Trimmomatic unknown trimmer
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.
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