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  • Trimmomatic - unknown trimmer error?

    Hi all,

    I am really struggling with Trimmomatic these days and the frustration level is rising (I have to meet a deadline). For multiple days Trimmomatic, on usegalaxy.org, has given me an error as soon as I apply the IlluminaClip:

    Fatal error: Exit code 1 () Trimmomatic did not finish successfully
    It works like a charm when applying the options for quality trimming, head-crop etc. I reported the error a few days ago, but it is still not working. In order to move along, I installed Trimmomatic on my computer (mac OS Sierra) through the homebrew/science command line application.

    When I run Trimmomatic, I continue to get an "unknown trimmer" error and cannot figure out how to fix it. Usage of command line and coding are still fairly new to me.

    I have applied following in the folder where the data is:

    Code:
     
    ENSPAC1515:01_Raw_data user$ 
    Trimmomatic PE -trimlog L001_adapter.txt  
    -basein Reference-Sample-index27_S1_L001_R1_001.fastq.gz 
    Reference-Sample-index27_S1_L001_R2_001.fastq.gz 
    -baseout L001_adapter_R1_P.fastq.gz L001_adapter_R1_U.fastq.gz
    L001_adapter_R2_P.fastq.gz L001_adapter_R2_U.fastq.gz 
    ILLUMINACLIP: TruSeq3-PE.fa:2:40:15
    And this happens:

    Code:
    TrimmomaticPE: Started with arguments:
    -trimlog L001_adapter.txt 
    -basein Reference-Sample-index27_S1_L001_R1_001.fastq.gz 
               Reference-Sample-index27_S1_L001_R2_001.fastq.gz
    -baseout L001_adapter_R1_P.fq.gz 
                  L001_adapter_R1_U.fq.gz 
                  L001_adapter_R2_P.fq.gz 
                  L001_adapter_R2_U.fq.gz 
    ILLUMINACLIP: TruSeq3-PE.fa:2:40:15
    
    Multiple cores found: Using 4 threads
    
    Using templated Input files: 
    Reference-Sample-index27_S1_L001_R1_001.fastq.gz 
    Reference-Sample-index27_S1_L001_R2_001.fastq.gz
    
    Using templated Output files: 
    L001_adapter_R1_P_1P.fq.gz L001_adapter_R1_P_1U.fq.gz
    L001_adapter_R1_P_2P.fq.gz L001_adapter_R1_P_2U.fq.gz
    
    Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: 
    Reference-Sample-index27_S1_L001_R2_001.fastq.gz
    
    at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer
    (TrimmerFactory.java:70)
    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)
    I also tried to download the Truseq3-PE.fa and use the path to it in the Illuminaclip (but I get the same error). Hopefully some of you, know how to fix this? You will save my day if you do

    Thank you!!

  • #2
    Remove '-basein' and '-baseout', and leave the rest of your command the way it is, I think it should then work. When you specify the full names of all the input and output files, you don't need to use -basein and -baseout.

    Comment


    • #3
      Hi Mastal,

      Thank you so much for responding. I tried as you suggested, but it is still not working

      Code:
      java -jar trimmomatic-0.36.jar PE –trimlog logfile L001_R1.fastq L001_R2.fastq L001_R1_P.fastq L001_R1_U.fastq L001_R2_P.fastq L001_R2_U.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:40:15
      Code:
      TrimmomaticPE: Started with arguments:
       –trimlog logfile L001_R1.fastq L001_R2.fastq L001_R1_P.fastq L001_R1_U.fastq L001_R2_P.fastq L001_R2_U.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:40:15
      Multiple cores found: Using 4 threads
      Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: L001_R2_P.fastq
      	at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:70)
      	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)
      I have no idea what is the issue. This time I tried directly with the java file.

      Comment


      • #4
        I solved it!!!

        I deleted the -trimlog part, and suddenly it worked!

        This is the code I used, in case others have similar issues:

        I solved it! By deleting -trimlog, -inbase and -outbase - as well as found a space that should not be there, it worked!

        In case others have the same issue, this is how my code looked like (this time I used the homebrew version):

        Trimmomatic PE L001_R1.fastq L001_R2.fastq out_L001_R1_P.fastq out_L001_R1_U.fastq out_L001_R2_P.fastq L001_R2_U.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:40:15

        Comment

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