~300MB genome 2 librarires of paires (hiseq2000) (2nd library on 2 lanes) 96499384 x 2 47407253 x 2 13776832 x 2
2 libraries of mates 5kb (done with GAIIx) 26300454 x 2 25851346 x 2 Total 419670538 reads, 41967053800 bases, 139x (I know it's a bit high) On Mammouth, if you know the cluster, using 75 nodes, 10 of 24 cores (because of ram, I cannot use all 24 cores). 120hours walltime is not enough command (I removed file names and some PBS settings for brievety): #PBS -l nodes=100 #PBS -l walltime=120:00:00 export ppn=10 mpiexec -n $[PBS_NUM_NODES*ppn] -npernode $ppn Ray-v2.0.0-rc8/Ray -k 23 -p pairs -p pairs -p pairs -p mates -p mates -o combined_23 -one-color-per-file -write-checkpoints > combined_23.out 2>&1 Louis On 6/12/2012 2:47 PM, Sébastien Boisvert wrote: > Yes, it does that. > > There will be binary files with the ".ray" extension in the > directory where you launched Ray. > > > You can not change the k-mer length when starting from old checkpoints. > > The command needs to have the same number of arguments in the same order. > > > On what kind of dataset are you exceeding time limits ? > > > Louis Letourneau a écrit : >> I saw these options on Ray >> Checkpointing >> -write-checkpoints >> Write checkpoint files >> -read-checkpoints >> Read checkpoint files >> -read-write-checkpoints >> Read and write checkpoint files >> >> >> >> I'm hitting walltimes on the cluster I'm using and I'm wondering if by >> setting: >> -read-write-checkpoints >> >> I can resume where Ray got killed because of walltime? >> >> If that's the purpose, what a great feature! :-) >> >> Louis >> >> ------------------------------------------------------------------------------ >> 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 > > > ------------------------------------------------------------------------------ > 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 ------------------------------------------------------------------------------ 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
