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sebhtml / ray

Ray -- Parallel genome assemblies for parallel DNA sequencing
http://denovoassembler.sf.net
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Test Ray Communities #215

Closed sebhtml closed 10 years ago

sebhtml commented 10 years ago

...

sebhtml commented 10 years ago

bits to add:

-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 \ -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

job:

$ pwd /rap/nne-790-ab/projects/seb/NIH_Human_Microbiome_Project-Phase-1-shotgun

$ cat Ray-Communities-Template.sh-SRS011134.sh

PBS -S /bin/bash

PBS -N RayMicrobiome-SRS011134-colosse-3

PBS -o RayMicrobiome-SRS011134-colosse-3.stdout

PBS -e RayMicrobiome-SRS011134-colosse-3.stderr

PBS -A fsi-440-ab

PBS -l walltime=02:00:00:00

PBS -l nodes=12:ppn=8

cd $PBS_O_WORKDIR

module use /rap/nne-790-ab/modulefiles module load nne-790-ab/apps/ray/7001ab2e06f2bd827d3caf1ab44e86f731966906-1

mpiexec -n 96 \ Ray \ -k 31 \ -write-kmers \ -o RayMicrobiome-SRS011134-colosse-3 \ -detect-sequence-files SRS011134 \ -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 \ -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 \

$ msub Ray-Communities-Template.sh-SRS011134.sh

10514917

sebhtml commented 10 years ago

THis works.

And the code have not changed for a while.

$ pwd /rap/nne-790-ab/projects/seb/NIH_Human_Microbiome_Project-Phase-1-shotgun $ find RayMicrobiome-SRS011134-colosse-3/BiologicalAbundances/|grep taxono $ find RayMicrobiome-SRS011134-colosse-3/BiologicalAbundances/|grep Taxon RayMicrobiome-SRS011134-colosse-3/BiologicalAbundances/_Taxonomy RayMicrobiome-SRS011134-colosse-3/BiologicalAbundances/_Taxonomy/Taxons.xml RayMicrobiome-SRS011134-colosse-3/BiologicalAbundances/0.Profile.TaxonomyRank=no rank.tsv RayMicrobiome-SRS011134-colosse-3/BiologicalAbundances/0.Profile.TaxonomyRank=genus.tsv RayMicrobiome-SRS011134-colosse-3/BiologicalAbundances/0.Profile.TaxonomyRank=species.tsv RayMicrobiome-SRS011134-colosse-3/BiologicalAbundances/0.Profile.TaxonomyRank=order.tsv RayMicrobiome-SRS011134-colosse-3/BiologicalAbundances/0.Profile.TaxonomyRank=family.tsv RayMicrobiome-SRS011134-colosse-3/BiologicalAbundances/0.Profile.TaxonomyRank=subspecies.tsv RayMicrobiome-SRS011134-colosse-3/BiologicalAbundances/0.Profile.TaxonomyRank=phylum.tsv RayMicrobiome-SRS011134-colosse-3/BiologicalAbundances/0.Profile.TaxonomyRank=class.tsv RayMicrobiome-SRS011134-colosse-3/BiologicalAbundances/0.Profile.TaxonomyRank=kingdom.tsv RayMicrobiome-SRS011134-colosse-3/BiologicalAbundances/0.Profile.TaxonomyRank=species group.tsv