[mira_talk] Memory problem with MIRA

Hi,

I am trying to use mira for a de novo assembly of a transcriptome but after
running for a few minutes, it gives me a memory related error.

     Writing temporary hstat files:
     [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%] done

     Analysing hstat files:
     [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
     Ouch, out of memory detected.

My data is from 454 GS FLX Titanium series and I have nearly 650,000 reads
with associated quality file. I am using a strong server with 32 gb RAM. Any
idea why this might be happening?

I am using the following command to run mira:
     mira -project=1TCA --job=denovo,est,normal,454 -fasta -notraceinfo
-noclipping >&log_assembly.txt

Also I am unable to figure out how to invoke the miraMEM memory call. When I
try giving this as command, my shell returns with command not found and mira
doesn't seem to accept is as an option or argument. Can you tell me what
linux command should I give to invoke miraMEM to get an estimate of how much
memory my project might need ?

I am attaching the log assembly results for convenience

Thanks
Ankit Gupta
Graduate Student at Virginia Tech
This is MIRA V3rc4 (development version).

Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on
Bioinformatics (GCB) 99, pp. 45-56.

Mail general questions to the MIRA talk mailing list:
        mira_talk@xxxxxxxxxxxxx

To (un-)subsubcribe the MIRA mailing lists, see:
        http://www.chevreux.org/mira_mailinglists.html

To report bugs or ask for features, please use the new ticketing system at:
        http://sourceforge.net/apps/trac/mira-assembler/
This ensures that requests don't get lost.
Compiled in 32 bit mode.
Compiled in boundtracking mode.
Compiled in bugtracking mode.



Parsing parameters: -project=1TCA --job=denovo,est,normal,454 -fasta 
-notraceinfo -noclipping



Using quickmode switch -notraceinfo : 
SANGER_SETTINGS
            -LR:mxti=no
454_SETTINGS
            -LR:mxti=no
SOLEXA_SETTINGS
            -LR:mxti=no
SOLID_SETTINGS
            -LR:mxti=no

Using quickmode switch -noclipping : 
SANGER_SETTINGS
            
-CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:llc=no:emlc=no:emrc=no:cpat=no
454_SETTINGS
            
-CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:llc=no:emlc=no:emrc=no:cpat=no
SOLEXA_SETTINGS
            
-CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:llc=no:emlc=no:emrc=no:cpat=no
SOLID_SETTINGS
            
-CL:msvs=no:pvlc=no:qc=no:bsqc=no:mbc=no:llc=no:emlc=no:emrc=no:cpat=no



Parameters parsed without error, perfect.

------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data (also common parameters), 454 data

Used parameter settings:
  General (-GE):
        Project name in (proin)                  : 1TCA
        Project name out (proout)                : 1TCA
        Number of threads (not)                  : 2
        Automatic memory management (amm)        : yes
            Keep percent memory free (kpmf)      : 10
            Max. process size (mps)              : 0
        Keep contigs in memory (kcim)            : no
        EST SNP pipeline step (esps)             : 1
        Use template information (uti)           :  [san]  yes
                                                    [454]  yes
            Template insert size minimum (tismin):  [san]  -1
                                                    [454]  -1
            Template insert size maximum (tismax):  [san]  -1
                                                    [454]  -1
        Colour reads by hash frequency (crhf)    : no

  Load reads options (-LR):
        Load sequence data (lsd)                    :  [san]  no
                                                       [454]  yes
            File type (ft)                          :  [san]  fasta
                                                       [454]  fasta
            External quality (eq)                   : from SCF (scf)
                Ext. qual. override (eqo)           : no
                Discard reads on e.q. error (droeqe): no
            Solexa scores in qual file (ssiqf)      : yes
            FASTQ qual offset (fqqo)                :  [san]  0
                                                       [454]  0

        Wants quality file (wqf)                    :  [san]  yes
                                                       [454]  yes

        Read naming scheme (rns)                    :  [san] Sanger Institute 
(sanger)
                                                       [454] forward/reverse 
(fr)

        Merge with XML trace info (mxti)            :  [san]  no
                                                       [454]  no

        Filecheck only (fo)                         : no

  Assembly options (-AS):
        Number of passes (nop)                      : 4
            Skim each pass (sep)                    : yes
        Maximum number of RMB break loops (rbl)     : 2

