Unknown trimmer, paired end, other solutions not working

Question

[Archan]

Good afternoon,

I"d like to know how to solve some software error in trimmomatic, "Unknown trimmer: SLIDINGWINDOW", i'd tried other solutions that i found in the forum.;

This is my code:

trimmomatic PE 91614_ATTCAGAA-TATAGCCT_S1_L003_R1_001.fastq.gz 91614_ATTCAGAA-TATAGCCT_S1_L003_R2_001.fastq.gz \ 91614_ATTCAGAA-TATAGCCT_S1_L003_R1_001.trim.fastq.gz 91614_ATTCAGAA-TATAGCCT_S1_L003_R1_001un.trim.fastq.gz \ 91614_ATTCAGAA-TATAGCCT_S1_L003_R2_001.trim.fastq.gz 91614_ATTCAGAA-TATAGCCT_S1_L003_R2_001un.trim.fastq.gz \ SLIDINGWINDOW:4:20 MINLEN:25

This is my error:

 TrimmomaticPE: Started with arguments:
 91614_ATTCAGAA-TATAGCCT_S1_L003_R1_001.fastq.gz 91614_ATTCAGAA-TATAGCCT_S1_L003_R2_001.fastq.gz  91614_ATTCAGAA-TATAGCCT_S1_L003_R1_001.trim.fastq.gz 91614_ATTCAGAA-TATAGCCT_S1_L003_R1_001un.trim.fastq.gz  91614_ATTCAGAA-TATAGCCT_S1_L003_R2_001.trim.fastq.gz 91614_ATTCAGAA-TATAGCCT_S1_L003_R2_001un.trim.fastq.gz  SLIDINGWINDOW:4:20 MINLEN:25
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer:  SLIDINGWINDOW
    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)

Answer 1

[GenoMax]

Your command is incomplete. You are missing the part where you specify the adapter sequence file e.g. ILLUMINACLIP:/software/bin/Trimmomatic-0.39/adapters/TruSeq3-SE.fa:2:30:10

[Archan]

Thank you so much. That seemed to do that trick.