[DrYak]

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.

$ 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

Any suggestions as to what might be the issue?

Thank you.