Question: Trimmomatic - unknown trimmer?
1
gravatar for BioBing
2.0 years ago by
BioBing100
Denmark
BioBing100 wrote:

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!!

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by BioBing100

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.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by James Ashmore2.6k
1
gravatar for BioBing
2.0 years ago by
BioBing100
Denmark
BioBing100 wrote:

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
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by BioBing100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1316 users visited in the last hour