Java Error "Concurrent.Executionexception" While Running Trimmomatic V0.32

Question

[arnstrm]

Hi all,

I am trying to run trimmomatic to clip and quality trim the hiseq reads. I ran this command:

java -jar trimmomatic-0.32.jar PE -threads 16  -phred33 R1.fastq R2.fastq R1.trimmed_paired.fq R1.trimmed_unpaired.fq R2.trimmed_paired.fq R2.trimmed_unpaired.fq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25

And I got this error:

TrimmomaticPE: Started with arguments: -threads 16 T2-200-1_L2_I200012.R1.clean.trimmed.fastq T2-200-1_L2_I200012.R2.clean.trimmed.fastq T2-200-1_L2_I200012.R1.clean.trimmed_paired.fq T2-200-1_L2_I200012.R1.clean.trimmed_unpaired.fq T2-200-1_L2_I200012.R2.clean.trimmed_paired.fq T2-200-1_L2_I200012.R2.clean.trimmed_unpaired.fq ILLUMINACLIP:/data004/software/GIF/GIF/packages/trimmomatic/0.32/adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Quality encoding detected as phred33
Exception processing reads: HWI-ST1106:786:H0V70ADXX:2:1101:20230:4963 1:N:0:CTTGTN and HWI-ST1106:786:H0V70ADXX:2:1101:20230:4963 2:N:0:CTTGTN
Exception processing reads: HWI-ST1106:786:H0V70ADXX:2:1101:8228:5420 1:N:0:CTTGTN and HWI-ST1106:786:H0V70ADXX:2:1101:8228:5420 2:N:0:CTTGTN
java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34
        at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:252)
        at java.util.concurrent.FutureTask.get(FutureTask.java:111)
        at org.usadellab.trimmomatic.threading.SerializerWorker.run(SerializerWorker.java:48)
        at java.lang.Thread.run(Thread.java:722)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 34
        at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer$IlluminaPrefixPair.palindromeReadsCompare(IlluminaClippingTrimmer.java:377)
        at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer$IlluminaPrefixPair.access$100(IlluminaClippingTrimmer.java:319)
        at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.processRecords(IlluminaClippingTrimmer.java:252)
        at org.usadellab.trimmomatic.threading.BlockOfWork.call(BlockOfWork.java:93)
        at org.usadellab.trimmomatic.threading.BlockOfWork.call(BlockOfWork.java:11)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
        at java.util.concurrent.FutureTask.run(FutureTask.java:166)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        ... 1 more
..
..
..
output trimmed for brevity

I tried using the older version of trimmomatic, specifying memory (-Xms100g -Xmx-128g) etc., but nothing worked. Any help will greatly be appreciated. Thanks very much!

[Pierre Lindenbaum]

the main error is a java.lang.ArrayIndexOutOfBoundsException and it is a programming exception. You should ask the author for help.

[arnstrm]

Thanks, Pierre. I will write to the author then.

[rens.holmer]

I am curious to the response you got from the author, I am running into the exact same error.

[arnstrm]

@rens.holmer, yes. This happened because I was trying to filter/trim the paired end reads that had pairs of unequal length (since these reads were already trimmed/filtered). I hope this helps!

[rens.holmer]

Most certainly, thanks!