HiSeq-2500-NA12878-demo-2x150 on colosse

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Step Date Elapsed time Since Beginning

Network testing 2014-01-23T09:22:12 7 seconds 7 seconds Counting sequences to assemble 2014-01-23T09:30:30 8 minutes, 18 seconds 8 minutes, 25 seconds Sequence loading 2014-01-23T10:42:38 1 hours, 12 minutes, 8 seconds 1 hours, 20 minutes, 33 seconds K-mer counting 2014-01-23T11:13:55 31 minutes, 17 seconds 1 hours, 51 minutes, 50 seconds Coverage distribution analysis 2014-01-23T11:14:09 14 seconds 1 hours, 52 minutes, 4 seconds Graph construction 2014-01-23T12:08:51 54 minutes, 42 seconds 2 hours, 46 minutes, 46 seconds Null edge purging 2014-01-23T12:15:59 7 minutes, 8 seconds 2 hours, 53 minutes, 54 seconds Selection of optimal read markers 2014-01-23T13:14:12 58 minutes, 13 seconds 3 hours, 52 minutes, 7 seconds Detection of assembly seeds 2014-01-23T14:40:16 1 hours, 26 minutes, 4 seconds 5 hours, 18 minutes, 11 seconds Estimation of outer distances for paired reads 2014-01-23T14:50:31 10 minutes, 15 seconds 5 hours, 28 minutes, 26 seconds Bidirectional extension of seeds 2014-01-23T21:35:54 6 hours, 45 minutes, 23 seconds 12 hours, 13 minutes, 49 seconds Merging of redundant paths 2014-01-24T19:09:38 21 hours, 33 minutes, 44 seconds 1 days, 9 hours, 47 minutes, 33 seconds Generation of contigs 2014-01-24T19:38:26 28 minutes, 48 seconds 1 days, 10 hours, 16 minutes, 21 seconds Scaffolding of contigs 2014-01-25T04:31:49 8 hours, 53 minutes, 23 seconds 1 days, 19 hours, 9 minutes, 44 seconds Counting sequences to search 2014-01-25T04:31:49 0 seconds 1 days, 19 hours, 9 minutes, 44 seconds Graph coloring 2014-01-25T04:32:04 15 seconds 1 days, 19 hours, 9 minutes, 59 seconds Counting contig biological abundances 2014-01-25T04:38:37 6 minutes, 33 seconds 1 days, 19 hours, 16 minutes, 32 seconds Counting sequence biological abundances 2014-01-25T04:38:37 0 seconds 1 days, 19 hours, 16 minutes, 32 seconds Loading taxons 2014-01-25T04:38:50 13 seconds 1 days, 19 hours, 16 minutes, 45 seconds Loading tree 2014-01-25T04:39:04 14 seconds 1 days, 19 hours, 16 minutes, 59 seconds Processing gene ontologies 2014-01-25T04:39:29 25 seconds 1 days, 19 hours, 17 minutes, 24 seconds Computing neighbourhoods 2014-01-25T04:39:29 0 seconds 1 days, 19 hours, 17 minutes, 24 seconds

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/rap/nne-790-ab/projects/seb/human-compare-with-titan/HiSeq-2500-NA12878-demo-2x150-4

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$ cat RaySmartCommand.txt mpiexec -n 512 Ray \ -k \ 31 \ -route-messages \ -detect-sequence-files \ HiSeq-2500-NA12878-demo-2x150/ \ -o \ HiSeq-2500-NA12878-demo-2x150-4 \ LoadPairedEndReads \ HiSeq-2500-NA12878-demo-2x150/sorted_S1_L001_R1_001.fastq.gz \ HiSeq-2500-NA12878-demo-2x150/sorted_S1_L001_R2_001.fastq.gz \ LoadPairedEndReads \ HiSeq-2500-NA12878-demo-2x150/sorted_S1_L001_R1_002.fastq.gz \ HiSeq-2500-NA12878-demo-2x150/sorted_S1_L001_R2_002.fastq.gz \ LoadPairedEndReads \ HiSeq-2500-NA12878-demo-2x150/sorted_S1_L002_R1_001.fastq.gz \ HiSeq-2500-NA12878-demo-2x150/sorted_S1_L002_R2_001.fastq.gz \ LoadPairedEndReads \ HiSeq-2500-NA12878-demo-2x150/sorted_S1_L002_R1_002.fastq.gz \ HiSeq-2500-NA12878-demo-2x150/sorted_S1_L002_R2_002.fastq.gz