trimmomatic error

I have paired 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: There is some error, how can I solve this problem?

 java -jar /mnt/d/trimomatic/Trimmomatic-0.39/Trimmomatic-0.39.jar PE -basein /mnt/d/raw/2023nudi/01.RawData/Nudivirus/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1_1.fq /mnt/d/raw/2023nudi/01.RawData/Nudivirus/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1_2.fq /mnt/d/raw/2023nudi/01.RawData/Nudivirus/output_forward_paired.fastq /mnt/d/raw/2023nudi/01.RawData/Nudivirus/output_forward_unpaired.fastq /mnt/d/raw/2023nudi/01.RawData/Nudivirus/output_reverse_paired.fastq /mnt/d/raw/2023nudi/01.RawData/Nudivirus/output_reverse_unpaired.fastq SLIDINGWINDOW:4:15

This is the error message:

Using templated Input files: /mnt/d/raw/2023nudi/01.RawData/Nudivirus/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1_1.fq /mnt/d/raw/2023nudi/01.RawData/Nudivirus/Nudivirus_DKDN230027457-1A_HJHVHDSX7_L1_2.fq
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: /mnt/d/raw/2023nudi/01.RawData/Nudivirus/output_reverse_unpaired.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)

trimmomatic whole-genome-sequencing linux

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updated 3.0 years ago by Ram

• written 3.0 years ago by jiyoung •

Since you are using -basein only provide the first read file. Second read file name is automatically inferred. If you want to provide both names then remove -basein option.

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written 3.0 years ago by GenoMax

0 answers

No answers yet.

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