Trimmomatic - unknown trimmer?
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Entering edit mode
4.1 years ago
BioBing ▴ 130

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\$
-basein Reference-Sample-index27_S1_L001_R1_001.fastq.gz
Reference-Sample-index27_S1_L001_R2_001.fastq.gz
ILLUMINACLIP: TruSeq3-PE.fa:2:40:15


And this happened:

    TrimmomaticPE: Started with arguments:
-basein Reference-Sample-index27_S1_L001_R1_001.fastq.gz
Reference-Sample-index27_S1_L001_R2_001.fastq.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

Exception in thread "main" java.lang.RuntimeException: Unknown trimmer:
Reference-Sample-index27_S1_L001_R2_001.fastq.gz



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!!

RNA-Seq software error sequence next-gen • 6.4k views
0
Entering edit mode

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.

2
Entering edit mode
4.1 years ago
BioBing ▴ 130

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