Re: [Seqan-dev] question about mason

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Dear Sonia, with the RNG seeds parameter, you can start multiple mason processes (e.g. in parallel) resulting in different, but reproduceable, FASTA files. Generating packages of fewer reads should decrease the running time, even when run sequentially.

Currently there is no option to not generate the SAM file. We are working on a solution to this.

HTH,
Manuel
________________________________________
From: Sonia Vivas [vivas@molecularhealth.com]
Sent: Wednesday, October 24, 2012 5:10 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] question about mason

Hi!
I'm using seqan mason to generate mate pairs reads:

./build/Release/core/apps/mason/mason illumina -i -s $i -N 10000000 -n
50 -mp -hM 8 -hnN -o ./reads.fa ./fake_patient.fasta

I do not need the sam file as output, is there any way of avoiding that
is generated? ( I didn't find any option...)
I need high coverage, therefore the 10 million reads. This is taking a
lot of time and memory (50 minutes and up to 30Gb), is there a reason
for this to take so much memory? am I doing something wrong? (my fasta
file is 2.9Gb).

Thank you for your help,

--
Sonia Vivas


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