        Minimum read length (mrl)                   :  [san]  80
                                                       [454]  40
        Base default quality (bdq)                  :  [san]  10
                                                       [454]  10
        Enforce presence of qualities (epoq)        :  [san]  yes
                                                       [454]  yes

        Automatic repeat detection (ard)            : no
            Coverage threshold (ardct)              :  [san]  2
                                                       [454]  2
            Minimum length (ardml)                  :  [san]  400
                                                       [454]  200
            Grace length (ardgl)                    :  [san]  40
                                                       [454]  20
            Use uniform read distribution (urd)     : no
              Start in pass (urdsip)                : 3
              Cutoff multiplier (urdcm)             :  [san]  1.5
                                                       [454]  1.5
        Keep long repeats separated (klrs)          : no

        Spoiler detection (sd)                      : no
            Last pass only (sdlpo)                  : yes

        Use genomic pathfinder (ugpf)               : no

        Use emergency search stop (uess)            : yes
            ESS partner depth (esspd)               : 500
        Use emergency blacklist (uebl)              : yes
        Use max. contig build time (umcbt)          : yes
            Build time in seconds (bts)             : 3600

  Strain and backbone options (-SB):
        Load straindata (lsd)                       : no
        Load backbone (lb)                          : no
            Start backbone usage in pass (sbuip)    : 3
            Backbone file type (bft)                : fasta
            Backbone base quality (bbq)             : 30
            Backbone strain name (bsn)              : 
                Force for all (bsnffa)              : no
            Backbone rail from strain (brfs)        : 
            Backbone rail length (brl)              : 0
            Backbone rail overlap (bro)             : 0
            Also build new contigs (abnc)           : yes

  Dataprocessing options (-DP):
        Use read extensions (ure)                   :  [san]  no
                                                       [454]  no
            Read extension window length (rewl)     :  [san]  30
                                                       [454]  15
            Read extension w. maxerrors (rewme)     :  [san]  2
                                                       [454]  2
            First extension in pass (feip)          :  [san]  0
                                                       [454]  0
            Last extension in pass (leip)           :  [san]  0
                                                       [454]  0

  Clipping options (-CL):
        Merge with SSAHA vector screen (msvs)       :  [san]  no
                                                       [454]  no
            Gap size (msvsgs)                       :  [san]  10
                                                       [454]  8
            Max front gap (msvsmfg)                 :  [san]  30
                                                       [454]  8
            Max end gap (msvsmeg)                   :  [san]  60
                                                       [454]  12
            Strict front clip (msvssfc)             :  [san]  0
                                                       [454]  0
            Strict end clip (msvssec)               :  [san]  0
                                                       [454]  0
        Possible vector leftover clip (pvlc)        :  [san]  no
                                                       [454]  no
            maximum len allowed (pvcmla)            :  [san]  18
                                                       [454]  18
        Quality clip (qc)                           :  [san]  no
                                                       [454]  no
            Minimum quality (qcmq)                  :  [san]  20
                                                       [454]  20
            Window length (qcwl)                    :  [san]  30
                                                       [454]  30
        Bad stretch quality clip (bsqc)             :  [san]  no
                                                       [454]  no
            Minimum quality (bsqcmq)                :  [san]  20
                                                       [454]  5
            Window length (bsqcwl)                  :  [san]  30
                                                       [454]  20
        Masked bases clip (mbc)                     :  [san]  no
                                                       [454]  no
            Gap size (mbcgs)                        :  [san]  20
                                                       [454]  5
            Max front gap (mbcmfg)                  :  [san]  40
                                                       [454]  12
            Max end gap (mbcmeg)                    :  [san]  60
                                                       [454]  12
        Lower case clip (llc)                       :  [san]  no
                                                       [454]  no
        Clip poly A/T at ends (cpat)                :  [san]  no
                                                       [454]  no
            Keep poly-a signal (cpkps)              :  [san]  no
                                                       [454]  no
            Minimum signal length (cpmsl)           :  [san]  12
                                                       [454]  12
            Max errors allowed (cpmea)              :  [san]  1
                                                       [454]  1
            Max gap from ends (cpmgfe)              :  [san]  20000
                                                       [454]  20000
        Ensure minimum left clip (emlc)             :  [san]  no
                                                       [454]  no
            Minimum left clip req. (mlcr)           :  [san]  25
                                                       [454]  4
            Set minimum left clip to (smlc)         :  [san]  30
                                                       [454]  4
        Ensure minimum right clip (emrc)            :  [san]  no
                                                       [454]  no
            Minimum right clip req. (mrcr)          :  [san]  10
                                                       [454]  10
            Set minimum right clip to (smrc)        :  [san]  20
                                                       [454]  15

