Question: Exception in thread "main" java.lang.RuntimeException: Unknown trimmer
0
gravatar for mailard
3 months ago by
mailard 0
mailard 0 wrote:

Hi!

I'm trying to run trimmomatic:

java -jar /home/usr/program/Trimmomatic-0.39/trimmomatic-0.39.jar SE file_input.fastq.gz file_output.fastq.gz LLUMINACLIP:TruSeq3-SE.fa:2:30:10

and running into the following error:

TrimmomaticSE: Started with arguments: hepg_1.fastq.gz h_1.fastq.gz LLUMINACLIP:TruSeq3-SE.fa:2:30:1
Automatically using 1 threads **Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: LLUMINACLIP** 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)

How do I fix this? Or you can explain me what does trimmer mean?

Thanks in advance!

trimmomatic • 258 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by mailard 0
2

Shouldn't be ILLUMINACLIP???

ADD REPLYlink written 3 months ago by brunobsouzaa490

Yes, but i solved my problem! Thank you for your answer!

ADD REPLYlink written 3 months ago by mailard 0

Sure! Plz, post your solution, it may help others who face the same issue!

ADD REPLYlink written 3 months ago by brunobsouzaa490

of course! i add my solution

ADD REPLYlink written 3 months ago by mailard 0
0
0
gravatar for mailard
3 months ago by
mailard 0
mailard 0 wrote:

The solution to this problem: I just added the argument "-phred33". java -jar /home/katya/program/Trimmomatic-0.39/trimmomatic-0.39.jar SE -phred33 hepg_2.fastq.gz output2.fastq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10

ADD COMMENTlink modified 3 months ago • written 3 months ago by mailard 0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2753 users visited in the last hour
_