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Old 06-23-2014, 06:07 PM   #16
muol
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Location: USA

Join Date: Jun 2012
Posts: 10
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Brian,

I ran into a smaller issue with bbnorm. When trying to input and output separate files for a PE library like this:

Code:
bbnorm.sh in1=R1.fastq.gz in2=R2.fastq.gz out1=R1.bbnorm.fastq.gz out2=R2.bbnorm.fastq.gz prefilter=t tossbadreads=t ecc=t fixspikes=t qin=33 -Xmx72g target=40
I receive this error during pass 2:

Code:
Exception in thread "main" java.lang.AssertionError: Please do not set 'interleaved=true' with dual input files.
	at stream.ConcurrentGenericReadInputStream.<init>(ConcurrentGenericReadInputStream.java:132)
	at stream.ConcurrentGenericReadInputStream.getReadInputStream(ConcurrentGenericReadInputStream.java:661)
	at stream.ConcurrentGenericReadInputStream.getReadInputStream(ConcurrentGenericReadInputStream.java:641)
	at kmer.KmerCount7MTA.countFastq(KmerCount7MTA.java:355)
	at kmer.KmerCount7MTA.makeKca(KmerCount7MTA.java:222)
	at jgi.KmerNormalize.runPass(KmerNormalize.java:1006)
	at jgi.KmerNormalize.main(KmerNormalize.java:736)
Setting interleaved=false doesn't change that. Outputting to a single, interleaved file (in1=xxx in2=xxx out=xxx) on the other hand works fine. Any ideas?

Olaf
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