UGENE
  1. UGENE
  2. UGENE-5533

WD: Crash in "Trim and align Sanger reads" when reference contains wrong symbols

    Details

    • Story Points:
      1
    • Epic Link:
    • Sprint:
      DEV-27-5, DEV-27-6, DEV-27-7
    • Affect Type:
      Userdefined

      Description

      Reproducible on 1.26.1 release

      1. Select "Trim and аlign Sanger reads" in Workflow Designer
      2. Set Reference =.../test/general/_common_data/alphabets/standards_rna_1000.gb where first symbols changed with illegal value ="*".
      3. Set correct reads from .../test/general/_common_data/sanger
      4. Push Run on Results page
      Crash

        Issue Links

          Activity

          Hide
          Denis Kandrov
          added a comment -

          I get a bellow error message:

          (1) No reference sequence in the file: /home/dkandrov/ugene/trunk_new/test/general/_common_data/alphabets/standard_rna_1000_copy1.gb

          I checked on commit https://github.com/ugeneunipro/ugene/commit/6a4e188b198c57b436fd08b23a07203d61046c67

          Show
          Denis Kandrov
          added a comment - I get a bellow error message: (1) No reference sequence in the file: /home/dkandrov/ugene/trunk_new/test/general/_common_data/alphabets/standard_rna_1000_copy1.gb I checked on commit https://github.com/ugeneunipro/ugene/commit/6a4e188b198c57b436fd08b23a07203d61046c67
          Hide
          Denis Kandrov
          added a comment -

          Please attach an incorrect file with reference. It maybe help to reproduce.

          Show
          Denis Kandrov
          added a comment - Please attach an incorrect file with reference. It maybe help to reproduce.
          Hide
          Yuliya Algaer
          added a comment -

          Reviewed.

          Show
          Yuliya Algaer
          added a comment - Reviewed.
          Hide
          Aleksey Tiunov
          added a comment -

          It is reproducable on the release branch. It should be fixed for the minor release.
          Check, that everything is OK for modified reference in FASTA format.
          Ensure, that error messages are meaningful in master branch.

          Show
          Aleksey Tiunov
          added a comment - It is reproducable on the release branch. It should be fixed for the minor release. Check, that everything is OK for modified reference in FASTA format. Ensure, that error messages are meaningful in master branch.
          Hide
          Dmitrii Sukhomlinov
          added a comment - - edited

          Error message is not meaningful for user

          Subtask

          Unknown macro: {Align reads with BLAST & SW task}

          is failed: Subtask

          Unknown macro: {Align one read with BLAST & SW task}

          is failed: Subtask

          Unknown macro: {Run NCBI BlastAll task}

          is failed: [blastall 2.2.26] FATAL ERROR: Database C:/Users/dsukhomlinov/AppData/Local/Temp/ugene_tmp/p9804/align_to_ref/d_0 was not found or does not exist

          Show
          Dmitrii Sukhomlinov
          added a comment - - edited Error message is not meaningful for user Subtask Unknown macro: {Align reads with BLAST & SW task} is failed: Subtask Unknown macro: {Align one read with BLAST & SW task} is failed: Subtask Unknown macro: {Run NCBI BlastAll task} is failed: [blastall 2.2.26] FATAL ERROR: Database C:/Users/dsukhomlinov/AppData/Local/Temp/ugene_tmp/p9804/align_to_ref/d_0 was not found or does not exist
          Hide
          Aleksey Tiunov
          added a comment -

          The error message fix should be done in UGENE-5620.

          Show
          Aleksey Tiunov
          added a comment - The error message fix should be done in UGENE-5620 .
          Hide
          Yuliya Algaer
          added a comment -

          Reviewed.

          Show
          Yuliya Algaer
          added a comment - Reviewed.

            People

            • Assignee:
              Aleksey Tiunov
              Reporter:
              Svetlana Samoilenko
              Assigned Tester:
              Dmitrii Sukhomlinov
            • Votes:
              0 Vote for this issue
              Watchers:
              6 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved:

                Agile