        Propose end clips (pec)                     : no
            Bases per hash (pecbph)                 : 0

  Parameters for SKIM algorithm (-SK):
        Number of threads (not)                     : 2

        Bases per hash (bph)                        : 17
        Hash save stepping (hss)                    : 4
        Percent required (pr)                       :  [san]  70
                                                       [454]  80

        Max hits per read (mhpr)                    : 30
        Mask nasty repeats (mnr)                    : no
            Nasty repeat ratio (nrr)                : 100
        Max. megahub ratio (mmhr)                   : 0

        Max hashes in memory (mhim)                 : 15000000
        MemCap: hit reduction (mchr)                : 2048

  Pathfinder options (-PF):
        Use quick rule (uqr)                        :  [san]  yes
                                                       [454]  yes
            Quick rule min len 1 (qrml1)            :  [san]  200
                                                       [454]  80
            Quick rule min sim 1 (qrms1)            :  [san]  90
                                                       [454]  90
            Quick rule min len 2 (qrml2)            :  [san]  100
                                                       [454]  60
            Quick rule min sim 2 (qrms2)            :  [san]  95
                                                       [454]  95
        Backbone quick overlap min len (bqoml)      :  [san]  150
                                                       [454]  80

  Align parameters for Smith-Waterman align (-AL):
        Bandwidth in percent (bip)             :  [san]  15
                                                  [454]  20
        Bandwidth max (bmax)                   :  [san]  100
                                                  [454]  80
        Bandwidth min (bmin)                   :  [san]  25
                                                  [454]  20
        Minimum score (ms)                     :  [san]  30
                                                  [454]  15
        Minimum overlap (mo)                   :  [san]  15
                                                  [454]  40
        Minimum relative score in % (mrs)      :  [san]  80
                                                  [454]  80
        Solexa_hack_max_errors (shme)          :  [san]  0
                                                  [454]  0
        Extra gap penalty (egp)                :  [san]  yes
                                                  [454]  yes
            extra gap penalty level (egpl)     :  [san]  reject_codongaps
                                                  [454]  reject_codongaps
            Max. egp in percent (megpp)        :  [san]  100
                                                  [454]  100

  Contig parameters (-CO):
        Name prefix (np)                                         : 1TCA
        Reject on drop in relative alignment score in % (rodirs) :  [san]  20
                                                                    [454]  30
        Mark repeats (mr)                                        : yes
            Only in result (mroir)                               : no
            Assume SNP instead of repeats (asir)                 : no
            Minimum reads per group needed for tagging (mrpg)    :  [san]  2
                                                                    [454]  4
            Minimum neighbour quality needed for tagging (mnq)   :  [san]  20
                                                                    [454]  20
            Minimum Group Quality needed for RMB Tagging (mgqrt) :  [san]  30
                                                                    [454]  25
            End-read Marking Exclusion Area in bases (emea)      :  [san]  25
                                                                    [454]  10
            Also mark gap bases (amgb)                           :  [san]  yes
                                                                    [454]  no
                Also mark gap bases - even multicolumn (amgbemc) :  [san]  yes
                                                                    [454]  yes
                Also mark gap bases - need both strands (amgbnbs):  [san]  yes
                                                                    [454]  yes
        Force non-IUPAC consensus per sequencing type (fnicpst)  :  [san]  no
                                                                    [454]  no
        Merge short reads (msr)                                  :  [san]  no
                                                                    [454]  no
        Gap override ratio (gor)                                 :  [san]  66
                                                                    [454]  66

  Edit options (-ED):
        Automatic contig editing (ace)              :  [san]  no
                                                       [454]  yes
     Sanger only:
        Strict editing mode (sem)                   : no
        Confirmation threshold in percent (ct)      : 50

