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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.

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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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                Updated:
                Resolved: