[Seqan-dev] razers3 memory problem

[Matthias Lienhard <lienhard@molgen.mpg.de>]

Hi,
when runnig razers3 on my paired end HiSeq fastq files I get the 
following errors


razers3 -i 94 -rr 95 -tc 20 -o sample.sam reads1.fastq reads2.fastq
terminate called recursively
terminate called recursively
Aborted

or

terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted

It seems as memory usage is very high (>50gb). Each of the fastq files 
is about 7 gb. When I take the first 100000 reads, the razers3 seems to 
work fine. However, I don't want to split the files in small chucks and 
merge them together afterwards (because of disk usage and convenience - 
I have about 50 samples to process)
Is there another way to handle this issue?

Also, it would be very convienient if gzipped fastq files could be used 
as input directly - and output in bam-format would be nice as well.

Best wishes, Matthias