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:
Trimmomatic PE -trimlog L001_adapter.txt
And this happened:
TrimmomaticPE: Started with arguments:
Multiple cores found: Using 4 threads
Using templated Input files: Reference-Sample-index27_S1_L001_R1_001.fastq.gz
Using templated Output files: L001_adapter_R1_P_1P.fq.gz L001_adapter_R1_P_1U.fq.gz
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer:
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 :-)