Question: unknown trimmer in trimmomatic software
0
gravatar for modarzi
2.8 years ago by
modarzi140
modarzi140 wrote:

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

rna-seq • 1.5k views
ADD COMMENTlink modified 2.8 years ago by toralmanvar900 • written 2.8 years ago by modarzi140
1
gravatar for toralmanvar
2.8 years ago by
toralmanvar900
toralmanvar900 wrote:

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".

ADD COMMENTlink written 2.8 years ago by toralmanvar900

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

ADD REPLYlink written 2.8 years ago by modarzi140

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
Upvote|Bookmark|Accept

ADD REPLYlink written 2.8 years ago by WouterDeCoster45k
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