Re: [Denovoassembler-devel] RE : surveyor negative loaded sequence

[Maxime D. <max...@gm...>]

Hi Seb,

I fixed an endless loop that happened in some cases in
GenomeAssemblyReader when scaffolds were given in entry instead of contigs.

I also renamed the option to write the kmer matrix into a file, now
"-write-kmer-matrix".
Used to be "-run-kmer-matrix".

Please pull from :

https://github.com/Zorino/ray.git

fix-assembly-reader

Cheers,

Maxime


On 03/12/2014 04:13 PM, Sébastien Boisvert wrote:
> On 11 mars 2014 05:58, Maxime Deraspe [ma...@de...] wrote:
>> À : Sébastien Boisvert
>> Objet : surveyor negative loaded sequence
>>
>> Salut Seb,
>>
>> je me demandais comment est ce que le storekeeper pouvait loader une
>> valeur négative de sequence.
> The StoreKeeper actor is designed to only manage kmers in the distributed de Bruijn graph.
> It does not load sequences from files directly. In fact, StoreKeeper actors
> receive their payload from the aggregator (called Coa
>
>> /actors/1668 ->  loaded -1246000000 sequences
>> /actors/1768 ->  loaded 1739000000 sequences
>> /actors/1756 ->  loaded -1138000000 sequences
>> /actors/1807 ->  loaded -2084000000 sequences
>
> If you look in the code, it is not a StoreKeeper actor that loads sequences from files and
> that prints the "loaded XXX sequences" lines.
>
> [boiseb01@ls30 Surveyor]$ grep loaded *.cpp|grep sequences 
> GenomeAssemblyReader.cpp:       cout << " loaded " << m_loaded << " sequences" << endl;
> GenomeGraphReader.cpp:                  cout << " loaded " << m_loaded << " sequences" << endl;
>
>>
>> Est-ce que tu as une idée du problème qui peut survenir ?
> It is in GenomeAssemblyReader.cpp or in GenomeGraphReader.cpp. GenomeGraphReader.cpp loads a graph file
> and I tested it thoroughly.
>
> My guess would be that it is GenomeAssemblyReader.cpp, or code being used by this class.
> More specifically, maybe you should look in SequenceKmerReader.cpp.
>
> In that file, SequenceKmerReader::hasAnotherKmer returns the value of m_hasKmerLeft.
> The problem is presumably around that.
>
> What happens when your buffer has k symbols 'N' and you reached eof ?
>
> m_hasKmerLeft changes value on lines 67 and 118 in your code.
>
>
> In your case, there is one thing to do to go forward:
>
>
> Write a unit test for SequenceKmerReader.cpp.
>
>
> You can add your unit test in https://github.com/sebhtml/Ray-TestSuite/tree/master/unit-tests if you want too.
>
>
>
>> Aussi je crois que j'ai mal compilé ray pour cette run, j'obtiens ces
>> erreurs dans le stderr :
>>
>> Ray: /opt/pgi/linux86-64/11.8/libso/libnuma.so.1: no version information
>> available (required by /opt/mpi/gcc/openmpi-1.6.4/lib64/libmpi.so.1)
>>
>> Maxime
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