor_test_0025_3 GUITest_common_scenarios_mca_editor_test_0026_1 GUITest_common_scenarios_mca_editor_test_0026_2 GUITest_common_scenarios_mca_editor_test_0026_3 GUITest_common_scenarios_mca_editor_test_0027_1 GUITest_common_scenarios_mca_editor_test_0027_2 GUITest_common_scenarios_mca_editor_test_0027_3 GUITest_common_scenarios_mca_editor_test_0028 GUITest_common_scenarios_mca_editor_test_0029 GUITest_common_scenarios_mca_editor_test_0030 GUITest_common_scenarios_mca_editor_test_0034 GUITest_common_scenarios_mca_editor_test_0038 process:7500>Subtask {Align reads with BLAST & SW task} is failed: Subtask {Align one read with BLAST & SW task} is failed: Subtask {Run NCBI Blast+ task} is failed: Error: NCBI C++ Exception:
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          yalgaer Yuliya Algaer added a comment -

          Reviewed.

          Show
          yalgaer Yuliya Algaer added a comment - Reviewed.

            People

            Assignee:
            epushkova Eugenia Pushkova [X] (Inactive)
            Reporter:
            s.samoilenko Svetlana Samoilenko
            Assigned Tester:
            Aleksey Tiunov [X] (Inactive)
            Watchers:
            2 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: