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When I run Trimmomatic, I continue to get an "unknown trimmer" error and cannot figure out how to fix it.

I have applied following in the folder where the data is:

java -jar Trimmomatic-0.39/trimmomatic-0.39.jar PE phred33 /home/*/*R1.fastq.gz /home/*/*R2.fastq.gz *R1.trimmed.fastq.gz *R1.untrimmed.fastq.gz *R2.trimmed.fastq.gz *R2.untrimmed.fastq.gz ILLUMINACLIP:/home/Trimmomatic/adapters/TruSeq3-SE.fa:2:30:7 MINLEN:15

the output i got:

TrimmomaticPE: Started with arguments:
phred64 /home/*/*R1.fastq.gz /home/*/*R2.fastq.gz *R1.trimmed.fastq.gz *R1.untrimmed.fastq.gz *R2.trimmed.fastq.gz *R2.untrimmed.fastq.gz ILLUMINACLIP:/home/trimmomatic/adapters/TruSeq3-SE.fa:2:30:7 MINLEN:15
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: *R2.untrimmed.fastq.gz
    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
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updated by Ram Ram • written by littlemicrobiologist • littlemicrobiologist

don't use those stars and use the real files without globbing , and then update your post for a start.

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written by Pierre Lindenbaum Pierre Lindenbaum

Hi, I used real files only. here I just pasted the format that I used while trimming.

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updated by Ram Ram • written by littlemicrobiologist • littlemicrobiologist

Even if you used real file names, home/*/ seems like a suspect path. Do you have a directory called home in which ever directory you are running this from? Looks like that may need to start with a /home if you are referring to files in your home directory.

A similar issue may exist in this path trimmomatic/adapters/TruSeq3-SE.fa.

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written by GenoMax GenoMax

Assuming you have the right number of options provided this is going to be a path issue. Make sure the file with adapter sequence exists. Provide full path to /full_path_to/TruSeq3-SE.fa.

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written by GenoMax GenoMax

Can you post the commandline again here, after you have fixed/implemented all of GenoMax remarks.

Thanks

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updated by Ram Ram • written by lieven.sterck lieven.sterck

Do not delete posts that have received feedback. Interact with the people that have invested effort into helping you, and work towards providing closure to your post.

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written by Ram Ram

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