Issue with Trimmomatic "Unknown Trimmer"

Question

[Jake]

Hi all, I am trying to use Trimmomatic with paired end Illumina transcriptomic data (151 bp reads).

I am running the code

java -jar /hpc/group/vilgalyslab/jan58/samsa2/programs/Trimmomatic-0.36/trimmomatic-0.36.jar PE –phred33 Nash_6890_210407B6/305_S1_L001_R1_001.fastq.gz Nash_6890_210407B6/305_S1_L001_R2_001.fastq.gz Trimmomatic_reads/305_S1_L001_R1_001_forward_paired.fq.gz Trimmomatic_reads/305_S1_L001_R1_001_forward_unpaired.fq.gz Trimmomatic_reads/305_S1_L001_R2_001_reverse_paired.fq.gz Trimmomatic_reads/305_S1_L001_R2_001_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36

And getting the error

TrimmomaticPE: Started with arguments: –phred33 Nash_6890_210407B6/305_S1_L001_R1_001.fastq.gz Nash_6890_210407B6/305_S1_L001_R2_001.fastq.gz Trimmomatic_reads/305_S1_L001_R1_001_forward_paired.fq.gz Trimmomatic_reads/305_S1_L001_R1_001_forward_unpaired.fq.gz Trimmomatic_reads/305_S1_L001_R2_001_reverse_paired.fq.gz Trimmomatic_reads/305_S1_L001_R2_001_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36 Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: Trimmomatic_reads/305_S1_L001_R2_001_reverse_unpaired.fq.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 know this quetion has been asked many times but I looked through a number of threads and really couldn't solve my issue. Thanks for the help!

Answer 1

[shelkmike]

Try to use "-phred33" instead of "–phred33". There is an en-dash in your command, while it should be a hyphen.

[Jake]

That seems to have fixed it! Wow what a silly mistake. Thanks a bunch!

[GenoMax]

If you are using macOS you should turn off smart quotes/hyphens in keyboard preference menu to precent this from happening.