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Type: Bug
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Status: Closed
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Priority: Minor
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Resolution: Won't Fix
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Affects Version/s: master
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Fix Version/s: None
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Labels:
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Affect Type:Userdefined
Scenario:
- Open ".../_common_data/cmdline/external-tool-support/trimmomatic/se_trimmomatic.uwl".
- Input ".../_common_data/cmdline/external-tool-support/small-R1.fastq" to the "Read NGS SE Reads" element.
- Set value of the "Trimming steps" parameter in "Improve Reads with Trimmomatic" to "HEADCROP:111111111".
- 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).
- relates to
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UGENE-6091 VEME 2018 issues
- Closed