mac trimmomatic problem.

Question

[sehriban.buyukkilic]

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)

[Ram]

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

Answer 1

[GenoMax]

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.