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  1. UGENE
  2. UGENE-6142

Error on "HEADCROP:111111111" for Trimmomatic ILLUMINACLIP step

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    • Affect Type:
      Userdefined

      Description

      Scenario:

      1. Open ".../_common_data/cmdline/external-tool-support/trimmomatic/se_trimmomatic.uwl".
      2. Input ".../_common_data/cmdline/external-tool-support/small-R1.fastq" to the "Read NGS SE Reads" element.
      3. Set value of the "Trimming steps" parameter in "Improve Reads with Trimmomatic" to "HEADCROP:111111111".
      4. Run the workflow.
        Current state: a runtime exception occurs in Trimmomatic:
        Subtask {Trimmomatic tool} is failed: Caused by: java.lang.RuntimeException: Attempting invalid trim on HWI-ST1309F:161:C584UANXX:1:1101:5575:1993 1:N:0:GTCCTTC with length 125: Wanted -1073741698 to 125
        

      Note that the error occurs on this particular value of the HEADCROP parameter. Also, it does not make sense to input such big value as the value should be less than a sequencing read length. So, one of the way to fix the issue is to set limitation on the max value of the HEADCROP parameter (for now, it is not clear enough what should be the value).

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              Assignee:
              Unassigned
              Reporter:
              oigl Olga Golosova
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