Exception in thread "main" java.lang.RuntimeException: Unknown trimmer

Question

[mailard]

Hi!

I'm trying to run trimmomatic:

java -jar /home/usr/program/Trimmomatic-0.39/trimmomatic-0.39.jar SE file_input.fastq.gz file_output.fastq.gz LLUMINACLIP:TruSeq3-SE.fa:2:30:10

and running into the following error:

TrimmomaticSE: Started with arguments: hepg_1.fastq.gz h_1.fastq.gz LLUMINACLIP:TruSeq3-SE.fa:2:30:1
Automatically using 1 threads **Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: LLUMINACLIP** 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)

How do I fix this? Or you can explain me what does trimmer mean?

Thanks in advance!

[brunobsouzaa]

Shouldn't be ILLUMINACLIP???

[mailard]

Yes, but i solved my problem! Thank you for your answer!

[brunobsouzaa]

Sure! Plz, post your solution, it may help others who face the same issue!

[mailard]

of course! i add my solution

Answer 1

[ATpoint]

Unknown trimmer, single end, i tried other solutions but not soved.

Trimmomatic error: Unknown trimmer: unpaired.fastq.gz

unknown trimmer in trimmomatic software

Trimmomatic - unknown trimmer?

Trimmomatic Unknown Trimmer Error for Output File

trimmomatic error with unknown trimmer

[mailard]

Thank you for your answer! Its help me!

Answer 2

[mailard]

The solution to this problem: I just added the argument "-phred33". java -jar /home/katya/program/Trimmomatic-0.39/trimmomatic-0.39.jar SE -phred33 hepg_2.fastq.gz output2.fastq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10