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Trimmomatic Error (Exception in thread "main" java)

I have been struggling with trimmomatic. I am getting an error which others have also got, however, I am unable to detect the error in my code. Please suggest.

This is the code I am running:

   java -jar /home/sohini/happy_bin/Trimmomatic-0.39/trimmomatic-0.39.jar PE phred33 100-15-Mat-Orl_1_sequence.txt.gz 100-15-Mat-Orl_2_sequence.txt.gz paired_100-15-Mat-Orl_1_sequence.txt.gz unpaired_100-15-Mat-Orl_1_sequence.txt.gz paired_100-15-Mat-Orl_2_sequence.txt.gz paired_100-15-Mat-Orl_2_sequence.txt.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15

and the error I am receiving is as follows:

TrimmomaticPE: Started with arguments:
 phred33 100-15-Mat-Orl_1_sequence.txt.gz 100-15-Mat-Orl_2_sequence.txt.gz paired_100-15-Mat-Orl_1_sequence.txt.gz unpaired_100-15-Mat-Orl_1_sequence.txt.gz paired_100-15-Mat-Orl_2_sequence.txt.gz unpaired_100-15-Mat-Orl_2_sequence.txt.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:151
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: unpaired_100-15-Mat-Orl_2_sequence.txt.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)
next-gen trimmomatic
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updated by GenoMax GenoMax • written by sohinibanerjee.rs • sohinibanerjee.rs

1 answer

You need to have -phred33 and not bare word like you have in your command line.

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written by GenoMax GenoMax

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