On 17/11/13 01:09 PM, Adrian Pelin wrote:
> Hello,
>
> My assembly at a kmer 59 failed. I used 5 libraries of paired end data
> as input:
The failure is probably unrelated to GenomeNeighbourhood being disable as it is
disabled by default.
GenomeNeighbourhood is enabled with this option:
-enable-neighbourhoods
Computes contig neighborhoods in the de Bruijn graph
Output file: RayOutput/NeighbourhoodRelations.txt
>
> mpiexec -n 32 Ray -k 59 -p /shared/reads/LIB/NC2/GDR-18_NC2_1.fastq
> /shared/reads/LIB/NC2/GDR-18_NC2_2.fastq -p
> /shared/reads/LIB/NC2/GDR-19_NC2_1.fastq
> /shared/reads/LIB/NC2/GDR-19_NC2_2.fastq -p
> /shared/reads/LIB/NC2/GDR-20_NC2_1.fastq
> /shared/reads/LIB/NC2/GDR-20_NC2_2.fastq -p
> /shared/reads/LIB/NC2/GDR-21_NC2_1.fastq
> /shared/reads/LIB/NC2/GDR-21_NC2_2.fastq -p
> /shared/reads/LIB/NC2/GDR-22_NC2_1.fastq
> /shared/reads/LIB/NC2/GDR-22_NC2_2.fastq -p
> /shared/reads/LIB/NC2/GDR-23_NC2_1.fastq
> /shared/reads/LIB/NC2/GDR-23_NC2_2.fastq -o all_libraries
>
> ...
> Rank 20: 0 have some biological signal
> Number of dereferenced alternate handles: 0
> Number of k-mer observations with gene ontology terms: 0
> Rank 20: synced ontology term profiles with master
> Rank 3: 0 have some biological signal
> Number of dereferenced alternate handles: 0
> Number of k-mer observations with gene ontology terms: 0
> Rank 3: synced ontology term profiles with master
> Rank 17: 0 have some biological signal
> Number of dereferenced alternate handles: 0
> Number of k-mer observations with gene ontology terms: 0
> Rank 17: synced ontology term profiles with master
> Rank 8: 0 have some biological signal
> Number of dereferenced alternate handles: 0
> Number of k-mer observations with gene ontology terms: 0
> Rank 8: synced ontology term profiles with master
> Rank 16: 0 have some biological signal
> Number of dereferenced alternate handles: 0
> Number of k-mer observations with gene ontology terms: 0
> Rank 16: synced ontology term profiles with master
> Rank 10: 0 have some biological signal
> Number of dereferenced alternate handles: 0
> Number of k-mer observations with gene ontology terms: 0
> Rank 10: synced ontology term profiles with master
> Rank 7: 0 have some biological signal
> Number of dereferenced alternate handles: 0
> Number of k-mer observations with gene ontology terms: 0
> Rank 7: synced ontology term profiles with master
> Rank Rank Rank 1: the CorePlugin GenomeNeighbourhood is disabled...
> Rank Rank 7Rank 108Rank : the CorePlugin GenomeNeighbourhood is
> disabled...: the CorePlugin GenomeNeighbourhood is disabled...Rank : the
> CorePlugin GenomeNeighbourhood is disabled...Rank 919Rank Rank Rank Rank
> 16Rank 1718Rank : the CorePlugin GenomeNeighbourhood is disabled...21:
> the CorePlugin GenomeNeighbourhood is disabled...22
> 31: the CorePlugin GenomeNeighbourhood is disabled...: the CorePlugin
> GenomeNeighbourhood is disabled...: the CorePlugin GenomeNeighbourhood
> is disabled...
> 20
> : the CorePlugin GenomeNeighbourhood is disabled...
> : the CorePlugin GenomeNeighbourhood is disabled...
>
> 15: the CorePlugin GenomeNeighbourhood is disabled...
>
> : the CorePlugin GenomeNeighbourhood is disabled...
> : the CorePlugin GenomeNeighbourhood is disabled...
>
> Rank
>
> 43: the CorePlugin GenomeNeighbourhood is disabled...
> : the CorePlugin GenomeNeighbourhood is disabled...
> -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> 12:14:27
> @NC2 ~/programs/ray $
>
>
> I'm wondering what went wrong here.
>
> Adrian
>
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