Trimmomatic error

Question

[4117837]

Hi everyone. I'm trying to trim some read data but I'm getting an error message. This is my input:

trimmomatic PE -threads 24 -phred 33 /home/tbeckett/lustre/practice/output_data/ Filtered2S1_L3_R1.fastq.gz /home/tbeckett/lustre/practice/output_data/ Filtered2S1_L3_R2.fastq.gz /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R1_p.fastq /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R1_un.fastq /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R2_p.fastq /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R2_un.fastq ILLUMINACLIP:NexteraPE-PE.fa LEADING:20 TRAILING:20 MINLEN:60

This is the error I'm getting:

TrimmomaticPE: Started with arguments:
 -threads 24 -phred33 /home/tbeckett/lustre/practice/output_data/Filtered2S1_L3_R1.fastq.gz /home/tbeckett/lustre/practice/output_data/Filtered2S1_L3_R2.fastq.gz /home$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)

Any help understanding what is wrong is highly appreciated.

Answer 1

[Istvan Albert]

ILLUMINACLIP needs to have more fields, see the manual

• ILLUMINACLIP:<fastaWithAdaptersEtc>:<seed mismatches>:<palindrome clip threshold>:<simple clip threshold>

for example

ILLUMINACLIP:adapter.fa:2:30:5