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  1. UGENE
  2. UGENE-4304

Tools for multiple sequence alignment may hang a system

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    • Affect Type:
      Userdefined

      Description

      See a scenario from UGENE-4067:

      1. Provide a valid path to MAFFT.
      2. Open COI.aln.
      3. Do not select anything in the Project View.
      4. Select more than one file in the opened dialog, e.g. "murine.gb" and "sars.gb" and approve the dialog.
        Expected result: both sequences are aligned to the original alignment.
        Current result: UGENE hangs and hangs the operating system (only Ctrl+Alt+Del and termination of ugeneui process helps).

      The error occured because MAFFT uses too much memory.

      Adding of the option "memsave" may improve the program behavior, but there are still may be problems on big enough data.

      The same problem occurs when aligning COI.aln with the added sequences "murine", "sars" inside the Alignment Editor.

      Also, the problem was detected not only when MAFFT is used, but when other multiple sequence aligners are used: KAlign, MUSCLE, etc.

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              Assignee:
              Unassigned
              Reporter:
              oigl Olga Golosova
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                Updated:
                Resolved: