Hi ! First, this is a git development snapshot and may not work as expected.
This bug occurred when the output path was absolute, which produced an infinite loop. Sorry for that. It has been fixed. Thanks for the extensive testing ! Sébastien Boisvert On Tue, 2012-03-13 at 18:30 -0700, habibr wrote: > Hi Sebastien, > > I have tried ray on 20 million, 100bp paired-end reads yesterday. But it > seems it stopped > for long time, at "Global observations" > > I did this command: > > nohup mpiexec -machinefile /illumina/software/tools/mpi-test/machinefile -np > 25 ./Ray -k 19 > -p > /illumina/OLB/111220/Project_D0GM7ACXX/Sample_lane1/lane1_R1.fastq_uniq1.20M.subset.fastq > > /illumina/OLB/111220/Project_D0GM7ACXX/Sample_lane1/lane1_R1.fastq_uniq2.20M.subset.fastq > 350 60 > -o /illumina/OLB/111220/Project_D0GM7ACXX/RayOutput,20M,uniq,k19,v2 & > > The last line in nohup.out (last modified about 8 hours ago) is "Global > observations" > > Is it safe to stop Ray, or what is it doing right now? I already see the > Scaffold.fasta file in > the output folder. > > At the end of this message is the content of ElapsedTime.txt in the output > folder. > > Best regards, > > Habib > > ****** > > > *** > Step: Network testing > Date: Tue Mar 13 15:44:30 2012 > Elapsed time: 7 seconds > Since beginning: 7 seconds > *** > > > *** > Step: Counting sequences to assemble > Date: Tue Mar 13 15:45:12 2012 > Elapsed time: 42 seconds > Since beginning: 49 seconds > *** > > > *** > Step: Sequence loading > Date: Tue Mar 13 15:48:41 2012 > Elapsed time: 3 minutes, 29 seconds > Since beginning: 4 minutes, 18 seconds > *** > > > *** > Step: K-mer counting > Date: Tue Mar 13 17:27:39 2012 > Elapsed time: 1 hours, 38 minutes, 58 seconds > Since beginning: 1 hours, 43 minutes, 16 seconds > *** > > > *** > Step: Coverage distribution analysis > Date: Tue Mar 13 17:27:46 2012 > Elapsed time: 7 seconds > Since beginning: 1 hours, 43 minutes, 23 seconds > *** > > > *** > Step: Graph construction > Date: Tue Mar 13 21:21:44 2012 > Elapsed time: 3 hours, 53 minutes, 58 seconds > Since beginning: 5 hours, 37 minutes, 21 seconds > *** > > > *** > Step: Null edge purging > Date: Tue Mar 13 21:52:17 2012 > Elapsed time: 30 minutes, 33 seconds > Since beginning: 6 hours, 7 minutes, 54 seconds > *** > > > *** > Step: Selection of optimal read markers > Date: Tue Mar 13 22:22:53 2012 > Elapsed time: 30 minutes, 36 seconds > Since beginning: 6 hours, 38 minutes, 30 seconds > *** > > > *** > Step: Detection of assembly seeds > Date: Tue Mar 13 23:11:19 2012 > Elapsed time: 48 minutes, 26 seconds > Since beginning: 7 hours, 26 minutes, 56 seconds > *** > > > *** > Step: Estimation of outer distances for paired reads > Date: Tue Mar 13 23:12:15 2012 > Elapsed time: 56 seconds > Since beginning: 7 hours, 27 minutes, 52 seconds > *** > > > *** > Step: Bidirectional extension of seeds > Date: Tue Mar 13 23:34:30 2012 > Elapsed time: 22 minutes, 15 seconds > Since beginning: 7 hours, 50 minutes, 7 seconds > *** > > > *** > Step: Merging of redundant paths > Date: Tue Mar 13 23:59:03 2012 > Elapsed time: 24 minutes, 33 seconds > Since beginning: 8 hours, 14 minutes, 40 seconds > *** > > > *** > Step: Generation of contigs > Date: Tue Mar 13 23:59:09 2012 > Elapsed time: 6 seconds > Since beginning: 8 hours, 14 minutes, 46 seconds > *** > > > *** > Step: Scaffolding of contigs > Date: Wed Mar 14 00:10:03 2012 > Elapsed time: 10 minutes, 54 seconds > Since beginning: 8 hours, 25 minutes, 40 seconds > *** > > > *** > Step: Counting sequences to search > Date: Wed Mar 14 00:10:09 2012 > Elapsed time: 6 seconds > Since beginning: 8 hours, 25 minutes, 46 seconds > *** > > > *** > Step: Graph coloring > Date: Wed Mar 14 00:10:09 2012 > Elapsed time: 0 seconds > Since beginning: 8 hours, 25 minutes, 46 seconds > *** > > > *** > Step: Counting contig biological abundances > Date: Wed Mar 14 00:11:52 2012 > Elapsed time: 1 minutes, 43 seconds > Since beginning: 8 hours, 27 minutes, 29 seconds > *** > > > *** > Step: Counting sequence biological abundances > Date: Wed Mar 14 00:11:52 2012 > Elapsed time: 0 seconds > Since beginning: 8 hours, 27 minutes, 29 seconds > *** > > > *** > Step: Loading taxons > Date: Wed Mar 14 00:11:59 2012 > Elapsed time: 7 seconds > Since beginning: 8 hours, 27 minutes, 36 seconds > *** > > -- > Reply to this email directly or view it on GitHub: > http://github.com/inbox/35551148#reply ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users