Trimmomatic unknown trimmer

Trimmomatic unknown trimmer

1

Hi all,

I am really struggling with Trimmomatic these days and getting confused.
I’m trying to run trimmomatic:

java -jar trimmomatic-0.39.jar PE -threads 2 -phred33  ly1_1.fq ly1_2.fq  ly1_paired_1.trimmed.fq ly1_unpaired_1.trimmed.fq ly1_paired_2.trimmed.fq ly1_unpaired_2.trimmed.fq HEADCROP:9

This is my error:

        TrimmomaticPE: Started with arguments:`
-threads 2 -phred64  ly1_1.fq ly1_2.fq  ly1_paired_1.trimmed.fq ly1_unpaired_1.trimmed.fq ly1_paired_2.trimmed.fq ly1_unpaired_2.trimmed.fq HEADCROP:9
Exception in thread "main" java.io.FileNotFoundException:  ly1_1.fq (No such file or directory)`
        at java.io.FileInputStream.open0(Native Method)
        at java.io.FileInputStream.open(FileInputStream.java:195)
        at java.io.FileInputStream.<init>(FileInputStream.java:138)
        at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:135)
        at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:265)
        at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:555)
        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

Any help would be appreciated.


Trimmomatic

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