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