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Ray -- Parallel genome assemblies for parallel DNA sequencing
http://denovoassembler.sf.net
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Ray not writing Neighborhood relations #207

Closed fredericraymond closed 10 years ago

fredericraymond commented 10 years ago

I used the function -enable-neighbourhood to write Neighborhood relation between contigs but the file came out with only the header.

Path of analysis : /rap/nne-790-ab/projects/Project_CQDM2/Participant3-indepth/Sample_P3J7-SilverRayFR-2013-10-02/Assembly

The full command for ray was :

mpiexec -n 128 Ray \ -o \ Assembly \ -k \ 31 \ -enable-neighbourhood \ -amos \ -write-kmers \ -p \ Sample/P3J7_Lane3_R1_10.fastq \ Sample/P3J7_Lane3_R2_10.fastq \ -p \ Sample/P3J7_Lane3_R1_11.fastq \ Sample/P3J7_Lane3_R2_11.fastq \ -p \ Sample/P3J7_Lane3_R1_12.fastq \ Sample/P3J7_Lane3_R2_12.fastq \ -p \ Sample/P3J7_Lane3_R1_13.fastq \ Sample/P3J7_Lane3_R2_13.fastq \ -p \ Sample/P3J7_Lane3_R1_14.fastq \ Sample/P3J7_Lane3_R2_14.fastq \ -p \ Sample/P3J7_Lane3_R1_15.fastq \ Sample/P3J7_Lane3_R2_15.fastq \ -p \ Sample/P3J7_Lane3_R1_16.fastq \ Sample/P3J7_Lane3_R2_16.fastq \ -p \ Sample/P3J7_Lane3_R1_17.fastq \ Sample/P3J7_Lane3_R2_17.fastq \ -p \ Sample/P3J7_Lane3_R1_18.fastq \ Sample/P3J7_Lane3_R2_18.fastq \ -p \ Sample/P3J7_Lane3_R1_19.fastq \ Sample/P3J7_Lane3_R2_19.fastq \ -p \ Sample/P3J7_Lane3_R1_1.fastq \ Sample/P3J7_Lane3_R2_1.fastq \ -p \ Sample/P3J7_Lane3_R1_20.fastq \ Sample/P3J7_Lane3_R2_20.fastq \ -p \ Sample/P3J7_Lane3_R1_2.fastq \ Sample/P3J7_Lane3_R2_2.fastq \ -p \ Sample/P3J7_Lane3_R1_3.fastq \ Sample/P3J7_Lane3_R2_3.fastq \ -p \ Sample/P3J7_Lane3_R1_4.fastq \ Sample/P3J7_Lane3_R2_4.fastq \ -p \ Sample/P3J7_Lane3_R1_5.fastq \ Sample/P3J7_Lane3_R2_5.fastq \ -p \ Sample/P3J7_Lane3_R1_6.fastq \ Sample/P3J7_Lane3_R2_6.fastq \ -p \ Sample/P3J7_Lane3_R1_7.fastq \ Sample/P3J7_Lane3_R2_7.fastq \ -p \ Sample/P3J7_Lane3_R1_8.fastq \ Sample/P3J7_Lane3_R2_8.fastq \ -p \ Sample/P3J7_Lane3_R1_9.fastq \ Sample/P3J7_Lane3_R2_9.fastq \ -search \ /rap/nne-790-ab/genomes/EMBL_CDS+GO/EMBL_CDS_Sequences \ -gene-ontology \ /rap/nne-790-ab/genomes/EMBL_CDS+GO/000-Ontologies.txt \ /rap/nne-790-ab/genomes/EMBL_CDS+GO/000-Annotations.txt \ -search \ /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/ARDB \ -search \ /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/Bacteria-Genomes \ -search \ /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/HumanChromosomes \ -search \ /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/NCBI-Bacteria_DRAFT \ -search \ /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/Viruses-Genomes \ -search \ /scratch/nne-790-ac/CQDM-Production/Search-Datasets/MERGEM_2013-04-29/RG-genes \ -search \ /scratch/nne-790-ac/CQDM-Production/Search-Datasets/MERGEM_2013-04-29/IS-genes \ -search \ /rap/nne-790-ab/genomes/RayKmerSearchStuff-dev/2013-01-30/VFDB_13-01-24 \ -with-taxonomy \ /rap/nne-790-ab/genomes/taxonomy/last-build/Genome-to-Taxon.tsv \ /rap/nne-790-ab/genomes/taxonomy/last-build/TreeOfLife-Edges.tsv \ /rap/nne-790-ab/genomes/taxonomy/last-build/Taxon-Names.tsv

sebhtml commented 10 years ago

What are the last lines of stdout ?

fredericraymond commented 10 years ago

Tail de StdOut

BEGIN Wed Oct 2 18:02:37 EDT 2013 running in /rap/nne-790-ab/projects/Project_CQDM2/Participant3-indepth/Sample_P3J7-SilverRayFR-2013-10-02 command= ln -s ../Sample_P3J7 Sample END Wed Oct 2 18:02:37 EDT 2013

