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 :-)