Any update on this? I would like to know if there is any data I should retain for further analysis, or anything I can do as a temporary workaround. On Mon, Oct 3, 2011 at 8:48 AM, Artemus Harper <subanark@xxxxxxxxx> wrote: > Mira stopped this morning. Please tell me if you need anything else from > the output file. It is taking up 167G of HD space right now. > > GOOD: 165481297 0 0 > GOOD: 165481298 0 0 > GOOD: 165481299 0 0 > > > ========================== Memory self assessment > ============================== > Running in 64 bit mode. > > Dump from /proc/meminfo > > -------------------------------------------------------------------------------- > MemTotal: 528624708 kB > MemFree: 302086772 kB > Buffers: 222388 kB > Cached: 1874972 kB > SwapCached: 0 kB > Active: 224022116 kB > Inactive: 1580080 kB > HighTotal: 0 kB > HighFree: 0 kB > LowTotal: 528624708 kB > LowFree: 302086772 kB > SwapTotal: 8289532 kB > SwapFree: 8289532 kB > Dirty: 156 kB > Writeback: 0 kB > AnonPages: 223504776 kB > Mapped: 113260 kB > Slab: 199664 kB > PageTables: 511132 kB > NFS_Unstable: 0 kB > Bounce: 0 kB > CommitLimit: 272601884 kB > Committed_AS: 262788128 kB > VmallocTotal: 34359738367 kB > VmallocUsed: 361348 kB > VmallocChunk: 34359376347 kB > HugePages_Total: 0 > HugePages_Free: 0 > HugePages_Rsvd: 0 > Hugepagesize: 2048 kB > > -------------------------------------------------------------------------------- > > Dump from /proc/self/status > > -------------------------------------------------------------------------------- > Name: mira > State: R (running) > SleepAVG: 78% > Tgid: 9648 > Pid: 9648 > PPid: 9644 > TracerPid: 0 > Uid: 5018 5018 5018 5018 > Gid: 5005 5005 5005 5005 > FDSize: 256 > Groups: 5005 > VmPeak: 262164656 kB > VmSize: 261867580 kB > VmLck: 0 kB > VmHWM: 258686184 kB > VmRSS: 222888736 kB > VmData: 261862184 kB > VmStk: 88 kB > VmExe: 5272 kB > VmLib: 0 kB > VmPTE: 505312 kB > StaBrk: 06fa8000 kB > Brk: 3e73c8c000 kB > StaStk: 7fff449a6770 kB > Threads: 1 > SigQ: 0/4210688 > SigPnd: 0000000000000000 > ShdPnd: 0000000000000000 > SigBlk: 0000000000000000 > SigIgn: 0000000000001000 > SigCgt: 0000000180000000 > CapInh: 0000000000000000 > CapPrm: 0000000000000000 > CapEff: 0000000000000000 > Cpus_allowed: > 00000000,00000000,00000000,00000000,00000000,00000000,ffffffff,ffffffff > Mems_allowed: 00000000,0000000f > > -------------------------------------------------------------------------------- > > Information on current assembly object: > > AS_readpool: 165481300 reads. > AS_contigs: 0 contigs. > AS_bbcontigs: 0 contigs. > Mem used for reads: 141753391872 (132.0 GiB) > > Memory used in assembly structures: > Eff. Size Free cap. > LostByAlign > AS_writtenskimhitsperid: 165481300 631 MiB 0 B 0 > B > AS_skim_edges: 563714456 16.8 GiB 32 B 0 > B > AS_adsfacts: 0 24 B 0 B 0 > B > AS_confirmed_edges: 0 24 B 0 B 0 > B > AS_permanent_overlap_bans: 1 24 B 0 B 0 > B > AS_readhitmiss: 0 24 B 0 B 0 > B > AS_readhmcovered: 0 24 B 0 B 0 > B > AS_count_rhm: 0 24 B 0 B 0 > B > AS_clipleft: 165481300 631 MiB 0 B 0 > B > AS_clipright: 165481300 631 MiB 0 B 0 > B > AS_used_ids: 165481300 158 MiB 0 B 4 > B > AS_multicopies: 0 158 MiB 158 MiB 4 > B > AS_hasmcoverlaps: 0 158 MiB 158 MiB 4 > B > AS_maxcoveragereached: 165481300 631 MiB 0 B 0 > B > AS_coverageperseqtype: 0 24 B 0 B 0 > B > AS_istroublemaker: 165481300 158 MiB 0 B 4 > B > AS_isdebris: 165481300 158 MiB 0 B 4 > B > AS_needalloverlaps: 165481300 158 MiB 44 B 0 > B > AS_readsforrepeatresolve: 0 40 B 0 B 0 > B > AS_allrmbsok: 0 631 MiB 631 MiB 0 > B > AS_probablermbsnotok: 0 631 MiB 631 MiB 0 > B > AS_weakrmbsnotok: 0 631 MiB 631 MiB 0 > B > AS_readmaytakeskim: 165481300 158 MiB 44 B 0 > B > AS_skimstaken: 5226841530 4.9 GiB 6 B 0 > B > AS_numskimoverlaps: 165481300 631 MiB 0 B 0 > B > AS_numleftextendskims: 165481300 631 MiB 0 B 0 > B > AS_rightextendskims: 165481300 631 MiB 0 B 0 > B > AS_skimleftextendratio: 165481300 158 MiB 0 B 4 > B > AS_skimrightextendratio: 165481300 158 MiB 0 B 4 > B > AS_usedtmpfiles: 10 336 B 0 B 0 > B > Total: 173127680944 (161.2 GiB) > > > ================================================================================ > Dynamic allocs: 0 > Align allocs: 0 > > Internal logic/programming/debugging error (*sigh* this should not have > happened). > Please file a bug report on > http://sourceforge.net/apps/trac/mira-assembler/ > > "Would extend memory of AS_skim_edges? Shouldn't be. File: > Chemdawg_mira_1_assembly/Chemdawg_mira_1_d_tmp/Chemdawg_mira_1_int_posmatchc_pass.1.bin > Line: > 854458193 > SE: 62697086 103812658 24 10890 2177922329 1 -1 33 0 0 0 0 1 > > " > > ->Thrown: uint32 Assembly::rsh4_loadSkimHitBlock(const string & filename, > int32 blockstartid, int32 blockendid, int8 rid1dir, int8 rid2dir) > ->Caught: main > > Aborting process, probably due to an internal error. > > If you want to report the error, please do so on > http://sourceforge.net/apps/trac/mira-assembler/ > and also give a short notice on the mira talk mailing list. > > If reporting, please do not delete the log and checkpoint directories, > there may > be files in them which could be needed to find the problem. > > Subscribing / unsubscribing to mira talk, see: > //www.freelists.org/list/mira_talk > > CWD: /home/dhingralab/artemus_harper > Thank you for noticing that this is *NOT* a crash, but a > controlled program stop. > -- > Artemus Harper > -- Artemus Harper