BEGIN Wed Oct 2 18:02:38 EDT 2013 running in /rap/nne-790-ab/projects/Project_CQDM2/Participant3-indepth/Sample_P3J7-SilverRayFR-2013-10-02 command= mpiexec -output-filename ComputeCore -n 128 Ray -o Assembly -k 31 -enable-neighbourhood -amos -write-kmers -p Sample/P3J7_Lane3_R1_10.fastq Sample/P3J7_Lane3_R2_10.fastq -p Sample/P3J7_Lane3_R1_11.fastq Sample/P3J7_Lane3_R2_11.fastq -p Sample/P3J7_Lane3_R1_12.fastq Sample/P3J7_Lane3_R2_12.fastq -p Sample/P3J7_Lane3_R1_13.fastq Sample/P3J7_Lane3_R2_13.fastq -p Sample/P3J7_Lane3_R1_14.fastq Sample/P3J7_Lane3_R2_14.fastq -p Sample/P3J7_Lane3_R1_15.fastq Sample/P3J7_Lane3_R2_15.fastq -p Sample/P3J7_Lane3_R1_16.fastq Sample/P3J7_Lane3_R2_16.fastq -p Sample/P3J7_Lane3_R1_17.fastq Sample/P3J7_Lane3_R2_17.fastq -p Sample/P3J7_Lane3_R1_18.fastq Sample/P3J7_Lane3_R2_18.fastq -p Sample/P3J7_Lane3_R1_19.fastq Sample/P3J7_Lane3_R2_19.fastq -p Sample/P3J7_Lane3_R1_1.fastq Sample/P3J7_Lane3_R2_1.fastq -p Sample/P3J7_Lane3_R1_20.fastq Sample/P3J7_Lane3_R2_20.fastq -p Sample/P3J7_Lane3_R1_2.fastq Sample/P3J7_Lane3_R2_2.fastq -p Sample/P3J7_Lane3_R1_3.fastq Sample/P3J7_Lane3_R2_3.fastq -p Sample/P3J7_Lane3_R1_4.fastq Sample/P3J7_Lane3_R2_4.fastq -p Sample/P3J7_Lane3_R1_5.fastq Sample/P3J7_Lane3_R2_5.fastq -p Sample/P3J7_Lane3_R1_6.fastq Sample/P3J7_Lane3_R2_6.fastq -p Sample/P3J7_Lane3_R1_7.fastq Sample/P3J7_Lane3_R2_7.fastq -p Sample/P3J7_Lane3_R1_8.fastq Sample/P3J7_Lane3_R2_8.fastq -p Sample/P3J7_Lane3_R1_9.fastq Sample/P3J7_Lane3_R2_9.fastq -search /rap/nne-790-ab/genomes/EMBL_CDS+GO/EMBL_CDS_Sequences -gene-ontology /rap/nne-790-ab/genomes/EMBL_CDS+GO/000-Ontologies.txt /rap/nne-790-ab/genomes/EMBL_CDS+GO/000-Annotations.txt -search /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/ARDB -search /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/Bacteria-Genomes -search /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/HumanChromosomes -search /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/NCBI-Bacteria_DRAFT -search /rap/nne-790-ab/genomes/RayKmerSearchStuff/last-build/Viruses-Genomes -search /scratch/nne-790-ac/CQDM-Production/Search-Datasets/MERGEM_2013-04-29/RG-genes -search /scratch/nne-790-ac/CQDM-Production/Search-Datasets/MERGEM_2013-04-29/IS-genes -search /rap/nne-790-ab/genomes/RayKmerSearchStuff-dev/2013-01-30/VFDB_13-01-24 -with-taxonomy /rap/nne-790-ab/genomes/taxonomy/last-build/Genome-to-Taxon.tsv /rap/nne-790-ab/genomes/taxonomy/last-build/TreeOfLife-Edges.tsv /rap/nne-790-ab/genomes/taxonomy/last-build/Taxon-Names.tsv END Thu Oct 3 02:29:57 EDT 2013

sebhtml commented 10 years ago

If you are using the SilverRay wrapper, you should look into ComputeCore.1.* for stdout.

Which version of Ray is it ?

fredericraymond commented 10 years ago

Version : Ray 2.2.0-rc0

Oh...

Rank 0: the CorePlugin GenomeNeighbourhood is disabled... [GenomeNeighbourhood] in final list: 0

Step: Computing neighbourhoods Date: Thu Oct 3 02:29:56 2013 Elapsed time: 0 seconds Since beginning: 8 hours, 27 minutes, 16 seconds

sebhtml commented 10 years ago

The manual says:

   -enable-neighbourhoods
          Computes contig neighborhoods in the de Bruijn graph
          Output file: RayOutput/NeighbourhoodRelations.txt

But you used -enable-neighbourhood

Alignment:

-enable-neighbourhood
|||||||||||||||||||||
-enable-neighbourhoods
fredericraymond commented 10 years ago

Oh crap, sorry! Thanks for your help!