[mira_talk] Re: Where is my assembly at?

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:
http://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

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