[mira_talk] Re: MIRA (V3.0.3 (production version)) does not recognize my fastaq illumina data

Dear Bestien,
I have implemented the suggestions and the assembly seem to be working
okay... just that I seem to be getting a memory allocation problem...I
have attached the log of events..
Kind regards
Mireji PO



On Tue, Sep 20, 2011 at 5:37 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Sep 20, 2011, at 23:03 , Paul Mireji wrote:
>> I am  using Mira for the first time to assemble illumina trancriptome data.
>
> Hello Paul,
>
> and then you use 3.0.3? Ouch, ouch. Don't! You absolutely do want to switch 
> at least to 3.4.0 or, if the transcriptome data you have is from a higher 
> eukaryote (mamal, plant) - perhaps wait for an upcoming update.
>
> But do yourself a favour: ditch that old version. The 3.0.x series is not 
> suited for Illumina RNASeq data. That became somewhat usable in 3.2.x and 
> even more in 3.4.0. I now have plant data to work on and the next update will 
> also allow a more or less usable assembly of these with 20 to 50m reads.
>
>> I have separately tried  the parameters below as indicated in the
>> manual (http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.htm)
>> to  get started
>>
>> mira --project=data.fastq  --job=denovo,est,accurate,solexa
>>
>> and
>>
>> mira --project=data.fastq  --job=denovo,est,accurate,solexa
>
> These are identical command lines. Copy paste error? :-)
>
>> and I only get the  error message below.... where could I be going wrong?
>>
>> Loading data (Solexa) from FASTQ files,
>>
>> Fatal Error (may be due to problems of the input data):
>> "Could not open FASTQ file 'Test_CLC_export.fastq_in.solexa.fastq'. Is
>> it present? Is it readable? Did you want to load your data in another
>> format?"
>
> Hmmm, is there anything unclear with that error message? MIRA tried to open a 
> file called "Test_CLC_export.fastq" but there wasn't any, so it stopped.
>
> Which, by the way, tells me you have not started MIRA with the lines you 
> pasted above, but with something else. Because if you had started MIRA with 
> what you wrote you did (mira --project=data.fastq 
>  --job=denovo,est,accurate,solexa), MIRA would have complained with the same 
> error message but complained about a non-existent file 
> "data.fastq_in.solexa.fastq". You do not need to be afraid to write the term 
> "CLC" on this mailing list ... I don't bite when reading about other 
> assemblers :-)
>
> Back to your problem:
>
> 1) Name your FASTQ file like this:    "Test_CLC_export_in.solexa.fastq"
> 2) Start MIRA with: "mira --project=Test_CLC_export 
> --job=denovo,est.accurate,solexa >&log_assembly.txt"
>
> And that's it.
>
> Hope this helped,
>  Bastien
>
>
>
>
> --
> You have received this mail because you are subscribed to the mira_talk 
> mailing list. For information on how to subscribe or unsubscribe, please 
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>
This is MIRA V3.4.0 (production 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.

To (un-)subscribe the MIRA mailing lists, see:
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Compiled by: bach
Sun Aug 21 17:50:30 CEST 2011
On: Linux arcadia 2.6.38-11-generic #48-Ubuntu SMP Fri Jul 29 19:02:55 UTC 2011 
x86_64 x86_64 x86_64 GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compiled with ENABLE64 activated.
Runtime settings (sorry, for debug):
        Size of size_t  : 8
        Size of uint32  : 4
        Size of uint32_t: 4
        Size of uint64  : 8
        Size of uint64_t: 8
Current system: Linux mireji-desktop 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 
29 21:07:13 UTC 2011 x86_64 GNU/Linux



Parsing parameters: --project=Test_CLC_export --job=denovo,est,accurate,solexa




Parameters parsed without error, perfect.

