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  • Trimmomatic not working correctly

    Hello all,
    I am very new to trimmomatic and running into problems. My command line is:

    C:\Users\Munster>java -jar "c:\Program Files\Trimmomatic-0.36\trimmomatic-0.36.jar" PE -phred33 -threads 8 -trimlog 33_blood_log.txt 33_blood_67__brain_R1_001.fastq.gz 33_blood_67__brain_R2_001.fastq.gz 33_blood_TRSW_1P.fq 33_blood_TRSW_1U.fq 33_blood_TRSW_2P.fq 33_blood_TRSW_2U.fq ILLUMINACLIP:"c:\Program Files\Trimmomatic-0.36\adapters\TruSeq3-PE.fa":2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

    This is what I get when I run the command:

    TrimmomaticPE: Started with arguments:
    -phred33 -threads 8 -trimlog 33_blood_log.txt 33_blood_67__brain_R1_001.fastq.g
    z 33_blood_67__brain_R2_001.fastq.gz 33_blood_TRSW_1P.fq 33_blood_TRSW_1U.fq 33_
    blood_TRSW_2P.fq 33_blood_TRSW_2U.fq ILLUMINACLIP:c:\Program Files\Trimmomatic-0
    .36\adapters\TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLE
    N:36
    Exception in thread "main" java.lang.NumberFormatException: For input string: "\
    Program Files\Trimmomatic-0.36\adapters\TruSeq3-PE.fa"
    at java.lang.NumberFormatException.forInputString(NumberFormatException.
    java:65)
    at java.lang.Integer.parseInt(Integer.java:580)
    at java.lang.Integer.parseInt(Integer.java:615)
    at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaCl
    ippingTrimmer(IlluminaClippingTrimmer.java:54)
    at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFact
    ory.java:32)
    at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java
    :59)
    at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:536)
    at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)


    What do these errors mean? Any suggestions for how to get this to work correctly? I am working on a PC and using the command window to run commands. THANKS!!!

  • #2
    Hello munsters,

    I guess the problem is the path to the adapter file, as it contains "c:" and trimmomatic understand the ":" as a delimiter.

    Try using a path without the device name.

    fin swimmer

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