Re: [Seqan-dev] Failed to build FM index with hg19

["Siragusa, Enrico" <Enrico.Siragusa@fu-berlin.de>]

Hi Hieu,

This incomprehensible error message means that the index construction algorithm run out of disk space! The suffix array construction algorithm implemented in SeqAn (Skew7) works on external memory and requires at least 20-25 times the disk space of the input text. The algorithm writes such temporary data to the system’s temporary folder (usually /tmp). In general, you can change this folder by (re)defining the environment variable TMPDIR.

Concerning any application that you write using SeqAn (or the MiniBowtie demo): you should redefine the SAValue metafunction to squeeze the size of the suffix array. By default, SAValue is a Pair<__uint64, __uint64>. For hg19, you can redefine SAValue as follows:

namespace seqan {

template <typename TString, typename TSpec>

struct SAValue<StringSet<TString, TSpec> >

{

    typedef Pair<__uint8, __uint32, Pack>   Type;

};

}

In this way each SA value will consume only 5 bytes (1 byte to index any sequence in the text collection + 4 bytes to index any position within any sequence).

Concerning Masai: please upgrade to Yara (http://www.seqan.de/projects/yara/) if you didn’t!

Enrico

On 27 Nov 2014, at 05:26, Tran Ngoc Hieu (Dr) <NHTran@ntu.edu.sg> wrote:

Dear SeqAn Team,

 

I often encounter the following error when trying to build the FM index of the human genome (UCSC hg19) by using the tool “masai_indexer” or by following your online tutorial “MiniBowtie”. The process sometimes runs smoothly, but sometimes fails, thus I don’t know what’s going on. Everything is fine with smaller genomes. Could you please give some advices? Thank you very much!

 

 

Building FM index...

Asynchronous I/O operation failed (waitFor): "Success"

fildes:  9

buffer:  7f7e3a5d6000

offset:  3298d0000

nbytes:  28000

event:   1

Raddr:   0x1def098

../../core/include/seqan/file/file_page.h:740 FAILED!  (WRITING operation could not be completed: "Success")

Aborted (core dumped)

 

 

Regards,

Hieu

 

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