-CL:pec and -CO:emeas1clpec are set, setting -CO:emea values to 1.
------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data (also common parameters), Solexa data

Used parameter settings:
  General (-GE):
        Project name in (proin)                     : Test_CLC_export
        Project name out (proout)                   : Test_CLC_export
        Number of threads (not)                     : 2
        Automatic memory management (amm)           : yes
            Keep percent memory free (kpmf)         : 15
            Max. process size (mps)                 : 0
        EST SNP pipeline step (esps)                : 0
        Use template information (uti)              :  [san]  yes
                                                       [sxa]  yes
            Template insert size minimum (tismin)   :  [san]  -1
                                                       [sxa]  -1
            Template insert size maximum (tismax)   :  [san]  -1
                                                       [sxa]  -1
            Template partner build direction (tpbd) :  [san]  -1
                                                       [sxa]  -1
        Colour reads by hash frequency (crhf)       : no

  Load reads options (-LR):
        Load sequence data (lsd)                    :  [san]  no
                                                       [sxa]  yes
            File type (ft)                          :  [san]  fasta
                                                       [sxa]  fastq
            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)      : no
            FASTQ qual offset (fqqo)                :  [san]  0
                                                       [sxa]  0

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

        Read naming scheme (rns)                    :  [san] Sanger Institute 
(sanger)
                                                       [sxa] Solexa (solexa)

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

        Filecheck only (fo)                         : no

  Assembly options (-AS):
        Number of passes (nop)                      : 3
            Skim each pass (sep)                    : yes
        Maximum number of RMB break loops (rbl)     : 1
        Maximum contigs per pass (mcpp)             : 0

        Minimum read length (mrl)                   :  [san]  80
                                                       [sxa]  20
        Minimum reads per contig (mrpc)             :  [san]  2
                                                       [sxa]  4
        Base default quality (bdq)                  :  [san]  10
                                                       [sxa]  10
        Enforce presence of qualities (epoq)        :  [san]  yes
                                                       [sxa]  yes

        Automatic repeat detection (ard)            : no
            Coverage threshold (ardct)              :  [san]  2
                                                       [sxa]  2.5
            Minimum length (ardml)                  :  [san]  400
                                                       [sxa]  300
            Grace length (ardgl)                    :  [san]  40
                                                       [sxa]  20
            Use uniform read distribution (urd)     : no
              Start in pass (urdsip)                : 3
              Cutoff multiplier (urdcm)             :  [san]  1.5
                                                       [sxa]  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
        Assign default strain (ads)                 :  [san]  no
                                                       [sxa]  no
            Default strain name (dsn)               :  [san]  StrainX
                                                       [sxa]  StrainX
        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)              : ReferenceStrain
                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]  yes
                                                       [sxa]  no
            Read extension window length (rewl)     :  [san]  30
                                                       [sxa]  30
            Read extension w. maxerrors (rewme)     :  [san]  2
                                                       [sxa]  2
            First extension in pass (feip)          :  [san]  0
                                                       [sxa]  0
            Last extension in pass (leip)           :  [san]  0
                                                       [sxa]  0

