trimmomatic Errors : "Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1"

Question

[om2021]

I am running the command on cluster for trimming reads as provided below:

module load trimmomatic

trimmomatic PE -trimlog At -phred33 ../data/rnaSeq/ERR754059_1.fastq.gz ../data/rnaSeq/ERR754059_2.fastq.gz ERR754059_1.paired.fastq.gz ERR754059_1.unpaired.fastq.gz ERR754059_2.{paired,unpaired}.fastq.gz ILLUMINACLIP: /data/apps/trimmomatic/0.36/adapters/TruSeq2-PE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:30 >& At.ouput

Unfortunately , I am getting errors printed to At.ouput file:

TrimmomaticPE: Started with arguments:
 -trimlog At -phred33 ../data/rnaSeq/ERR754059_1.fastq.gz ../data/rnaSeq/ERR754059_2.fastq.gz ERR754059_1.paired.fastq.gz  ERR754059_1.unpaired.fastq.gz ERR754059_2.paired.fastq.gz ERR754059_2.unpaired.fastq.gz ILLUMINACLIP: /data/apps/trimmomatic/0.36/adapters/TruSeq2-PE.fa:2:30:10 SLIDINGWINDOW:4:15
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.TrimmomaticPE.run(TrimmomaticPE.java:536)
        at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

No, luck yet on troubleshooting. Would appreciate any help or insights..

I also tested the same command with SE option on one of the read sample ...and it didn't show errors!

Answer 1

[GenoMax]

It looks like you have a space between ILLUMINACLIP: directive and the adapter file path that follows in your command. Remove that and try again.

ILLUMINACLIP:/data/apps/trimmomatic/0.36/adapters/TruSeq2-PE.fa