Uploaded image for project: 'UGENE'
  1. UGENE
  2. UGENE-8114

Sanger alignment fails if path to files contains semicolon (;)

    XMLWordPrintable

    Details

    • Type: Bug
    • Status: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: None
    • Labels:
      None
    • Sprint:
      DEV-51-3, DEV-51-4, DEV-51-5, DEV-51-RELEASE, DEV-52-1
    • Affect Type:
      Userdefined

      Description

      Scenario1: If the path to the reference contains a semicolon, then the alignment will start but fail with an error.

      1. Create folder with this name "Sanger;output".
      2. Put attached reference in this folder.
      3. Select Tools-> Sanger data analysis->Maps reads to reference.. menu item
      4. Add reference from "Sanger;output" folder.
      5. Add 2 attached reads
      6. Click Map button
        Process is not finished successfully.

      [ERROR][11:42] process:12824>Task

      {Workflow run from cmdline}

      finished with error: Map to Reference: 'D:/sanger' is not a file Map to Reference: File not found: 'D:/ugene/src/ugeneui/outpit/reference.gb' see 'ugene --help=align-to-reference' for details

      Scenario2: If the path to the reference does not contain a semicolon, but the reads do, then the alignment will start, but reads whose path contains a semicolon will not participate in it.

      1. Create folder with this name "Sanger;output".
      2. Copy 2 attached reads in this folder.
      3. Select Tools-> Sanger data analysis->Maps reads to reference.. menu item
      4. Add reference from attachment
      5. Add read from Sanger;output folder
      6. Click Map button
        Process is not finished successfully.

      [ERROR][12:21] process:9700>The trimming was skipped for the sequences without quality information.
      [ERROR][12:21] process:9700>The trimming was skipped for the sequences without quality information.

      [[ERROR][12:12] process:3316>Subtask

      {Compose alignment} is failed: The related chromatogram not found
      [ERROR][12:12] process:3316>Subtask {Map to reference} is failed: Subtask {Compose alignment}

      is failed: The related chromatogram not found
      [ERROR][12:12] Task

      {Map Sanger reads to reference}

      finished with error: Subtask

      {Compose alignment}

      is failed: The related chromatogram not found

      Scenario3: Sanger data analysis in Worklow Designer

      1. Put all 3 attached files in "Sanger;output" folder.
      2. Open WD
      3. Open workflow sample Trim and map Sanger reads.
      4. Select Read Sequence item and add one read from "Sanger;output" folder.
      5. Select Map to reference item and add reference from "Sanger;output" folder.
        Error dialog appears, see attachment shapshort1.png
        One more issue: no Russian translation for this dialog.

        Attachments

        1. reference.gb
          20 kB
        2. sanger_01.ab1
          283 kB
        3. sanger_02.ab1
          284 kB
        4. screenshot-1.png
          screenshot-1.png
          45 kB

          Issue Links

            Activity

              People

              Assignee:
              kir Kirill Rasputin
              Reporter:
              s.samoilenko Svetlana Samoilenko
              Watchers:
              2 Start watching this issue

                Dates

                Created:
                Updated: