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mac trimmomatic problem.

Hi everyone, I'm struggling with Trimmomatic on Mac.

I'm trying do trim my FastQC file but it giving errors. Maybe my code is not correct I'm not sure. Please help me.

(base) Sehribans-MacBook-Air:~ sehriban$ Trimmomatic PE in_SRR22302419_1.fastq in_SRR22302419_2.fastq out_SRR22302419_1.fastq out_SRR22302419_2.fastq out_SRR22302419_1_2.fastq out_ SRR22302419_2_2.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:40:15
TrimmomaticPE: Started with arguments:
 in_SRR22302419_1.fastq in_SRR22302419_2.fastq out_SRR22302419_1.fastq out_SRR22302419_2.fastq out_SRR22302419_1_2.fastq out_ SRR22302419_2_2.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:40:15
Multiple cores found: Using 4 threads
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: SRR22302419_2_2.fastq
    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)
trim rna-seq
• 1,161 views • link
updated by Ram Ram • written by sehriban.buyukkilic • sehriban.buyukkilic

You can trim FASTQ files but not FASTQC files (FASTQC output is a report, not raw data).

• 0 views • link
written by Ram Ram

1 answer

It looks like you have a stray (extra) space in your file name here out_ SRR22302419_2_2.fastq (between out_ and rest). Remove that and try again.

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written by GenoMax GenoMax

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