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usadellab / Trimmomatic

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Not executable - Reg. #64

Open bioramg opened 6 months ago

bioramg commented 6 months ago

Hello Sir, I'm trying to trim my genome sequence, but I'm encountering an error. I've installed Trimmomatic both individually and through Anaconda, but I still can't execute it. Can you please suggest where the issue might be?

Thank you. java -jar /home/bin/Trimmomatic-0.39/trimmomatic-0.39.jar PE /home/2024/EFA_1.fastq.gz /home/2024/EFA_2.fastq.gz /home/2024/forward_trim.fastq.gz /home/2024/forward_unpaired.fastq.gz /home/2024/reverse_trim.fastq.gz /home/2024/reverse_unpaired.fastq.gz -threads 40 /home/bin/Trimmomatic-0.39/adapters/ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36

TrimmomaticPE: Started with arguments: /home/2024/EFA_1.fastq.gz /home/2024/EFA_2.fastq.gz /home/2024/forward_trim.fastq.gz /home/2024/forward_unpaired.fastq.gz /home/2024/reverse_trim.fastq.gz /home/2024/reverse_unpaired.fastq.gz -threads 40 /home/bin/Trimmomatic-0.39/adapters/ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36 Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: /home/bin/Trimmomatic-0.39/adapters/ILLUMINACLIP 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)