Trimmomatic: Unknown trimmer error

0

I'm trying to trun trimmomatic on all of my fastq files at the same time, this is my command:

trimmomatic SE Samplemerge.fastq.gz Sample_trimmed.fastq.gz ILLUMINACLIP:/mnt/scratch/c1818206/fastqs/merged_files/AdaptorsIF-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15

However, I get this error message:

TrimmomaticSE: Started with arguments:
Sample10merge.fastq.gz Sample11merge.fastq.gz Sample12merge.fastq.gz Sample13merge.fastq.gz Sample1merge.fastq.gz Sample2merge.fastq.gz Sample3merge.fastq.gz Sample4merge.fastq.gz Sample5merge.fastq.gz Sample6merge.fastq.gz Sample7merge.fastq.gz Sample8merge.fastq.gz Sample9merge.fastq.gz Sample*_trimmed.fastq.gz ILLUMINACLIP:/mnt/scratch/c1818206/fastqs/merged_files/AdaptorsIF-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15
Automatically using 4 threads
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: Sample12merge.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.TrimmomaticSE.run(TrimmomaticSE.java:318)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:85)

I'm not sure what this means? If I run trimmomatic on my files individually it works, so why doesn't it work when I try to run them together? Thanks!


fastq


trimmomatic


RNA-seq

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