  Directories (-DI):
        When loading EXP files            : 
        When loading SCF files            : 
        For writing result files          : 1TCA_d_results
        For writing result info files     : 1TCA_d_info
        For writing log files             : 1TCA_d_log
        For writing checkpoint files      : 1TCA_d_chkpt

  File names (-FN):
        When loading sequences from FASTA            :  [san]  
1TCA_in.sanger.fasta
                                                        [454]  1TCA_in.454.fasta
        When loading qualities from FASTA quality    :  [san]  
1TCA_in.sanger.fasta.qual
                                                        [454]  
1TCA_in.454.fasta.qual
        When loading sequences from FASTQ            :  [san]  
1TCA_in.sanger.fastq
                                                        [454]  1TCA_in.454.fastq
        When loading project from CAF                : 1TCA_in.sanger.caf
        When loading project from MAF (disabled)     : 1TCA_in.sanger.maf
        When loading EXP fofn                        : 1TCA_in.fofn
        When loading project from PHD                : 1TCA_in.phd.1
        When loading strain data                     : 1TCA_straindata_in.txt
        When loading XML trace info files            :  [san]  
1TCA_traceinfo_in.sanger.xml
                                                        [454]  
1TCA_traceinfo_in.454.xml
        When loading SSAHA vector screen results     : 
1TCA_ssahavectorscreen_in.txt

        When loading backbone from CAF               : 1TCA_backbone_in.caf
        When loading backbone from GenBank           : 1TCA_backbone_in.gbf
        When loading backbone from FASTA             : 1TCA_backbone_in.fasta


  Output files (-OUTPUT/-OUT):
        Save simple singlets in project (sssip)      :  [san]  no
                                                        [454]  no
        Save tagged singlets in project (stsip)      :  [san]  yes
                                                        [454]  yes

        Remove rollover logs (rrol)                  : yes
        Remove log directory (rld)                   : no

    Result files:
        Saved as CAF                       (orc)     : yes
        Saved as FASTA                     (orf)     : yes
        Saved as GAP4 (directed assembly)  (org)     : no
        Saved as phrap ACE                 (ora)     : yes
        Saved as HTML                      (orh)     : no
        Saved as Transposed Contig Summary (ors)     : yes
        Saved as simple text format        (ort)     : no
        Saved as wiggle                    (orw)     : no

    Temporary result files:
        Saved as CAF                       (otc)     : yes
        Saved as CAF                       (otm)     : no
        Saved as FASTA                     (otf)     : no
        Saved as GAP4 (directed assembly)  (otg)     : no
        Saved as phrap ACE                 (ota)     : no
        Saved as HTML                      (oth)     : no
        Saved as Transposed Contig Summary (ots)     : no
        Saved as simple text format        (ott)     : no

    Extended temporary result files:
        Saved as CAF                      (oetc)     : no
        Saved as FASTA                    (oetf)     : no
        Saved as GAP4 (directed assembly) (oetg)     : no
        Saved as phrap ACE                (oeta)     : no
        Saved as HTML                     (oeth)     : no
        Save also singlets               (oetas)     : no

    Alignment output customisation:
        TEXT characters per line (tcpl)              : 60
        HTML characters per line (hcpl)              : 60
        TEXT end gap fill character (tegfc)          :  
        HTML end gap fill character (hegfc)          :  

    File / directory output names:
        CAF             : 1TCA_out.caf
        MAF             : 1TCA_out.maf
        FASTA           : 1TCA_out.unpadded.fasta
        FASTA quality   : 1TCA_out.unpadded.fasta.qual
        FASTA (padded)  : 1TCA_out.padded.fasta
        FASTA qual.(pad): 1TCA_out.padded.fasta.qual
        GAP4 (directory): 1TCA_out.gap4da
        ACE             : 1TCA_out.ace
        HTML            : 1TCA_out.html
        Simple text     : 1TCA_out.txt
        TCS overview    : 1TCA_out.tcs
        Wiggle          : 1TCA_out.wig
------------------------------------------------------------------------------
Deleting old directory 1TCA_d_log ... done.
Creating directory 1TCA_d_log ... done.
Deleting old directory 1TCA_d_results ... done.
Creating directory 1TCA_d_results ... done.
Deleting old directory 1TCA_d_info ... done.
Creating directory 1TCA_d_info ... done.
Deleting old directory 1TCA_d_chkpt ... done.
Creating directory 1TCA_d_chkpt ... done.
Localtime: Thu Dec  3 13:42:15 2009

