Question: Java Error "Concurrent.Executionexception" While Running Trimmomatic V0.32
gravatar for arnstrm
7.0 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 • 6.0k views
ADD COMMENTlink written 7.0 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 7.0 years ago by Pierre Lindenbaum133k

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

ADD REPLYlink written 7.0 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 6.5 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 6.5 years ago by arnstrm1.8k

Most certainly, thanks!

ADD REPLYlink written 6.4 years ago by rens.holmer20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1621 users visited in the last hour