I tried to run Trimmomatic 0.39 but ran into
Error: Invalid or corrupt jarfile /storage/home/user/tools/Trimmomatic-0.39/. I went into the Trimmomatic directory and noticed that the decompressed binary
.jar was not created at all. Java is updated to the latest version.
I configured my PATH for this tool
export PATH=/storage/home/user/tools/Trimmomatic-0.39/adapters:$PATH and run trimmomatic but still failed....
The command I used to run trimmomatic is this
java -jar /storage/home/user/tools/Trimmomatic-0.39/ SE -phred33 S23_R1_001_.fastq.gz S23_R1_001_OP.fastq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
also tried this way
java -jar /storage/home/user/tools/Trimmomatic-0.39/adapters SE -phred33 3159_S23_R1_001_.fastq.gz 3159_S23_R1_001_.fastq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 after setting PATH to the adapters directory, still was not working...
Not sure where I did it wrong and why .jar was not there when I downloaded it or if missed something on my end. Note, the file is single-end read.
Any advice is appreciated.