I have very similar error as many of you encountered before when trimming using Trimmomatic v 0.38. I am following the examples from the book "Bioinformatics A Practical Handbook of Next Generation Sequencing ad its applications" - Chapter 6 Denovo Assembly of a Genome

1. First i need to trim the two fastq files s_6_1.fastq.gz and s_6_2.fastq.gz

I am running the following command in the folder where the 2 input fastq files and Illumina adapter files are.

java -jar /home/ivan/Desktop/BioTools/Trimmomatic/Trimmomatic-0.38/trimmomatic-0.38.jar PE s_6_1.fastq.gz s_6_2.fastq.gz s_6_1_paired.fastq.gz s_6_1_unpaired.fastq.gz s_6_2_paired.fastq.gz s_6_2_ unpaired.fastq.gz ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:30 MINLEN:30

TrimmomaticPE: Started with arguments:
 s_6_1.fastq.gz s_6_2.fastq.gz s_6_1_paired.fastq.gz s_6_1_unpaired.fastq.gz s_6_2_paired.fastq.gz s_6_2_ unpaired.fastq.gz ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:30 MINLEN:30

Multiple cores found: Using 4 threads

Exception in thread "main" java.lang.RuntimeException: **Unknown trimmer:** unpaired.fastq.gz
    at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:73)
    at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)
    at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:552)
    at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

Not sure what is wrong here as in previous chapter when running same command (with different input files) and same Illumina adapter files, programme runs with no errors.

Apreciate any inputs or suggestions