  Clipping options (-CL):
        Merge with SSAHA2/SMALT vector screen (msvs):  [san]  no
                                                       [sxa]  no
            Gap size (msvsgs)                       :  [san]  10
                                                       [sxa]  1
            Max front gap (msvsmfg)                 :  [san]  60
                                                       [sxa]  2
            Max end gap (msvsmeg)                   :  [san]  120
                                                       [sxa]  2
            Strict front clip (msvssfc)             :  [san]  0
                                                       [sxa]  0
            Strict end clip (msvssec)               :  [san]  0
                                                       [sxa]  0
        Possible vector leftover clip (pvlc)        :  [san]  yes
                                                       [sxa]  no
            maximum len allowed (pvcmla)            :  [san]  18
                                                       [sxa]  18
        Min qual. threshold for entire read (mqtfer):  [san]  0
                                                       [sxa]  5
            Number of bases (mqtfernob)             :  [san]  0
                                                       [sxa]  15
        Quality clip (qc)                           :  [san]  no
                                                       [sxa]  no
            Minimum quality (qcmq)                  :  [san]  20
                                                       [sxa]  20
            Window length (qcwl)                    :  [san]  30
                                                       [sxa]  30
        Bad stretch quality clip (bsqc)             :  [san]  yes
                                                       [sxa]  no
            Minimum quality (bsqcmq)                :  [san]  20
                                                       [sxa]  5
            Window length (bsqcwl)                  :  [san]  30
                                                       [sxa]  20
        Masked bases clip (mbc)                     :  [san]  yes
                                                       [sxa]  yes
            Gap size (mbcgs)                        :  [san]  20
                                                       [sxa]  5
            Max front gap (mbcmfg)                  :  [san]  40
                                                       [sxa]  12
            Max end gap (mbcmeg)                    :  [san]  60
                                                       [sxa]  12
        Lower case clip (lcc)                       :  [san]  no
                                                       [sxa]  no
        Clip poly A/T at ends (cpat)                :  [san]  no
                                                       [sxa]  yes
            Keep poly-a signal (cpkps)              :  [san]  no
                                                       [sxa]  no
            Minimum signal length (cpmsl)           :  [san]  12
                                                       [sxa]  15
            Max errors allowed (cpmea)              :  [san]  1
                                                       [sxa]  1
            Max gap from ends (cpmgfe)              :  [san]  9
                                                       [sxa]  20000
        Clip 3 prime polybase (c3pp)                :  [san]  no
                                                       [sxa]  yes
            Minimum signal length (c3ppmsl)         :  [san]  12
                                                       [sxa]  12
            Max errors allowed (c3ppmea)            :  [san]  2
                                                       [sxa]  2
            Max gap from ends (c3ppmgfe)            :  [san]  9
                                                       [sxa]  9
        Clip known adaptors right (ckar)            :  [san]  no
                                                       [sxa]  yes
        Ensure minimum left clip (emlc)             :  [san]  yes
                                                       [sxa]  no
            Minimum left clip req. (mlcr)           :  [san]  25
                                                       [sxa]  0
            Set minimum left clip to (smlc)         :  [san]  30
                                                       [sxa]  0
        Ensure minimum right clip (emrc)            :  [san]  no
                                                       [sxa]  no
            Minimum right clip req. (mrcr)          :  [san]  10
                                                       [sxa]  10
            Set minimum right clip to (smrc)        :  [san]  20
                                                       [sxa]  20

        Apply SKIM chimera detection clip (ascdc)   : yes
        Apply SKIM junk detection clip (asjdc)      : no

        Propose end clips (pec)                     : yes
            Bases per hash (pecbph)                 : 31
            Handle Solexa GGCxG problem (pechsgp)   : yes

        Clip bad solexa ends (cbse)                 : yes

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

        Also compute reverse complements (acrc)     : yes
        Bases per hash (bph)                        : 17
        Hash save stepping (hss)                    : 1
        Percent required (pr)                       :  [san]  65
                                                       [sxa]  95

        Max hits per read (mhpr)                    : 30
        Max megahub ratio (mmhr)                    : 0

        SW check on backbones (swcob)               : no

        Freq. est. min normal (fenn)                : 0.4
        Freq. est. max normal (fexn)                : 1.6
        Freq. est. repeat (fer)                     : 1.9
        Freq. est. heavy repeat (fehr)              : 8
        Freq. est. crazy (fecr)                     : 20
        Mask nasty repeats (mnr)                    : yes
            Nasty repeat ratio (nrr)                : 100
        Repeat level in info file (rliif)           : 6

        Max hashes in memory (mhim)                 : 15000000
        MemCap: hit reduction (mchr)                : 4096

  Pathfinder options (-PF):
        Use quick rule (uqr)                        :  [san]  yes
                                                       [sxa]  yes
            Quick rule min len 1 (qrml1)            :  [san]  200
                                                       [sxa]  -95
            Quick rule min sim 1 (qrms1)            :  [san]  90
                                                       [sxa]  100
            Quick rule min len 2 (qrml2)            :  [san]  100
                                                       [sxa]  -85
            Quick rule min sim 2 (qrms2)            :  [san]  95
                                                       [sxa]  100
        Backbone quick overlap min len (bqoml)      :  [san]  150
                                                       [sxa]  20
        Max. start cache fill time (mscft)          : 5

