Questions concerning bbmerge

[finswimmer]

Hello all,
I have some question concerning bbmerge. I would like to merge overlapping read pairs. For this I use this command:

bbmerge-auto.sh in1=Sample_L001_R1_001.fastq.gz in2=Sample_L001_R2_001.fastq.gz out=merged/Sample.extendedFrags.fastq.gz outu1=merged/Sample.notCombined_1.fastq.gz outu2=merged/Sample.notCombined_2.fastq.gz qtrim2 trimq=10,20,30 ordered=t ftm=5

When having multiple values for trimq I get the following error

Exception in thread "Thread-6" java.lang.NullPointerException
	at jgi.BBMerge$MateThread.processReadPair(BBMerge.java:2341)
	at jgi.BBMerge$MateThread.findOverlapInThread(BBMerge.java:1643)
	at jgi.BBMerge$MateThread.processReads(BBMerge.java:1583)
	at jgi.BBMerge$MateThread.run(BBMerge.java:1557)
Output buffer became full; key 1250 waiting on 995.

And the program stop. If I remove the ordered=t option this appears:

Exception in thread "Thread-7" java.lang.NullPointerException
	at jgi.BBMerge$MateThread.processReadPair(BBMerge.java:2341)
	at jgi.BBMerge$MateThread.findOverlapInThread(BBMerge.java:1643)
	at jgi.BBMerge$MateThread.processReads(BBMerge.java:1583)
	at jgi.BBMerge$MateThread.run(BBMerge.java:1557)
Exception in thread "Thread-9" java.lang.NullPointerException
	at jgi.BBMerge$MateThread.processReadPair(BBMerge.java:2341)
	at jgi.BBMerge$MateThread.findOverlapInThread(BBMerge.java:1643)
	at jgi.BBMerge$MateThread.processReads(BBMerge.java:1583)
	at jgi.BBMerge$MateThread.run(BBMerge.java:1557)
Exception in thread "Thread-6" java.lang.NullPointerException
	at jgi.BBMerge$MateThread.processReadPair(BBMerge.java:2341)
	at jgi.BBMerge$MateThread.findOverlapInThread(BBMerge.java:1643)
	at jgi.BBMerge$MateThread.processReads(BBMerge.java:1583)
	at jgi.BBMerge$MateThread.run(BBMerge.java:1557)

But the program runs fine until it's finished.

What causes this trouble and can I fix it?

Another question is: Can I do quality trimming for reads that do not overlap directly with in this step?

fin swimmer

[finswimmer]

Ok, I could fix the error messages by setting qtrim2 to one of the values mentioned in the manual for qtrim.

qtrim=f              Trim read ends to remove bases with quality below minq.
                     Trims BEFORE merging.
                     Values: t (trim both ends), 
                             f (neither end), 
                             r (right end only), 
                             l (left end only).
qtrim2=f             May be specified instead of qtrim to perform trimming 
                     only if merging is unsuccessful, then retry merging.