Loading data (454) from FASTA files,
Counting sequences in FASTA file:
 [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... 
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... 
[100%] 
Found 636034 sequences.
454 will load 636034 reads.
Longest Sanger: 0
Longest 454: 644
Longest Solexa: 0
Longest Solid: 0
Longest overall: 644
Total reads to load: 636034
Reserving space for reads (this may take a while)
Reserved space for 636044 reads.
Loading data (454) from FASTA files,
Counting sequences in FASTA file:
 [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... 
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... 
[100%] 
Found 636034 sequences.
Loading data from FASTA file:
 [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... 
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... 
[100%] 
Loading quality data from FASTA quality file 1TCA_in.454.fasta.qual:
 [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... 
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... 
[100%] 

Done.
Loaded 636034 reads, 636034 of which have quality accounted for.
Loaded 636034 454 reads.
Total reads loaded: 636034


========================== Memory self assessment ==============================
Running in 64 bit mode.

Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal:     32429216 kB
MemFree:      21445252 kB
Buffers:           776 kB
Cached:        8252344 kB
SwapCached:          0 kB
Active:        7261480 kB
Inactive:      3360724 kB
HighTotal:    31815552 kB
HighFree:     21350704 kB
LowTotal:       613664 kB
LowFree:         94548 kB
SwapTotal:     8388600 kB
SwapFree:      8388600 kB
Dirty:            1164 kB
Writeback:           0 kB
AnonPages:     2368792 kB
Mapped:          18796 kB
Slab:           334864 kB
SReclaimable:   321968 kB
SUnreclaim:      12896 kB
PageTables:       5820 kB
NFS_Unstable:        0 kB
Bounce:              0 kB
WritebackTmp:        0 kB
CommitLimit:  24603208 kB
Committed_AS:  2434328 kB
VmallocTotal:   110584 kB
VmallocUsed:      9968 kB
VmallocChunk:    83808 kB
HugePages_Total:     0
HugePages_Free:      0
HugePages_Rsvd:      0
HugePages_Surp:      0
Hugepagesize:     2048 kB
DirectMap4k:      6144 kB
DirectMap2M:    911360 kB
--------------------------------------------------------------------------------

Dump from /proc/self/status
--------------------------------------------------------------------------------
Name:   mira
State:  R (running)
Tgid:   10488
Pid:    10488
PPid:   4454
TracerPid:      0
Uid:    20634   20634   20634   20634
Gid:    100     100     100     100
FDSize: 256
Groups: 100 
VmPeak:  2339020 kB
VmSize:  2325936 kB
VmLck:         0 kB
VmHWM:   2334968 kB
VmRSS:   2322008 kB
VmData:  2320044 kB
VmStk:        84 kB
VmExe:      2648 kB
VmLib:      3024 kB
VmPTE:      4552 kB
Threads:        1
SigQ:   0/262144
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed:   00000000,00000000,00000000,000000ff
Cpus_allowed_list:      0-7
Mems_allowed:   01
Mems_allowed_list:      0
voluntary_ctxt_switches:        9
nonvoluntary_ctxt_switches:     178
--------------------------------------------------------------------------------

Information on current assembly object:

AS_readpool: 636034 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 2355002064 (2.2 GiB)