  Align parameters for Smith-Waterman align (-AL):
        Bandwidth in percent (bip)             :  [san]  20
                                                  [sxa]  20
        Bandwidth max (bmax)                   :  [san]  130
                                                  [sxa]  80
        Bandwidth min (bmin)                   :  [san]  25
                                                  [sxa]  20
        Minimum score (ms)                     :  [san]  30
                                                  [sxa]  15
        Minimum overlap (mo)                   :  [san]  17
                                                  [sxa]  25
        Minimum relative score in % (mrs)      :  [san]  65
                                                  [sxa]  90
        Solexa_hack_max_errors (shme)          :  [san]  0
                                                  [sxa]  0
        Extra gap penalty (egp)                :  [san]  no
                                                  [sxa]  yes
            extra gap penalty level (egpl)     :  [san] low
                                                  [sxa] reject_codongaps
            Max. egp in percent (megpp)        :  [san]  100
                                                  [sxa]  100

  Contig parameters (-CO):
        Name prefix (np)                                         : 
Test_CLC_export
        Reject on drop in relative alignment score in % (rodirs) :  [san]  25
                                                                    [sxa]  15
        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
                                                                    [sxa]  4
            Minimum neighbour quality needed for tagging (mnq)   :  [san]  20
                                                                    [sxa]  20
            Minimum Group Quality needed for RMB Tagging (mgqrt) :  [san]  30
                                                                    [sxa]  30
            End-read Marking Exclusion Area in bases (emea)      :  [san]  1
                                                                    [sxa]  1
                Set to 1 on clipping PEC (emeas1clpec)           : yes
            Also mark gap bases (amgb)                           :  [san]  yes
                                                                    [sxa]  yes
                Also mark gap bases - even multicolumn (amgbemc) :  [san]  yes
                                                                    [sxa]  yes
                Also mark gap bases - need both strands (amgbnbs):  [san]  yes
                                                                    [sxa]  yes
        Force non-IUPAC consensus per sequencing type (fnicpst)  :  [san]  no
                                                                    [sxa]  no
        Merge short reads (msr)                                  :  [san]  no
                                                                    [sxa]  yes
            Keep ends unmerged (msrkeu)                          :  [san]  -1
                                                                    [sxa]  -1
        Gap override ratio (gor)                                 :  [san]  66
                                                                    [sxa]  66

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

  Misc (-MI):
        Stop on NFS (sonfs)                         : yes
        Extended log (el)                           : no
        Large contig size (lcs)                     : 500
        Large contig size for stats(lcs4s)          : 1000
        Stop on max read name length (somrnl)       : 40

  Directories (-DI):
        Working directory                 : 
        When loading EXP files            : 
        When loading SCF files            : 
        Top directory for writing files   : Test_CLC_export_assembly
        For writing result files          : 
Test_CLC_export_assembly/Test_CLC_export_d_results
        For writing result info files     : 
Test_CLC_export_assembly/Test_CLC_export_d_info
        For writing tmp files             : 
Test_CLC_export_assembly/Test_CLC_export_d_tmp
        Tmp redirected to (trt)           : 
        For writing checkpoint files      : 
Test_CLC_export_assembly/Test_CLC_export_d_chkpt

  File names (-FN):
        When loading sequences from FASTA            :  [san]  
Test_CLC_export_in.sanger.fasta
                                                        [sxa]  
Test_CLC_export_in.solexa.fasta
        When loading qualities from FASTA quality    :  [san]  
Test_CLC_export_in.sanger.fasta.qual
                                                        [sxa]  
Test_CLC_export_in.solexa.fasta.qual
        When loading sequences from FASTQ            :  [san]  
Test_CLC_export_in.sanger.fastq
                                                        [sxa]  
Test_CLC_export_in.solexa.fastq
        When loading project from CAF                : 
Test_CLC_export_in.sanger.caf
        When loading project from MAF (disabled)     : 
Test_CLC_export_in.sanger.maf
        When loading EXP fofn                        : 
Test_CLC_export_in.sanger.fofn
        When loading project from PHD                : Test_CLC_export_in.phd.1
        When loading strain data                     : 
Test_CLC_export_straindata_in.txt
        When loading XML trace info files            :  [san]  
Test_CLC_export_traceinfo_in.sanger.xml
                                                        [sxa]  
Test_CLC_export_traceinfo_in.solexa.xml
        When loading SSAHA2 vector screen results    : 
Test_CLC_export_ssaha2vectorscreen_in.txt
        When loading SMALT vector screen results     : 
Test_CLC_export_smaltvectorscreen_in.txt

