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  • On Trimmomatic Error. PE reads

    Hello!!

    I've got 12,438,019 Illumina paired end reads which I'm trying to preprocess in Trimommatic V 0.32 as follows:

    java -jar trimmomatic-0.32.jar PE -threads 8 -phred33 -basein /home/DMEL-2/SRR042489_H3_1.fastq -baseout /home/DMEL-2/MOSCAPP ILLUMINACLIP:TruSeq2-PE.fa:2:30:10:true SLIDINGWINDOW:6:10 HEADCROP:10 MINLEN:32

    However, I'm getting the below message.
    I've not seen this error before. Please advise.

    Thanks for your help.


    TrimmomaticPE: Started with arguments: -threads 8 -phred33 -basein /home/pcarvajal04/DMEL-2/SRR042489_H3_1.fastq -baseout /home/pcarvajal04/DMEL-2/MOSCAPP ILLUMINACLIP:./adapters/TruSeq2-PE.fa:2:30:10:true SLIDINGWINDOW:6:10 HEADCROP:10 MINLEN:32
    Using templated Input files: /home/DMEL-2/SRR042489_H3_1.fastq/home/DMEL-2/SRR042489_H3_2.fastq
    Using templated Output files: /home/DMEL-2/MOSCAPP_1P /home/DMEL-2/MOSCAPP_1U /home/DMEL-2/MOSCAPP_2P /home/DMEL-2/MOSCAPP_2U
    Exception in thread "main" java.lang.NumberFormatException: For input string: "true"
    at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
    at java.lang.Integer.parseInt(Integer.java:492)
    at java.lang.Integer.parseInt(Integer.java:527)
    at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:61)
    at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:27)
    at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:495)
    at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:35)

  • #2
    Have you used that version of the Illuminaclip command before?

    The error message looks like it's expecting a number instead of the string 'true'.

    According to the manual, the command is:
    LLUMINACLIP:<fastaWithAdaptersEtc>:<seed mismatches>:<palindrome clip threshold>:<simple clip threshold>:<minAdapterLength>:<keepBothReads>

    the default minAdapterLength is 8, so you could try rewriting the command as:

    ILLUMINACLIP:./adapters/TruSeq2-PE.fa:2:30:10:8:true

    and see if that works.

    Comment


    • #3
      Hello!!

      You're right, it worked.
      Thank you.

      In regards to the question, I think I've used it before, though it seems than I need to pay more attention to details on PE

      Thanks

      Comment

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