I am using trimmomatic for quality trimming of Paired reads. however, i am unable to get equal numbrer of reads in paired read files. Can anyone please help me out to resolve this issue. the command I am using is as follows:

    java -jar trimmomatic-0.36.jar -phred33 PE /path/to/dir/SRR9590_1.fastq /path/to/dir/SRR9590_2.fastq SRR9590_1P.fq SRR9590_1U.fq SRR9590_2P.fq SRR9590_2U.fq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Hello,

first let's check if there are the same number of line in both fastq files. So what's the output of `wc -l /path/to/dir/SRR9590_1.fastq` and `wc -l /path/to/dir/SRR9590_2.fastq`?

If it's the same number we can go on. In your output above you have this message:

    java.io.FileNotFoundException: /data/sata4/memona/Trimmomatic-0.36/TruSeq3-PE.fa

Check if this file realy doesn't exist. If there is a similar named file adopt your command line to this. I have found some threads where the authors guess that the error `thread "main" java.lang.RuntimeException: Sequence and quality length don't match:`  arise due to the missing adaptor file.

fin swimmer