Memory used in assembly structures:
                                           Eff. Size   Free cap. LostByAlign
     AS_writtenskimhitsperid:          0        12 B         0 B         0 B
               AS_skim_edges:          0        12 B         0 B         0 B
                 AS_adsfacts:          0        12 B         0 B         0 B
          AS_confirmed_edges:          0        12 B         0 B         0 B
   AS_permanent_overlap_bans:          0        12 B         0 B         0 B
              AS_readhitmiss:          0        12 B         0 B         0 B
            AS_readhmcovered:          0        12 B         0 B         0 B
                AS_count_rhm:          0        12 B         0 B         0 B
                 AS_clipleft:          0        12 B         0 B         0 B
                AS_clipright:          0        12 B         0 B         0 B
                 AS_used_ids:          0        12 B         0 B         0 B
              AS_multicopies:          0        12 B         0 B         0 B
            AS_hasmcoverlaps:          0        12 B         0 B         0 B
       AS_maxcoveragereached:          0        12 B         0 B         0 B
       AS_coverageperseqtype:          0        12 B         0 B         0 B
           AS_istroublemaker:          0        12 B         0 B         0 B
                 AS_isdebris:          0        12 B         0 B         0 B
          AS_needalloverlaps:          0        20 B         0 B         0 B
    AS_readsforrepeatresolve:          0        20 B         0 B         0 B
                AS_allrmbsok:          0        12 B         0 B         0 B
        AS_probablermbsnotok:          0        12 B         0 B         0 B
            AS_weakrmbsnotok:          0        12 B         0 B         0 B
          AS_readmaytakeskim:          0        20 B         0 B         0 B
               AS_skimstaken:          0        20 B         0 B         0 B
          AS_numskimoverlaps:          0        12 B         0 B         0 B
       AS_numleftextendskims:          0        12 B         0 B         0 B
         AS_rightextendskims:          0        12 B         0 B         0 B
      AS_skimleftextendratio:          0        12 B         0 B         0 B
     AS_skimrightextendratio:          0        12 B         0 B         0 B
             AS_usedlogfiles:          1        24 B         0 B         0 B
Total: 2355002468 (2.2 GiB)

================================================================================
Checking reads for trace data:
 [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... 
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... 
[100%] 
No SCF data present in any read, automatic contig editing for Sanger data is 
now switched off.
636034 reads with valid data for assembly.
Localtime: Thu Dec  3 13:45:14 2009

Generated 636034 unique template ids for 636034 valid reads.
No useful template information found, template routines will not be used.
Localtime: Thu Dec  3 13:45:26 2009

Generated 0 unique strain ids for 636034 reads.
Strain "default" has 636034 reads.
Have read pool with 636034 reads.

===========================================================================
Pool statistics:
Backbones: 0    Backbone rails: 0

                Sanger  454     Solexa  SOLiD
                ---------------------------------
Total reads     0       636034  0       0
Reads wo qual   0       0       0       0
Used reads      0       636034  0       0
Avg len used    0       387     0       0

With strain     0       0       0       0
W/o clips       0       636034  0       0
===========================================================================



===========================================================================
Pool statistics:
Backbones: 0    Backbone rails: 0

                Sanger  454     Solexa  SOLiD
                ---------------------------------
Total reads     0       636034  0       0
Reads wo qual   0       0       0       0
Used reads      0       636034  0       0
Avg len used    0       387     0       0

With strain     0       0       0       0
W/o clips       0       636034  0       0
===========================================================================


Writing temporary hstat files:
 [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... 
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... 
[100%] done

Analysing hstat files:
 [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... 
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... 
[100%] 
Ouch, out of memory detected.


========================== Memory self assessment ==============================
Running in 64 bit mode.

Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal:     32429216 kB
MemFree:      14659912 kB
Buffers:           776 kB
Cached:       14926184 kB
SwapCached:          0 kB
Active:        7289080 kB
Inactive:     10034884 kB
HighTotal:    31815552 kB
HighFree:     14648824 kB
LowTotal:       613664 kB
LowFree:         11088 kB
SwapTotal:     8388600 kB
SwapFree:      8388600 kB
Dirty:           43304 kB
Writeback:        8176 kB
AnonPages:     2396220 kB
Mapped:          19448 kB
Slab:           418832 kB
SReclaimable:   405444 kB
SUnreclaim:      13388 kB
PageTables:       5764 kB
NFS_Unstable:        0 kB
Bounce:              0 kB
WritebackTmp:        0 kB
CommitLimit:  24603208 kB
Committed_AS:  2466592 kB
VmallocTotal:   110584 kB
VmallocUsed:      9968 kB
VmallocChunk:    83808 kB
HugePages_Total:     0
HugePages_Free:      0
HugePages_Rsvd:      0
HugePages_Surp:      0
Hugepagesize:     2048 kB
DirectMap4k:      6144 kB
DirectMap2M:    911360 kB
--------------------------------------------------------------------------------

