Trimmomatic - unknown trimmer?

Question

[BioBing]

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:

 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.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

And this happened:

    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!!

[James Ashmore]

Perhaps remove the space between "ILLUMINACLIP:" and "TruSeq3-PE.fa". Also try manually specifying the input and output fastq files, rather than relying on the basename matching feature.

Answer 1

[BioBing]

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:

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