Caused by: java.lang.ArrayIndexOutOfBoundsException: 34

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Hossein Borhan

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May 29, 2015, 11:52:46 AM5/29/15
to trinityrn...@googlegroups.com
Hi 

I started a trinity run on PE RNA seq data  

Trinity --bypass_java_version_check --trimmomatic --seqType fq --max_memory 50G --left T-LepR1-00-100-6dai-S001C92_r1\ \(paired\)\ trimmed\ \(paired\)\ un-mapped\ reads\ \[no\ read\ group\]\ \(paired\).split1.fastq  --right T-LepR1-00-100-6dai-S001C92_r1\ \(paired\)\ trimmed\ \(paired\)\ un-mapped\ reads\ \[no\ read\ group\]\ \(paired\).split2.fastq --CPU 12 --output trinity-00-100-infected-nmapped-to-darmour



and soon after the run was initiated I got this message. there has been no progress since I left the run overnight. it seems to be caused when running trimmomatic


Exception processing reads: No name and No name

java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at java.util.concurrent.FutureTask.report(FutureTask.java:122)

at java.util.concurrent.FutureTask.get(FutureTask.java:192)

at org.usadellab.trimmomatic.threading.TrimStatsWorker.run(TrimStatsWorker.java:40)

at java.lang.Thread.run(Thread.java:745)

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.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

... 1 more

java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at java.util.concurrent.FutureTask.report(FutureTask.java:122)

at java.util.concurrent.FutureTask.get(FutureTask.java:192)

at org.usadellab.trimmomatic.threading.SerializerWorker.run(SerializerWorker.java:39)

at java.lang.Thread.run(Thread.java:745)

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.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

... 1 more

java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at java.util.concurrent.FutureTask.report(FutureTask.java:122)

at java.util.concurrent.FutureTask.get(FutureTask.java:192)

at org.usadellab.trimmomatic.threading.SerializerWorker.run(SerializerWorker.java:39)

at java.lang.Thread.run(Thread.java:745)

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.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

... 1 more

java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at java.util.concurrent.FutureTask.report(FutureTask.java:122)

at java.util.concurrent.FutureTask.get(FutureTask.java:192)

at org.usadellab.trimmomatic.threading.SerializerWorker.run(SerializerWorker.java:39)

at java.lang.Thread.run(Thread.java:745)

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.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

... 1 more

java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at java.util.concurrent.FutureTask.report(FutureTask.java:122)

at java.util.concurrent.FutureTask.get(FutureTask.java:192)

at org.usadellab.trimmomatic.threading.SerializerWorker.run(SerializerWorker.java:39)

at java.lang.Thread.run(Thread.java:745)

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.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

... 1 more

Exception in thread "Thread-3" Exception in thread "Thread-5" java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at org.usadellab.trimmomatic.threading.SerializerWorker.run(SerializerWorker.java:56)

at java.lang.Thread.run(Thread.java:745)

Caused by: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at java.util.concurrent.FutureTask.report(FutureTask.java:122)

at java.util.concurrent.FutureTask.get(FutureTask.java:192)

at org.usadellab.trimmomatic.threading.SerializerWorker.run(SerializerWorker.java:39)

... 1 more

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.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

... 1 more

Exception in thread "Thread-2" java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at org.usadellab.trimmomatic.threading.SerializerWorker.run(SerializerWorker.java:56)

at java.lang.Thread.run(Thread.java:745)

Caused by: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at java.util.concurrent.FutureTask.report(FutureTask.java:122)

at java.util.concurrent.FutureTask.get(FutureTask.java:192)

at org.usadellab.trimmomatic.threading.SerializerWorker.run(SerializerWorker.java:39)

... 1 more

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.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

... 1 more

Exception in thread "Thread-6" java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at org.usadellab.trimmomatic.threading.TrimStatsWorker.run(TrimStatsWorker.java:56)

at java.lang.Thread.run(Thread.java:745)

Caused by: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at java.util.concurrent.FutureTask.report(FutureTask.java:122)

at java.util.concurrent.FutureTask.get(FutureTask.java:192)

at org.usadellab.trimmomatic.threading.TrimStatsWorker.run(TrimStatsWorker.java:40)

... 1 more

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.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

... 1 more

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at org.usadellab.trimmomatic.threading.SerializerWorker.run(SerializerWorker.java:56)

at java.lang.Thread.run(Thread.java:745)

Caused by: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at java.util.concurrent.FutureTask.report(FutureTask.java:122)

at java.util.concurrent.FutureTask.get(FutureTask.java:192)

at org.usadellab.trimmomatic.threading.SerializerWorker.run(SerializerWorker.java:39)

... 1 more

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.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

... 1 more

Exception in thread "Thread-4" java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at org.usadellab.trimmomatic.threading.SerializerWorker.run(SerializerWorker.java:56)

at java.lang.Thread.run(Thread.java:745)

Caused by: java.util.concurrent.ExecutionException: java.lang.ArrayIndexOutOfBoundsException: 34

at java.util.concurrent.FutureTask.report(FutureTask.java:122)

at java.util.concurrent.FutureTask.get(FutureTask.java:192)

at org.usadellab.trimmomatic.threading.SerializerWorker.run(SerializerWorker.java:39)

... 1 more

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.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

... 1 more

Exception processing reads: No name and No name

Exception processing reads: No name and No name

Exception processing reads: No name and No name

Exception processing reads: No name and No name

Exception processing reads: No name and No name

Exception processing reads: No name and No name

Exception processing reads: No name and No name

Exception processing reads: No name and No name

Exception processing reads: No name and No name

Exception processing reads: No name and No name

Exception processing reads: No name and No name

Exception processing reads: No name and No name

Brian Haas

unread,
Jun 1, 2015, 10:15:24 AM6/1/15
to Hossein Borhan, trinityrn...@googlegroups.com
Hi Hossein

Those fastq file paths look fairly strange.  Are you running this on a linux system?

If Trimmomatic is giving you trouble, try running it separately from Trinity, and then run Trinity using the trimmed files.  The Trimmomatic authors can provide support as needed.

best,

~brian


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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 
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