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  1. UGENE
  2. UGENE-5878

Filter out Sanger reads that consist of gaps ('-') or unknown characters ('N') only

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    • Tests Type:
      GUI automatic
    • Epic Link:
    • Sprint:
      DEV-29-1, DEV-29-2
    • Affect Type:
      Userdefined

      Description

      When the attached "pFB7-CDK5RAP2_P1713799_043.ab1" read is mapped to the to reference, the BLAST+ step in the Sanger reads mapping task fails with the following error:

      [ERROR][15:49] Task {Map Sanger reads to reference} finished with error: 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: 
      

      The error happens when a read consists of gaps or N characters only.

      Check a read in advance before using BLAST+. If a read consists of gaps/N's, consider that it's similarity with the reference is "0". Put the read into the "Filtered by low similarity" group in the Sanger reads mapping task report.

        Attachments

        1. reference.gb
          19 kB
          Dmitrii Sukhomlinov

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              Assignee:
              atiunov Aleksey Tiunov [X] (Inactive)
              Reporter:
              dsukhomlinov Dmitrii Sukhomlinov
              Assigned Tester:
              Eugenia Pushkova [X] (Inactive)
              Watchers:
              3 Start watching this issue

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                Created:
                Updated:
                Resolved: