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

Question

[Adriel Rosa]

Good afternoon,

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

that's my code:

$trimmomatic SE -threads 10 /../00-Fastq_analise/ T1R2_6H.fastq T1R2_6H_trimm ILLUMINACLIP:/software/bin/Trimmomatic-0.39/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:10:20 MINLEN:70

that's the error: TrimmomaticSE: Started with arguments:

 -threads 10 /../00-Fastq_analise/ T1R2_6H.fastq T1R2_6H_trimm ILLUMINACLIP:/software/bin/Trimmomatic-0.39/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:10:20 MINLEN:70
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: T1R2_6H_trimm
        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)

[ATpoint]

What is /../00-Fastq_analise/?

[Adriel Rosa]

the path to archive

Answer 1

[JC]

If this is your command, you have a space between directory and Fastq filename, also the directory relative path could be incorrect:

$trimmomatic SE -threads 10 /../00-Fastq_analise/ T1R2_6H.fastq T1R2_6H_trimm ILLUMINACLIP:/software/bin/Trimmomatic-0.39/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:10:20 MINLEN:70

It should be:

$trimmomatic SE -threads 10 ../00-Fastq_analise/T1R2_6H.fastq T1R2_6H_trimm ILLUMINACLIP:/software/bin/Trimmomatic-0.39/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:10:20 MINLEN:70

[Adriel Rosa]

i really love you, its work, thanks. S2