Dump from /proc/self/status
--------------------------------------------------------------------------------
Name:   mira
State:  R (running)
Tgid:   10488
Pid:    10488
PPid:   4454
TracerPid:      0
Uid:    20634   20634   20634   20634
Gid:    100     100     100     100
FDSize: 256
Groups: 100 
VmPeak:  2752996 kB
VmSize:  2359972 kB
VmLck:         0 kB
VmHWM:   2741832 kB
VmRSS:   2347900 kB
VmData:  2354080 kB
VmStk:        84 kB
VmExe:      2648 kB
VmLib:      3024 kB
VmPTE:      4620 kB
Threads:        1
SigQ:   0/262144
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed:   00000000,00000000,00000000,000000ff
Cpus_allowed_list:      0-7
Mems_allowed:   01
Mems_allowed_list:      0
voluntary_ctxt_switches:        1574
nonvoluntary_ctxt_switches:     11828
--------------------------------------------------------------------------------

Information on current assembly object:

AS_readpool: 636034 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 2355002064 (2.2 GiB)

Memory used in assembly structures:
                                           Eff. Size   Free cap. LostByAlign
     AS_writtenskimhitsperid:          0        12 B         0 B         0 B
               AS_skim_edges:          0        12 B         0 B         0 B
                 AS_adsfacts:          0        12 B         0 B         0 B
          AS_confirmed_edges:          0        12 B         0 B         0 B
   AS_permanent_overlap_bans:          0      15 MiB         0 B         0 B
              AS_readhitmiss:          0        12 B         0 B         0 B
            AS_readhmcovered:          0        12 B         0 B         0 B
                AS_count_rhm:          0        12 B         0 B         0 B
                 AS_clipleft:     636034       2 MiB         0 B         0 B
                AS_clipright:     636034       2 MiB         0 B         0 B
                 AS_used_ids:     636034     621 KiB         0 B         2 B
              AS_multicopies:          0     621 KiB     621 KiB         2 B
            AS_hasmcoverlaps:          0     621 KiB     621 KiB         2 B
       AS_maxcoveragereached:     636034       2 MiB         0 B         0 B
       AS_coverageperseqtype:          0        12 B         0 B         0 B
           AS_istroublemaker:     636034     621 KiB         0 B         2 B
                 AS_isdebris:     636034     621 KiB         0 B         2 B
          AS_needalloverlaps:     636034     621 KiB        30 B         0 B
    AS_readsforrepeatresolve:          0        20 B         0 B         0 B
                AS_allrmbsok:          0       2 MiB       2 MiB         0 B
        AS_probablermbsnotok:          0       2 MiB       2 MiB         0 B
            AS_weakrmbsnotok:          0       2 MiB       2 MiB         0 B
          AS_readmaytakeskim:          0        20 B         0 B         0 B
               AS_skimstaken:          0        20 B         0 B         0 B
          AS_numskimoverlaps:          0        12 B         0 B         0 B
       AS_numleftextendskims:          0        12 B         0 B         0 B
         AS_rightextendskims:          0        12 B         0 B         0 B
      AS_skimleftextendratio:          0        12 B         0 B         0 B
     AS_skimrightextendratio:          0        12 B         0 B         0 B
             AS_usedlogfiles:          2        40 B         0 B         0 B
Total: 2389348360 (2.2 GiB)

================================================================================


========================== Memory self assessment ==============================
Running in 64 bit mode.

Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal:     32429216 kB
MemFree:      14590624 kB
Buffers:           776 kB
Cached:       14926300 kB
SwapCached:          0 kB
Active:        7358064 kB
Inactive:     10034604 kB
HighTotal:    31815552 kB
HighFree:     14579528 kB
LowTotal:       613664 kB
LowFree:         11096 kB
SwapTotal:     8388600 kB
SwapFree:      8388600 kB
Dirty:           43212 kB
Writeback:        8272 kB
AnonPages:     2465640 kB
Mapped:          20384 kB
Slab:           418844 kB
SReclaimable:   405444 kB
SUnreclaim:      13400 kB
PageTables:       5832 kB
NFS_Unstable:        0 kB
Bounce:              0 kB
WritebackTmp:        0 kB
CommitLimit:  24603208 kB
Committed_AS:  2548100 kB
VmallocTotal:   110584 kB
VmallocUsed:      9968 kB
VmallocChunk:    83808 kB
HugePages_Total:     0
HugePages_Free:      0
HugePages_Rsvd:      0
HugePages_Surp:      0
Hugepagesize:     2048 kB
DirectMap4k:      6144 kB
DirectMap2M:    911360 kB
--------------------------------------------------------------------------------

