Re: [Seqan-dev] razers3 memory problem
Hi Matthias,
RazerS keeps a q-gram index of reads in memory. Hence its memory consumption is directly proportional to the input size. And it requires about 10GB for 10M x 100bp reads. Unfortunately, there is currently no other option than to split the input file into chunks and map then independently one-after-another or in-parallel on a cluster.
BAM outputs will certainly be supported in the near future and gzipped fastq input could be supported but requires to benchmark the alternative I/O module before.
Cheers,
Dave
--
David Weese weese@inf.fu-berlin.de
Freie Universität Berlin http://www.inf.fu-berlin.de/
Institut für Informatik Phone: +49 30 838 75137
Takustraße 9 Algorithmic Bioinformatics
14195 Berlin Room 020
Am 05.06.2013 um 11:44 schrieb 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
>
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