[UGENE-5860] Sanger mapping does not work with a gapped reference Created: 01/Nov/17  Updated: 07/Dec/17  Resolved: 03/Nov/17

Status: Closed
Project: UGENE
Component/s: Basic-MSA, Basic-Nucl
Affects Version/s: 1.28
Fix Version/s: 1.28.1

Type: Bug Priority: Blocker
Reporter: Svetlana Samoilenko Assignee: Eugenia Pushkova [X] (Inactive)
Resolution: Fixed  
Labels: request, sanger
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified

Story Points: 3
Assigned Tester: Aleksey Tiunov [X] (Inactive)
Tests Type: GUI automatic
Epic Link: Sanger2
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


 Comments   
Comment by Svetlana Samoilenko [ 02/Nov/17 ]

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:
Comment by Yuliya Algaer [ 07/Dec/17 ]

Reviewed.

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