I am trying to use Trimmomatic-0.39 to perform trimming on miRNA generated using the Truseq small rna library prep kit. I've downloaded the trimmomatic package in the same folder as the FASTQ's. I've also downloaded the adapter sequence file TruSeq3-SE.fa and placed under the same folder as the package and FASTQ's. The following is my command. I've tried adding the whole path of the folder too but the error doesn't seem to change. I've made sure there are no extra spaces.
java -jar Trimmomatic-0.39/trimmomatic-0.39.jar SE -phred33 LCxxxxxx_RawData.fq.gz LCxxxxxx_trimmed.fq.gz ILLUMINACLIP:TruSeq3-SE.fa LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Automatically using 4 threads Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1 at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:54) at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32) at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59) at org.usadellab.trimmomatic.TrimmomaticSE.run(TrimmomaticSE.java:318) at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:85)