        When loading backbone from MAF               : 
Test_CLC_export_backbone_in.maf
        When loading backbone from CAF               : 
Test_CLC_export_backbone_in.caf
        When loading backbone from GenBank           : 
Test_CLC_export_backbone_in.gbf
        When loading backbone from GFF3              : 
Test_CLC_export_backbone_in.gff3
        When loading backbone from FASTA             : 
Test_CLC_export_backbone_in.fasta


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

        Remove rollover tmps (rrot)                  : yes
        Remove tmp directory (rtd)                   : no

    Result files:
        Saved as CAF                       (orc)     : yes
        Saved as MAF                       (orm)     : yes
        Saved as FASTA                     (orf)     : yes
        Saved as GAP4 (directed assembly)  (org)     : no
        Saved as phrap ACE                 (ora)     : yes
        Saved as GFF3                     (org3)     : no
        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 MAF                       (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             : Test_CLC_export_out.caf
        MAF             : Test_CLC_export_out.maf
        FASTA           : Test_CLC_export_out.unpadded.fasta
        FASTA quality   : Test_CLC_export_out.unpadded.fasta.qual
        FASTA (padded)  : Test_CLC_export_out.padded.fasta
        FASTA qual.(pad): Test_CLC_export_out.padded.fasta.qual
        GAP4 (directory): Test_CLC_export_out.gap4da
        ACE             : Test_CLC_export_out.ace
        HTML            : Test_CLC_export_out.html
        Simple text     : Test_CLC_export_out.txt
        TCS overview    : Test_CLC_export_out.tcs
        Wiggle          : Test_CLC_export_out.wig
------------------------------------------------------------------------------
Deleting old directory Test_CLC_export_assembly ... done.
Creating directory Test_CLC_export_assembly ... done.
Creating directory Test_CLC_export_assembly/Test_CLC_export_d_tmp ... done.
Creating directory Test_CLC_export_assembly/Test_CLC_export_d_results ... done.
Creating directory Test_CLC_export_assembly/Test_CLC_export_d_info ... done.
Creating directory Test_CLC_export_assembly/Test_CLC_export_d_chkpt ... done.

Tmp directory is not on a NFS mount, good.

Localtime: Thu Sep 22 11:49:39 2011

Loading data (Solexa) from FASTQ files,
Localtime: Thu Sep 22 11:49:39 2011
Counting sequences in FASTQ file: found 42325367 sequences.
Localtime: Thu Sep 22 11:52:04 2011
Solexa will load 42325367 reads.
Longest Sanger: 0
Longest 454: 0
Longest IonTor: 0
Longest PacBio: 0
Longest Solexa: 74
Longest Solid: 0
Longest overall: 74
Total reads to load: 42325367
Reserving space for reads (this may take a while)
tcmalloc: large alloc 9819488256 bytes == (nil) @ 


