Hello,
I am having an issue with a java error when trying to use BBDuk to remove low entropy sequences from a fastq file. The libraries were made using ribozero so there are a number of polyT sequences I would like to remove.
I have previously used BBDuk on the same library to remove PhiX an adapter sequences with no problem.
The file has ~135 million 100bp SE reads.
I am running on a node with 24 cores and 128 GiB RAM running CentOS Linux release 7.3.1611 and java version "1.7.0_131".
I get this error with or without the -Xmx flag.
Any suggestions as to what might be the issue?
Thank you.
I am having an issue with a java error when trying to use BBDuk to remove low entropy sequences from a fastq file. The libraries were made using ribozero so there are a number of polyT sequences I would like to remove.
I have previously used BBDuk on the same library to remove PhiX an adapter sequences with no problem.
The file has ~135 million 100bp SE reads.
I am running on a node with 24 cores and 128 GiB RAM running CentOS Linux release 7.3.1611 and java version "1.7.0_131".
I get this error with or without the -Xmx flag.
Code:
$ bbduk.sh in=seq.fq out=seq_0-1-entrop-filtered.fq outm=low_complexity-0-1.fq entropy=0.1 java -Djava.library.path=/apps/chpc/bio/bbmap/jni/ -ea -Xmx24052m -Xms24052m -cp /apps/chpc/bio/bbmap/current/ jgi.BBDukF in=fish-coral_1_filtered_clean.fq out=fish-coral_1_filtered_clean_0-1-entrop-filtered.fq outm=low_complexity-0-1.fq entropy=0.1 Executing jgi.BBDukF [in=seq.fq, out=seq_0-1-entrop-filtered.fq, outm=low_complexity-0-1.fq, entropy=0.1] Version 37.90 [in=seq.fq, out=seq_0-1-entrop-filtered.fq, outm=low_complexity-0-1.fq, entropy=0.1] Initial: Memory: max=24170m, free=23665m, used=505m Input is being processed as unpaired Started output streams: 0.051 seconds. Exception in thread "Thread-6" java.lang.ArrayIndexOutOfBoundsException: 39 at structures.EntropyTracker.averageEntropy(EntropyTracker.java:302) at structures.EntropyTracker.passes(EntropyTracker.java:348) at jgi.BBDukF$ProcessThread.run(BBDukF.java:2583) Exception in thread "Thread-28" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-8" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-11" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-27" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-24" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-16" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-10" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-13" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-21" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-23" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-22" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-12" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-17" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-20" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-18" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-15" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-26" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-19" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-29" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-7" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-14" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-9" java.lang.ArrayIndexOutOfBoundsException Exception in thread "Thread-25" java.lang.ArrayIndexOutOfBoundsException Processing time: 0.384 seconds. Input: 34841 reads 3436691 bases. Low entropy discards: 2157 reads (6.19%) 215168 bases (6.26%) Total Removed: 2181 reads (6.26%) 216121 bases (6.29%) Result: 32660 reads (93.74%) 3220570 bases (93.71%) Time: 0.459 seconds. Reads Processed: 34841 75.88k reads/sec Bases Processed: 3436k 7.48m bases/sec
Thank you.
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