Trimmomatic(0.33) java error [Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1]

Question

[ebogen]

Hi everyone, I am trying to use trimmomatic on a few RNAseq files but I keep getting the error below. I have tried changing the path and checked for any white spaces but I keep getting the same error.

java -jar /packages/7x/trimmomatic/0.33/trimmomatic.jar PE OBG0044-1-010_S37_L005_R1_001.fastq OBG0044-1-010_S37_L005_R2_001.fastq OBG0044-1_R1.paired.trim.fastq OBG0044-1_R1.unpaired.trim.fastq OBG0044-1_R2.paired.trim.fastq OBG0044-1_R2.unpaired.trim.fastq ILLUMINACLIP:adapter_other.fa SLIDINGWINDOW:4:30

Error

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
        at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:53)
        at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:27)
        at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:496)
        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:35)

Adapter file
>TruSeq_Universal_Adapter
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>TruSeq_Adapter_Index 1-64
GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG

[GenoMax]

Is adapter_other.fa the name of this adapter file (one that you show above)? That is what you have in your command line.

[ebogen]

yep, that is the one refed in the command line