Dump from /proc/self/status
--------------------------------------------------------------------------------
Name:   mira
State:  R (running)
Tgid:   10488
Pid:    10488
PPid:   4454
TracerPid:      0
Uid:    20634   20634   20634   20634
Gid:    100     100     100     100
FDSize: 256
Groups: 100 
VmPeak:  2752996 kB
VmSize:  2359972 kB
VmLck:         0 kB
VmHWM:   2741832 kB
VmRSS:   2347900 kB
VmData:  2354080 kB
VmStk:        84 kB
VmExe:      2648 kB
VmLib:      3024 kB
VmPTE:      4620 kB
Threads:        1
SigQ:   0/262144
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed:   00000000,00000000,00000000,000000ff
Cpus_allowed_list:      0-7
Mems_allowed:   01
Mems_allowed_list:      0
voluntary_ctxt_switches:        1574
nonvoluntary_ctxt_switches:     11829
--------------------------------------------------------------------------------

Information on current assembly object:

AS_readpool: 636034 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 2355002064 (2.2 GiB)

Memory used in assembly structures:
                                           Eff. Size   Free cap. LostByAlign
     AS_writtenskimhitsperid:          0        12 B         0 B         0 B
               AS_skim_edges:          0        12 B         0 B         0 B
                 AS_adsfacts:          0        12 B         0 B         0 B
          AS_confirmed_edges:          0        12 B         0 B         0 B
   AS_permanent_overlap_bans:          0      15 MiB         0 B         0 B
              AS_readhitmiss:          0        12 B         0 B         0 B
            AS_readhmcovered:          0        12 B         0 B         0 B
                AS_count_rhm:          0        12 B         0 B         0 B
                 AS_clipleft:     636034       2 MiB         0 B         0 B
                AS_clipright:     636034       2 MiB         0 B         0 B
                 AS_used_ids:     636034     621 KiB         0 B         2 B
              AS_multicopies:          0     621 KiB     621 KiB         2 B
            AS_hasmcoverlaps:          0     621 KiB     621 KiB         2 B
       AS_maxcoveragereached:     636034       2 MiB         0 B         0 B
       AS_coverageperseqtype:          0        12 B         0 B         0 B
           AS_istroublemaker:     636034     621 KiB         0 B         2 B
                 AS_isdebris:     636034     621 KiB         0 B         2 B
          AS_needalloverlaps:     636034     621 KiB        30 B         0 B
    AS_readsforrepeatresolve:          0        20 B         0 B         0 B
                AS_allrmbsok:          0       2 MiB       2 MiB         0 B
        AS_probablermbsnotok:          0       2 MiB       2 MiB         0 B
            AS_weakrmbsnotok:          0       2 MiB       2 MiB         0 B
          AS_readmaytakeskim:          0        20 B         0 B         0 B
               AS_skimstaken:          0        20 B         0 B         0 B
          AS_numskimoverlaps:          0        12 B         0 B         0 B
       AS_numleftextendskims:          0        12 B         0 B         0 B
         AS_rightextendskims:          0        12 B         0 B         0 B
      AS_skimleftextendratio:          0        12 B         0 B         0 B
     AS_skimrightextendratio:          0        12 B         0 B         0 B
             AS_usedlogfiles:          2        40 B         0 B         0 B
Total: 2389348360 (2.2 GiB)

================================================================================
Dynamic allocs: 0
Align allocs: 0
Out of memory detected, exception message is: std::bad_alloc


If you have questions on why this happened, please send the last 1000
lines (or better, the complete log) of the output log to the author
(together with a short summary of your assembly project).



For general help, you will probably get a quicker response on the
    MIRA talk mailing list
than if you mailed the author directly.

To report bugs or ask for features, please use the new ticketing system at:
        http://sourceforge.net/apps/trac/mira-assembler/
This ensures that requests don't get lost.

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