Question: Java Error "Concurrent.Executionexception" While Running Trimmomatic V0.32
gravatar for arnstrm
6.6 years ago by
Ames, IA
arnstrm1.8k wrote:

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
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$Sync.innerGet(
        at java.util.concurrent.FutureTask.get(
Caused by: java.lang.ArrayIndexOutOfBoundsException: 34
        at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer$IlluminaPrefixPair.palindromeReadsCompare(
        at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer$IlluminaPrefixPair.access$100(
        at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.processRecords(
        at java.util.concurrent.FutureTask$Sync.innerRun(
        at java.util.concurrent.ThreadPoolExecutor.runWorker(
        at java.util.concurrent.ThreadPoolExecutor$
        ... 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!

java qualitycontrol • 5.8k views
ADD COMMENTlink written 6.6 years ago by arnstrm1.8k

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

ADD REPLYlink written 6.6 years ago by Pierre Lindenbaum129k

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

ADD REPLYlink written 6.6 years ago by arnstrm1.8k

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

ADD REPLYlink written 6.0 years ago by rens.holmer20

@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!


ADD REPLYlink written 6.0 years ago by arnstrm1.8k

Most certainly, thanks!

ADD REPLYlink written 5.9 years ago by rens.holmer20
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