unknown trimmer in trimmomatic software

Question

[modarzi]

Hi, I have Single End fastq file and it needs trimming. So, I use trimmomatic software for this purpose.based on trimmomatic tutorial I write below code for my .fastq file:

java -jar /home/ubuntu/CIRI_v2.0.6/Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred64 sra_data_SRR1427482.fastq SRR1427482 LEADING=20 TRAILING=20 HEADCROP=14

but after run it in my Terminal, I see bellow error;

TrimmomaticSE: Started with arguments: -phred64 sra_data_SRR1427482.fastq SRR1427482 LEADING=20 TRAILING=20 HEADCROP=14 Automatically using 1 threads

Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: LEADING=20

at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:70)
at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)
at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:303)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:85)

I run this command in my data folder. so I appreciate if any body help me. Best Regars, Mohammad

Answer 1

[Tm]

You have not passed the parameters properly, trimmomatic takes ":" sign and not "=" for assignment of value. Below is the example given in trimmomatic website.

java -jar trimmomatic-0.35.jar SE -phred33 input.fq.gz output.fq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Even you should provide extension (.fastq) to the output file "SRR1427482".

[modarzi]

@toralmanvar , Hi, You are write.Thanks for your comment.

[WouterDeCoster]

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