trimmomatic unknown trimmer

Question

[Xiaoyun]

Hi all:

I'm trying to trim some read data but i'm getting an error message. This is my input

java -jar /home/yun/Downloads/Trimmomatic-0.39/trimmomatic-0.39.jar PE -threads 2 -phred33 ly1_1.fq ly1_2.fq \ly1_paired_1.trim.fq.gz ly1_unpaired_1.trim.fq.gz ly1_paired_2.trim.fq.gz ly1_unpaired_2.trim.fq,gz \ HEADCROP:9

This is my error:

    TrimmomaticPE: Started with arguments:
 -threads 2 -phred33 ly1_1.fq ly1_2.fq ly1_paired_1.trim.fq.gz ly1_unpaired_1.trim.fq.gz ly1_paired_2.trim.fq.gz ly1_unpaired_2.trim.fq,gz  HEADCROP:9
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer:  HEADCROP
    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)

Any help would be appreciated.

[GenoMax]

ly1_unpaired_2.trim.fq,gz

You have a comma in the last file name. Remove that and try again.

[Xiaoyun]

It didn't work.

java -jar /home/yun/Downloads/Trimmomatic-0.39/trimmomatic-0.39.jar PE -threads 2 -phred33 ly1_1.fq ly1_2.fq \ ly1_paired_1.trimmed.fq.gz ly1_unpaired_1.trimmed.fq.gz ly1_paired_2.trimmed.fq.gz ly1_unpaired_2.trimmed.fq.gz \ HEADCROP:9 

    TrimmomaticPE: Started with arguments:
 -threads 2 -phred33 ly1_1.fq ly1_2.fq  ly1_paired_1.trimmed.fq.gz ly1_unpaired_1.trimmed.fq.gz ly1_paired_2.trimmed.fq.gz ly1_unpaired_2.trimmed.fq.gz  HEADCROP:9
Exception in thread "main" java.lang.RuntimeException: Unknown trimmer:  HEADCROP
    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)

[GenoMax]

Can you try (use your own file names in correct spots)

java -jar /home/yun/Downloads/Trimmomatic-0.39/trimmomatic-0.39.jar PE file1.fq file2.fq -baseout basename_you_want HEADCROP:9

[Xiaoyun]

Thanks a lot! I think I have done it well.

java -jar /home/yun/Downloads/Trimmomatic-0.39/trimmomatic-0.39.jar PE ly1_1.fq ly1_2.fq -baseout sampleFiltered.fq.gz HEADCROP:9

I think maybe there is something wrong in output file name.

[GenoMax]

I think maybe there is something wrong in output file name.

You need to provide a basename which in this case should be just sampleFiltered.