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  1. UGENE
  2. UGENE-4812

SnpEff for x86: Java heap space out of memory

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 1.20
    • Component/s: None
    • Story Points:
      2
    • Tests Type:
      GUI automatic
    • Sprint:
      DEV-10/11/2015
    • Affect Type:
      Userdefined

      Description

      Run the test GUITest_regression_scenarios_test_3938 using x86 JRE. The workflow will fail with the error "SnpEff exited with code -1" and there will be a error about Java heap space out of memory in log.

      If you run that SnpEff command with command line and add the parameter -Xmx1024M (it means to use 1 Gb of RAM for the Java heap) then SnpEff finishes successfully.

      I think that the simplest solution is to pass this parameter to the SnpEff command. The value of this parameter must be the amount of RAM from the UGENE settings.

      In addition, parse the SnpEff error log and report the correct error to users when there is the OutOfMemory exception (task finish status, dashboard error, log error), e.g.:

      There is not enough memory to complete SnpEff execution.

      Unmute the test GUITest_regression_scenarios_test_3938 after fixing the problem.

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            People

            Assignee:
            kir Kirill Rasputin
            Reporter:
            ggrekhov German Grekhov
            Assigned Tester:
            Vladimir Malinovskiy
            Watchers:
            3 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: