Hello,
weijenc @ SEQanswers a écrit : > Dear Seb567, > > I have been trying to use Ray to assemble SRR131208 (containing paired-end, > 100 bp Illumina sequencing data). I have been >testing using 4 nodes x 8 processors, and 8 nodes x 8 processors with kmer = >21. The 4 x 8 > is still running, while the 8 x 8 kept generating error messages: > . > . > . > Rank 35 reached 400 vertices from seed 73, flow 1 > Speed RAY_SLAVE_MODE_EXTENSION 2320 units/second > Rank 35: assembler memory usage: 199388 KiB > Rank 61 reached 100 vertices from seed 69, flow 1 > Speed RAY_SLAVE_MODE_EXTENSION 25 units/second > Rank 61: assembler memory usage: 199360 KiB > Rank 12 reached 700 vertices from seed 27, flow 2 > Speed RAY_SLAVE_MODE_EXTENSION 19 units/second > Rank 12: assembler memory usage: 199128 KiB > mpiexec: Warning: tasks 0-39,41-63 died with signal 15 (Terminated). > mpiexec: Warning: task 40 died with signal 11 (Segmentation fault). > Which version are you using ? > Is there something I did wrongfully? Can you provide the command you used to launch Ray ? It should be something like: mpiexec -n 64 Ray -k 21 \ -o Test21 \ -s SRR131208.fastq \ -p SRR131208_1.fastq SRR131208_2.fastq The assembly I got: Contigs >= 100 nt Number: 149053 Total length: 75819372 Average: 508 N50: 822 Median: 319 Largest: 8701 Contigs >= 500 nt Number: 54663 Total length: 54570619 Average: 998 N50: 1068 Median: 849 Largest: 8701 Scaffolds >= 100 nt Number: 140427 Total length: 77365612 Average: 550 N50: 968 Median: 290 Largest: 16974 Scaffolds >= 500 nt Number: 46037 Total length: 56116859 Average: 1218 N50: 1466 Median: 887 Largest: 16974 > So far I have found Ray less memory demanding and hope > to be able to use it. Please let me know if you can help. > I think we will work it out. > Also, would you recommend me to trim or mask low quality sequences from the > data >(80M reads)? I saw your reply to another user, but did not specify whether trimming could help Ray significantly. > Better input should yield better assemblies [1], but it is not the reason why Ray is throwing an error here. [1] http://genome.cshlp.org/content/early/2012/01/12/gr.131383.111 > Thanks, > > > WJ ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users