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

Dump from /proc/meminfo
--------------------------------------------------------------------------------
MemTotal:        1598568 kB
MemFree:           13828 kB
Buffers:           25952 kB
Cached:           855056 kB
SwapCached:            0 kB
Active:           619732 kB
Inactive:         844384 kB
Active(anon):     444232 kB
Inactive(anon):   149224 kB
Active(file):     175500 kB
Inactive(file):   695160 kB
Unevictable:           0 kB
Mlocked:               0 kB
SwapTotal:       3191336 kB
SwapFree:        3191336 kB
Dirty:                16 kB
Writeback:             0 kB
AnonPages:        582996 kB
Mapped:           114540 kB
Shmem:             10460 kB
Slab:              40216 kB
SReclaimable:      19708 kB
SUnreclaim:        20508 kB
KernelStack:        3296 kB
PageTables:        24464 kB
NFS_Unstable:          0 kB
Bounce:                0 kB
WritebackTmp:          0 kB
CommitLimit:     3990620 kB
Committed_AS:    1641596 kB
VmallocTotal:   34359738367 kB
VmallocUsed:       39240 kB
VmallocChunk:   34359694792 kB
HardwareCorrupted:     0 kB
HugePages_Total:       0
HugePages_Free:        0
HugePages_Rsvd:        0
HugePages_Surp:        0
Hugepagesize:       2048 kB
DirectMap4k:       12224 kB
DirectMap2M:     1622016 kB
--------------------------------------------------------------------------------

Dump from /proc/self/status
--------------------------------------------------------------------------------
Name:   mira
State:  R (running)
Tgid:   3792
Pid:    3792
PPid:   3567
TracerPid:      0
Uid:    1000    1000    1000    1000
Gid:    1000    1000    1000    1000
FDSize: 64
Groups: 0 1 2 3 4 5 6 7 8 9 10 12 13 15 20 21 22 24 25 26 27 29 30 33 34 37 38 
39 40 41 42 43 
VmPeak:    11920 kB
VmSize:    11916 kB
VmLck:         0 kB
VmHWM:      7008 kB
VmRSS:      7008 kB
VmData:     6556 kB
VmStk:        88 kB
VmExe:      5236 kB
VmLib:         0 kB
VmPTE:        40 kB
Threads:        1
SigQ:   0/16382
SigPnd: 0000000000000000
ShdPnd: 0000000000000000
SigBlk: 0000000000000000
SigIgn: 0000000000000000
SigCgt: 0000000180000000
CapInh: 0000000000000000
CapPrm: 0000000000000000
CapEff: 0000000000000000
CapBnd: ffffffffffffffff
Cpus_allowed:   ff
Cpus_allowed_list:      0-7
Mems_allowed:   00000000,00000001
Mems_allowed_list:      0
voluntary_ctxt_switches:        61636
nonvoluntary_ctxt_switches:     790
--------------------------------------------------------------------------------

Information on current assembly object:

AS_readpool: 0 reads.
AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.
Mem used for reads: 64 (64 B)

Memory used in assembly structures:
                                           Eff. Size   Free cap. LostByAlign
     AS_writtenskimhitsperid:          0        24 B         0 B         0 B
               AS_skim_edges:          0        24 B         0 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:          0        24 B         0 B         0 B
                AS_clipright:          0        24 B         0 B         0 B
                 AS_used_ids:          0        24 B         0 B         0 B
              AS_multicopies:          0        24 B         0 B         0 B
            AS_hasmcoverlaps:          0        24 B         0 B         0 B
       AS_maxcoveragereached:          0        24 B         0 B         0 B
       AS_coverageperseqtype:          0        24 B         0 B         0 B
           AS_istroublemaker:          0        24 B         0 B         0 B
                 AS_isdebris:          0        24 B         0 B         0 B
          AS_needalloverlaps:          0        40 B         0 B         0 B
    AS_readsforrepeatresolve:          0        40 B         0 B         0 B
                AS_allrmbsok:          0        24 B         0 B         0 B
        AS_probablermbsnotok:          0        24 B         0 B         0 B
            AS_weakrmbsnotok:          0        24 B         0 B         0 B
          AS_readmaytakeskim:          0        40 B         0 B         0 B
               AS_skimstaken:          0        40 B         0 B         0 B
          AS_numskimoverlaps:          0        24 B         0 B         0 B
       AS_numleftextendskims:          0        24 B         0 B         0 B
         AS_rightextendskims:          0        24 B         0 B         0 B
      AS_skimleftextendratio:          0        24 B         0 B         0 B
     AS_skimrightextendratio:          0        24 B         0 B         0 B
             AS_usedtmpfiles:          1        48 B         0 B         0 B
Total: 872 (872 B)

================================================================================
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 of the output log (or better: the complete file) 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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